| W001 | Zn site | Protein (Zif268 Zinc Finger Peptide) | 1aay | HIS A129, HIS A125, CYS A107, CYS A112 | Cys2His2 zinc finger (Zif268): Zn ligation folds each finger so its helix can read DNA bases. |
| W002 | Zn site | Protein (P53 Tumor Suppressor) | 1tsr | HIS A179, CYS A242, CYS A238, CYS A176 | p53 DNA-binding domain Zn site holds the L2/L3 loops that contact DNA; often lost in cancer mutants. |
| W003 | Zn site | Protein (Glucocorticoid Receptor) | 1glu | CYS A440, CYS A460, CYS A457, CYS A443 | Nuclear receptor (glucocorticoid receptor) Cys4 zinc module positions the DNA recognition helix. |
| W004 | Zn site | Protein (Transcription Factor Iiia) | 1tf6 | HIS A37, HIS A33, CYS A20, CYS A15 | TFIIIA zinc finger Zn site, founding member of the C2H2 DNA/RNA-binding finger family. |
| W005 | Zn site | Signal Transduction Protein Cbl | 1fbv | CYS A381, CYS A384, CYS A404, CYS A401 | RING-finger E3 ligase (c-Cbl) Zn site; cross-brace Zn ligation builds the E2-binding surface. |
| W006 | Zn site | Carbonic Anhydrase Ii | 1ca2 | HIS A119, HIS A94, HIS A96 | Carbonic anhydrase II His3-Zn site that activates water for CO2 hydration. |
| W007 | Zn site | Copper,Zinc Superoxide Dismutase | 2sod | ASP O81, HIS O78, HIS O61, HIS O69 | Cu/Zn superoxide dismutase Zn site that rigidifies the active-site channel; ALS mutations perturb it. |
| W008 | Zn site | Sonic Hedgehog | 1vhh | HIS A141, HIS A183, ASP A148 | Sonic hedgehog N-terminal domain Zn site, a vestigial metalloprotease-like site on the signaling ligand. |
| W009 | Zn site | Apo-Liver Alcohol Dehydrogenase | 8adh | CYS A174, CYS A46, HIS A67 | Alcohol dehydrogenase catalytic Zn (Cys/His/Cys) that binds and polarizes the alcohol substrate. |
| W010 | Zn site | Carboxypeptidase A | 5cpa | HIS A196, HIS A69, GLU A72 | Carboxypeptidase A Zn site (His/Glu/His) that activates water for peptide hydrolysis. |
| W011 | Zn site | Thermolysin | 8tln | GLU E166, HIS E142, HIS E146 | Thermolysin HExxH zincin-motif Zn site, archetype of zinc metalloproteases. |
| W012 | Zn site | Alkaline Phosphatase | 1alk | HIS A412, ASP A327, HIS A331 | Alkaline phosphatase bimetallic Zn site that hydrolyzes phosphate monoesters. |
| W013 | Ca site | Calmodulin | 1cll | THR A26, GLU A31, ASP A24, ASP A20, ASP A22 | Calmodulin EF-hand Ca loop; Ca binding switches calmodulin on to regulate hundreds of targets. |
| W014 | Ca site | Calbindin D9K | 4icb | ASP A19, ALA A14, GLN A22, GLU A27, GLU A17 | Calbindin D9k EF-hand Ca site, a Ca buffer/transport protein in intestine. |
| W015 | Ca site | Calcium-Binding Parvalbumin | 4cpv | ASP A90, ASP A92, GLU A101, LYS A96, ASP A94 | Parvalbumin EF-hand Ca site that speeds muscle relaxation by buffering Ca. |
| W016 | Ca site | Troponin C | 1top | ASN A108, PHE A112, ASP A106, GLU A117, ASP A110 | Troponin C EF-hand Ca site, the Ca sensor that triggers skeletal muscle contraction. |
| W017 | Ca site | E-Cadherin | 1edh | ASP A195, ASN A104, ASN A143, ASP A136, ASN A102, ASP A134 | E-cadherin interdomain Ca site that rigidifies the ectodomain for cell-cell adhesion. |
| W018 | Ca site | Alpha-Lactalbumin | 1a4v | ASP A84, LYS A79, ASP A82, ASP A87, ASP A88 | Alpha-lactalbumin Ca 'elbow' site needed for folding and lactose synthase regulation. |
| W019 | Ca site | Phospholipase A2 | 1bp2 | TYR A28, GLY A32, GLY A30, ASP A49 | Secreted phospholipase A2 Ca-binding loop; Ca is an essential cofactor for catalysis. |
| W020 | Ca site | Subtilisin Bpn' | 2st1 | VAL A81, ILE A79, LEU A75, ASP A41, GLN A2, ASN A77 | Subtilisin high-affinity Ca site that stabilizes the protease fold. |
| W021 | Ca site | Alpha-Amylase | 1ppi | HIS A201, ARG A158, ASN A100, ASP A167 | Alpha-amylase Ca site required for structural integrity and activity. |
| W022 | Ca site | Proteinase K | 2prk | PRO A175, VAL A177, ASP A200 | Proteinase K Ca site that stabilizes this broadly used protease. |
| W023 | Ca site | Thermonuclease Precursor | 1snc | ASP A40, ASP A21, THR A41 | Staphylococcal nuclease Ca site that stabilizes the phosphodiester transition state. |
| W024 | Mg site | Integrin | 1ido | THR A209, SER A142, SER A144 | Integrin I-domain MIDAS metal site that grips the acidic residue of ligands such as ICAM. |
| W025 | Cu site | Plastocyanin | 1plc | HIS A37, HIS A87, CYS A84 | Plastocyanin type-1 blue copper site (His2CysMet) that shuttles electrons in photosynthesis. |
| W026 | Cu site | Azurin | 4azu | HIS A46, HIS A117, CYS A112 | Azurin type-1 blue copper site tuned for fast electron transfer. |
| W027 | Cu site | Amicyanin | 1aac | HIS A53, HIS A95, CYS A92 | Amicyanin type-1 copper site that relays electrons from methylamine dehydrogenase. |
| W028 | Cu site | Cucumber Stellacyanin | 1jer | HIS A46, HIS A94, CYS A89, GLN A99 | Stellacyanin type-1 copper site with an unusual Gln axial ligand. |
| W029 | Cu site | Rusticyanin | 1rcy | HIS A143, HIS A85, CYS A138 | Rusticyanin type-1 copper site with very high redox potential (iron oxidation). |
| W030 | Fe site | Rubredoxin | 1iro | CYS A42, CYS A9, CYS A39, CYS A6 | Rubredoxin Fe(Cys)4 site, the simplest iron-sulfur electron carrier. |
| W031 | Fe site | Serum Transferrin | 1a8e | TYR A188, TYR A95, ASP A63, HIS A249 | Transferrin N-lobe Fe site (Asp/Tyr/Tyr/His) that carries iron in blood. |
| W032 | Fe site | Lipoxygenase-1 | 1yge | HIS A690, HIS A499, HIS A504 | Lipoxygenase non-heme Fe site that oxygenates polyunsaturated fatty acids. |
| W033 | Fe site | Protocatechuate 3,4-Dioxygenase | 3pca | TYR M408, HIS M462, HIS M460 | Protocatechuate 3,4-dioxygenase Fe(III) site that cleaves aromatic rings. |
| W034 | Fe site | Isopenicillin N Synthase | 1bk0 | ASP A216, HIS A214, HIS A270 | Isopenicillin N synthase 2-His-1-carboxylate Fe site that forms the penicillin core. |
| W035 | Fe site | Iron(Ii) Superoxide Dismutase | 1isa | ASP A156, HIS A73, HIS A160, HIS A26 | Fe superoxide dismutase metal site that detoxifies superoxide. |
| W036 | Mn site | Superoxide Dismutase [Mn] | 1n0j | ASP A159, HIS A74, HIS A163, HIS A26 | Mitochondrial Mn superoxide dismutase Mn site, essential antioxidant defense. |
| W037 | Mn site | Concanavalin A | 3cna | HIS A24, ASP A19, ASP A10, GLU A8 | Concanavalin A Mn site that pre-organizes the carbohydrate-binding loop. |
| W038 | Mn site | Arginase | 1rla | ASP A124, ASP A128, HIS A101, ASP A232 | Arginase binuclear Mn site that hydrolyzes arginine in the urea cycle. |
| W039 | Ni site | Urease (Alpha Chain) | 2kau | HIS C136, ASP C360, HIS C134 | Urease binuclear Ni site that hydrolyzes urea. |
| W040 | Co site | Methionyl Aminopeptidase | 1mat | GLU A204, ASP A108, HIS A171, GLU A235 | Methionine aminopeptidase dinuclear Co site that removes initiator Met. |
| W041 | Cd site | Metallothionein Isoform Ii | 4mt2 | CYS A60, CYS A57, CYS A59, CYS A50 | Metallothionein Cd-thiolate cluster for heavy-metal sequestration. |
| W042 | Mg site | Enolase | 1one | GLU A295, ASP A246, ASP A320 | Enolase Mg site required for glycolytic dehydration of 2-phosphoglycerate. |
| W043 | Mg site | Chey | 1chn | ASP A13, ASN A59, ASP A57 | CheY receiver-domain Mg site that enables Asp phosphorylation in chemotaxis. |
| W044 | Fe-S cluster | Ferredoxin | 1a70 | CYS A77, CYS A44, CYS A39, CYS A47 | Plant ferredoxin [2Fe-2S] Cys4 site that delivers electrons from photosystem I. |
| W045 | Fe-S cluster | Rieske Iron-Sulfur Protein | 1rie | HIS A161, HIS A141, CYS A158, CYS A139 | Rieske [2Fe-2S] site (Cys2His2) of the cytochrome bc1 complex. |
| W046 | Fe-S cluster | Ferredoxin | 1fdn | CYS A47, CYS A14, CYS A8, CYS A11 | Bacterial ferredoxin [4Fe-4S] Cys4 site, a low-potential electron carrier. |
| W047 | Fe-S cluster | High Potential Iron Protein | 1hip | CYS A77, CYS A43, CYS A46, CYS A63 | High-potential iron-sulfur protein [4Fe-4S] site in photosynthetic electron transfer. |
| W048 | Heme pocket | Myoglobin | 1a6m | HIS A93, SER A92, HIS A97, ARG A45, PHE A43, LEU A89 | Myoglobin heme pocket with proximal His; stores O2 in muscle. |
| W049 | Heme pocket | Hemoglobin Subunit Alpha | 4hhb | HIS A87, HIS A45, TYR A42, HIS A58, LEU A101, LEU A91 | Hemoglobin heme pocket with proximal His; carries O2 in blood. |
| W050 | Heme pocket | Cytochrome C | 1hrc | CYS A14, CYS A17, HIS A18, MET A80, TRP A59, THR A49 | Cytochrome c heme (CXXCH, His/Met axial) in respiration and apoptosis signaling. |
| W051 | Heme pocket | Cytochrome P450-Cam | 2cpp | CYS A357, HIS A355, ARG A112, ASP A297, ARG A299, GLN A108 | Cytochrome P450cam heme with Cys thiolate ligand, the P450 oxygenase signature. |
| W052 | Heme pocket | Peroxidase C1A | 1atj | SER A73, SER A35, GLN A176, ARG A31, LYS A174, HIS A170 | Horseradish peroxidase heme pocket with proximal His and distal His/Arg. |
| W053 | Heme pocket | Cytochrome C Peroxidase | 2cyp | HIS A175, HIS A181, SER A185, LYS A179, GLY A178, TRP A51 | Cytochrome c peroxidase heme pocket, classic model of peroxidase catalysis. |
| W054 | Heme pocket | Catalase | 7cat | TYR A357, HIS A361, ASN A147, ALA A157, ARG A71, ARG A353 | Catalase heme pocket with Tyr proximal ligand that decomposes H2O2. |
| W055 | Heme pocket | Cytochrome B5 | 1cyo | HIS A63, HIS A39, SER A64, VAL A45, GLY A41, PHE A35 | Cytochrome b5 bis-His heme, electron donor for desaturases and P450s. |
| W056 | Heme pocket | Neuroglobin | 1oj6 | HIS A96, HIS A64, LYS A67, VAL A71, VAL A109, LEU A92 | Neuroglobin hexacoordinate heme pocket in neurons. |
| W057 | Heme pocket | Cytochrome B562 | 256b | HIS A102, MET A7, GLU A8, GLU A4, PHE A65, PHE A61 | Cytochrome b562 His/Met heme in a four-helix bundle. |
| W058 | Nucleotide site | C-H-Ras P21 Protein | 5p21 | GLY A12, GLY A13, LYS A16, SER A17, THR A35, GLY A60, GLN A61 | Ras P-loop and switch I/II residues binding GTP-Mg; G12, G13 and Q61 are oncogenic hotspots. |
| W059 | Kinase motif | Camp-Dependent Protein Kinase | 1atp | LYS E72, GLU E91, ASP E166, ASN E171, ASP E184 | Protein kinase A conserved motif: VAIK Lys, aC Glu, HRD Asp, catalytic-loop Asn and DFG Asp. |
| W060 | Nucleotide site | Human Cyclin-Dependent Kinase 2 | 1hck | GLN A131, ASP A145, GLU A81, ASN A132, THR A14, LYS A33 | CDK2 ATP pocket, target of cell-cycle kinase inhibitors. |
| W061 | Nucleotide site | Adenylate Kinase | 1ake | ARG A156, LYS A57, GLY A14, THR A15, ARG A167, ARG A123 | Adenylate kinase P-loop/lid site that balances cellular ATP/ADP/AMP. |
| W062 | Nucleotide site | G Protein Gi Alpha 1 | 1gia | GLY A203, LYS A46, THR A48, SER A47, LEU A175, GLU A43 | Heterotrimeric G-protein alpha subunit GTP pocket, the timer of GPCR signaling. |
| W063 | Cofactor site | Holo-D-Glyceraldehyde-3-Phosphate Dehydrogenase | 1gd1 | ASP O32, ILE O11, ASN O180, ASN O313, SER O119, ARG O10 | GAPDH Rossmann-fold NAD+ site in glycolysis. |
| W064 | Cofactor site | Ferredoxin-Nadp+ Reductase | 1fnb | SER A133, CYS A132, ARG A93, LEU A94, CYS A114, TYR A95 | Ferredoxin-NADP+ reductase FAD site that makes NADPH in photosynthesis. |
| W065 | Walker A | Rec A | 2reb | GLY A66, PRO A67, GLU A68, SER A69, SER A70, GLY A71, LYS A72, THR A73 | RecA Walker A (P-loop) motif that binds ATP to drive homologous recombination. |
| W066 | Walker A | Maltose/Maltodextrin Transport Atp-Binding Protein Malk | 1q12 | GLY A36, PRO A37, SER A38, GLY A39, CYS A40, GLY A41, LYS A42, SER A43 | ABC transporter (MalK) Walker A motif binding ATP to power transport. |
| W067 | DEAD box | Atp-Dependent Rna Helicase Vasa | 2db3 | ASP A399, GLU A400, ALA A401, ASP A402 | DEAD-box helicase motif II coordinating Mg-ATP for RNA unwinding. |
| W068 | Ligand pocket | Beta-Trypsin | 3ptb | GLY A219, ASP A189, SER A190, GLY A226, SER A195, GLN A192 | Trypsin S1 specificity pocket (Asp189) that selects Lys/Arg substrates. |
| W069 | Ligand pocket | Streptavidin Complex With Biotin | 1stp | TYR A43, SER A88, SER A27, ASP A128, ASN A49, ASN A23 | Streptavidin biotin pocket, among the tightest non-covalent interactions known. |
| W070 | Ligand pocket | Plasma Retinol-Binding Protein Precursor | 1rbp | LEU A63, LEU A35, PHE A36, ALA A55, GLN A98, VAL A61 | Retinol-binding protein pocket that transports vitamin A in plasma. |
| W071 | Ligand pocket | "Bacteriorhodopsin (Ground State Wild Type ""Br"")" | 1c3w | LYS A216, SER A141, TYR A185, ASP A212, TRP A182, TRP A86 | Bacteriorhodopsin retinal Schiff-base pocket, a light-driven proton pump. |
| W072 | Ligand pocket | Rhodopsin | 1f88 | LYS A296, THR A118, CYS A187, SER A186, MET A207, GLU A122 | Rhodopsin retinal pocket, the dim-light photoreceptor of vision. |
| W073 | Chromophore | Green Fluorescent Protein | 1ema | PHE A64, VAL A68, THR A203, ARG A96, VAL A61, THR A62 | GFP chromophore environment that tunes green fluorescence. |
| W074 | Ligand pocket | Hiv-1 Protease | 1hsg | ASP B25, ASP A25, GLY B27, ASP B29, GLY A48, VAL B32 | HIV-1 protease Asp25 dyad pocket bound to indinavir, an antiretroviral drug. |
| W075 | Ligand pocket | Estrogen Receptor | 1ere | GLU A353, HIS A524, ARG A394, LEU A525, LEU A346, LEU A387 | Estrogen receptor alpha ligand pocket bound to estradiol. |
| W076 | Ligand pocket | Progesterone Receptor | 1a28 | ARG A766, GLN A725, ASN A719, CYS A891, MET A759, LEU A718 | Progesterone receptor ligand pocket bound to progesterone. |
| W077 | Ligand pocket | Vitamin D Nuclear Receptor | 1db1 | SER A237, HIS A305, HIS A397, TYR A143, ARG A274, SER A278 | Vitamin D receptor pocket bound to calcitriol. |
| W078 | Ligand pocket | Peroxisome Proliferator Activated Receptor Gamma | 2prg | SER A289, HIS A323, GLN A286, HIS A449, TYR A473, ILE A341 | PPAR-gamma ligand pocket bound to rosiglitazone, an antidiabetic drug. |
| W079 | Ligand pocket | Acetylcholinesterase | 1acj | GLU A199, HIS A440, TRP A84, PHE A330, TRP A432, GLY A441 | Acetylcholinesterase aromatic gorge bound to tacrine (Alzheimer drug). |
| W080 | Ligand pocket | Dihydrofolate Reductase | 4dfr | ASP A27, ARG A57, ILE A5, ILE A94, ARG A52, PHE A31 | Dihydrofolate reductase pocket bound to methotrexate (anticancer drug). |
| W081 | Ligand pocket | Fk506 Binding Protein | 1fkj | GLU A54, TYR A82, ASP A37, ILE A56, VAL A55, PHE A36 | FKBP12 pocket bound to FK506, the immunosuppressant complex that inhibits calcineurin. |
| W082 | Ligand pocket | Maltodextrin-Binding Protein | 1anf | GLU A111, ASP A14, LYS A15, ALA A63, GLU A153, TRP A230 | Maltose-binding protein sugar pocket for ABC-transporter uptake. |
| W083 | Ligand pocket | L-Arabinose-Binding Protein | 1abe | ASN A232, LYS A10, GLU A14, ASP A90, ARG A151, ASN A205 | L-arabinose-binding protein pocket for periplasmic sugar transport. |
| W084 | Ligand pocket | Hen Egg White Lysozyme | 1hew | ALA A107, ASN A59, TRP A63, TRP A62, TRP A108, GLN A57 | Lysozyme sugar-binding cleft (subsites with NAG) for bacterial cell-wall hydrolysis. |
| W085 | pTyr pocket | V-Src Sh2 Domain | 1sha | GLU A35, ARG A12, ARG A32, THR A36, SER A34, HIS A58 | Src SH2 phosphotyrosine pocket that reads pTyr signaling marks. |
| W086 | Zn site | Nucleocapsid Protein | 1a1t | HIS A23, CYS A28, CYS A18, CYS A15 | HIV-1 nucleocapsid CCHC zinc knuckle that captures viral genomic RNA for packaging. |
| W087 | Ca site | Annexin V | 1avr | GLY A102, LEU A100, GLY A104, ASP A144 | Annexin V type-II Ca site that docks the protein onto phosphatidylserine membranes. |
| W088 | Cu site | Galactose Oxidase | 1gof | TYR A272, HIS A496, HIS A581, TYR A495 | Galactose oxidase Cu site with Tyr-Cys cross-linked radical cofactor. |
| W089 | Cofactor site | Flavodoxin | 1flv | THR A12, THR A10, THR A15, LYS A14, THR A56, GLY A60 | Flavodoxin FMN pocket, a low-potential electron carrier under iron limitation. |
| W090 | Ligand pocket | Tetracycline Repressor Class D | 2trt | HIS A64, ASN A82, HIS A100, VAL A113, SER A138, PHE A86 | Tet repressor tetracycline pocket that switches on antibiotic-resistance genes. |
| W091 | Ligand pocket | Transthyretin | 2rox | LEU A17, LEU A110, ALA A108, LYS A15, ALA A109, SER A117 | Transthyretin thyroxine channel; ligands here block amyloid-forming dissociation. |
| W092 | Ligand pocket | Acetylcholine-Binding Protein | 1uw6 | TRP A143, TYR A89, TYR A192, MET B114, TRP B53, LEU B112 | Acetylcholine-binding protein aromatic box bound to nicotine (nAChR agonist site model). |
| W093 | Selectivity filter | Potassium Channel Kcsa | 1k4c | THR C75, VAL C76, GLY C77, TYR C78, GLY C79 | K+ channel signature TVGYG; backbone carbonyls form the K+ selectivity filter. |
| W094 | Pore motif | Aquaporin 1 | 1j4n | ASN A78, PRO A79, ALA A80, ASN A194, PRO A195, ALA A196 | Aquaporin twin NPA motifs that meet mid-pore and block proton conduction. |
| W095 | Redox motif | Thioredoxin | 2trx | CYS A32, GLY A33, PRO A34, CYS A35 | Thioredoxin CGPC redox-active disulfide that reduces target proteins. |
| W096 | Redox motif | Dsba | 1dsb | CYS A30, PRO A31, HIS A32, CYS A33 | DsbA CPHC disulfide that oxidizes periplasmic proteins to form disulfides. |
| W097 | Redox motif | Protein Disulfide Isomerase | 1mek | CYS A36, GLY A37, HIS A38, CYS A39 | Protein disulfide isomerase CGHC active site for ER oxidative folding. |
| W098 | Redox motif | Glutaredoxin | 1egr | CYS A11, PRO A12, TYR A13, CYS A14 | Glutaredoxin CPYC glutathione-dependent redox site. |
| W099 | Adhesion motif | Fibronectin Cell-Adhesion Module Type Iii-10 | 1fna | ARG A78, GLY A79, ASP A80 | Fibronectin RGD loop recognized by integrins for cell adhesion. |
| W100 | Phospho-relay | Chey | 3chy | ASP A12, ASP A13, ASP A57, THR A87, LYS A109 | CheY receiver domain acidic pocket (D12/D13/D57) plus T87/K109 switch that controls flagellar rotation. |