SMTL ID : 7zxj.1

K563A Mutant of Recombinant CODH-II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 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 SF4.8: 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: 11 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.9, PEG.14 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.39, A:C.47 FES.9: 11 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, PEG.7 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.39, B:C.47

2 x WCC: FE(3)-NI(1)-S(4) CLUSTER(Non-covalent)

WCC.3: 14 residues within 4Å: Chain A: H.261, C.294, C.295, S.312, C.333, G.445, C.446, G.475, C.476, C.526, M.560, H.561, A.563 Ligands: FE2.4 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.333, A:C.446, A:C.476, A:C.526, H2O.19, H2O.26 WCC.10: 14 residues within 4Å: Chain B: H.261, C.294, C.295, S.312, C.333, G.445, C.446, G.475, C.476, C.526, M.560, H.561, A.563 Ligands: FE2.11 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.333, B:C.446, B:C.476, B:C.526, H2O.55, H2O.61

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

FE2.4: 4 residues within 4Å: Chain A: H.261, C.295, C.526 Ligands: WCC.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.261, A:C.295, H2O.19 FE2.11: 4 residues within 4Å: Chain B: H.261, C.295, C.526 Ligands: WCC.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.261, B:C.295, H2O.55

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: Q.38, C.39, G.40, F.41, T.44, P.60 Ligands: PEG.6, PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.38, A:G.40 PEG.6: 8 residues within 4Å: Chain A: Q.38, C.39, G.40, F.41, T.44, P.60 Ligands: PEG.5, PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.40 PEG.7: 9 residues within 4Å: Chain A: P.37, Q.38, C.39 Chain B: F.41, R.57 Ligands: PEG.5, PEG.6, FES.9, PEG.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.41 Hydrogen bonds: A:P.37 PEG.12: 8 residues within 4Å: Chain B: Q.38, C.39, G.40, F.41, T.44, P.60 Ligands: PEG.13, PEG.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.38, B:G.40 PEG.13: 8 residues within 4Å: Chain B: Q.38, C.39, G.40, F.41, T.44, P.60 Ligands: PEG.12, PEG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.40 PEG.14: 9 residues within 4Å: Chain A: F.41, R.57 Chain B: P.37, Q.38, C.39 Ligands: FES.2, PEG.7, PEG.12, PEG.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.37 Hydrophobic interactions: A:F.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, Y. et al., Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix. Acs Catalysis (2022)

Release Date

2023-03-15

Peptides

Carbon monoxide dehydrogenase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

Carbon monoxide dehydrogenase 2