SMTL ID : 8on0.1

NI,FE-CODH -600mV state : 90 min Dioxygen Exposure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 14 residues within 4Å: Chain A: C.48, R.49, H.50, C.51, Q.53, G.54, C.56, G.68, I.69, C.70, A.72, I.77, R.80, M.199 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.48, A:C.51, A:C.56, A:C.70 SF4.12: 14 residues within 4Å: Chain B: C.48, R.49, H.50, C.51, Q.53, G.54, C.56, G.68, I.69, C.70, A.72, I.77, R.80, M.199 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.48, B:C.51, B:C.56, B:C.70

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 10 residues within 4Å: Chain A: C.39, F.41, G.42, C.47, R.57 Chain B: C.39, C.47, R.49, P.55 Ligands: FES.13 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.39, A:C.47 FES.13: 10 residues within 4Å: Chain A: C.39, C.47, R.49, P.55 Chain B: C.39, F.41, G.42, C.47, R.57 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.39, B:C.47

2 x FE2: FE (II) ION(Non-covalent)

FE2.3: 10 residues within 4Å: Chain A: H.261, C.295, C.526, K.563 Ligands: FE.4, FE.6, FE.7, FE.8, FE.9, H2S.11 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.261, A:C.295, H2O.1, H2O.16, H2O.19 FE2.14: 10 residues within 4Å: Chain B: H.261, C.295, C.526, K.563 Ligands: FE.15, FE.17, FE.18, FE.19, FE.20, H2S.22 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.261, B:C.295, H2O.27, H2O.42, H2O.45

12 x FE: FE (III) ION(Non-covalent)

FE.4: 12 residues within 4Å: Chain A: H.261, C.333, M.560, H.561, K.563 Ligands: FE2.3, FE.5, FE.6, FE.7, FE.8, FE.9, H2S.11 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.333, H2O.16, H2O.19, H2O.20, H2O.24 FE.5: 9 residues within 4Å: Chain A: C.446, M.560, H.561 Ligands: FE.4, FE.6, FE.7, FE.9, H2S.10, H2S.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.446, H2O.19, H2O.20 FE.6: 10 residues within 4Å: Chain A: G.445, C.526, K.563 Ligands: FE2.3, FE.4, FE.5, FE.7, FE.9, H2S.10, H2S.11 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.526, H2O.1, H2O.20, H2O.20 FE.7: 9 residues within 4Å: Chain A: C.446, C.476 Ligands: FE2.3, FE.4, FE.5, FE.6, FE.8, FE.9, H2S.11 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.476, H2O.16, H2O.19, H2O.19 FE.8: 8 residues within 4Å: Chain A: C.294, S.312, C.333, C.476 Ligands: FE2.3, FE.4, FE.7, H2S.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.476, H2O.16, H2O.19 FE.9: 12 residues within 4Å: Chain A: G.445, C.446, G.475, C.476, C.526 Ligands: FE2.3, FE.4, FE.5, FE.6, FE.7, H2S.10, H2S.11 No protein-ligand interaction detected (PLIP) FE.15: 12 residues within 4Å: Chain B: H.261, C.333, M.560, H.561, K.563 Ligands: FE2.14, FE.16, FE.17, FE.18, FE.19, FE.20, H2S.22 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:C.333, H2O.42, H2O.46, H2O.46, H2O.50 FE.16: 9 residues within 4Å: Chain B: C.446, M.560, H.561 Ligands: FE.15, FE.17, FE.18, FE.20, H2S.21, H2S.22 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.446, H2O.46, H2O.46 FE.17: 10 residues within 4Å: Chain B: G.445, C.526, K.563 Ligands: FE2.14, FE.15, FE.16, FE.18, FE.20, H2S.21, H2S.22 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.526, H2O.27, H2O.46, H2O.46 FE.18: 9 residues within 4Å: Chain B: C.446, C.476 Ligands: FE2.14, FE.15, FE.16, FE.17, FE.19, FE.20, H2S.22 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.476, H2O.42, H2O.45, H2O.46 FE.19: 8 residues within 4Å: Chain B: C.294, S.312, C.333, C.476 Ligands: FE2.14, FE.15, FE.18, H2S.22 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.476, H2O.42, H2O.46 FE.20: 12 residues within 4Å: Chain B: G.445, C.446, G.475, C.476, C.526 Ligands: FE2.14, FE.15, FE.16, FE.17, FE.18, H2S.21, H2S.22 No protein-ligand interaction detected (PLIP)

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.10: 10 residues within 4Å: Chain A: G.445, C.446, C.526, H.561, K.563, A.564, I.567 Ligands: FE.5, FE.6, FE.9 No protein-ligand interaction detected (PLIP) H2S.11: 10 residues within 4Å: Chain A: H.261, C.333, K.563 Ligands: FE2.3, FE.4, FE.5, FE.6, FE.7, FE.8, FE.9 No protein-ligand interaction detected (PLIP) H2S.21: 10 residues within 4Å: Chain B: G.445, C.446, C.526, H.561, K.563, A.564, I.567 Ligands: FE.16, FE.17, FE.20 No protein-ligand interaction detected (PLIP) H2S.22: 10 residues within 4Å: Chain B: H.261, C.333, K.563 Ligands: FE2.14, FE.15, FE.16, FE.17, FE.18, FE.19, FE.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, Y. et al., Stepwise O 2 -Induced Rearrangement and Disassembly of the [NiFe 4 (OH)( mu 3 -S) 4 ] Active Site Cluster of CO Dehydrogenase. Angew.Chem.Int.Ed.Engl. (2023)

Release Date

2023-12-06

Peptides

Carbon monoxide dehydrogenase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

Carbon monoxide dehydrogenase 2

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