SMTL ID : 7zkv.1

F231A variant of the CODH/ACS complex of C. hydrogenoformans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-2-2-mer

Ligands

2 x RQM: Fe(3)-Ni(1)-S(4) cluster(Non-covalent)

RQM.1: 13 residues within 4Å: Chain A: H.281, C.315, F.332, C.353, G.465, C.466, C.496, C.545, M.579, S.580, K.582 Ligands: OH.4, OH.5 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.281, A:C.315, A:C.353, A:C.466, A:C.496, A:C.545, OH.4, OH.5 RQM.8: 13 residues within 4Å: Chain B: H.281, C.315, F.332, C.353, G.465, C.466, C.496, C.545, M.579, S.580, K.582 Ligands: OH.11, OH.12 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:H.281, B:C.315, B:C.353, B:C.466, B:C.496, B:C.545, OH.11, OH.12

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

SF4.2: 9 residues within 4Å: Chain A: C.58, F.60, G.61, C.66, R.76 Chain B: C.58, C.66, R.68 Ligands: SF4.9 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.58, A:C.66 SF4.3: 11 residues within 4Å: Chain A: C.67, F.69, C.70, G.73, C.75, G.86, I.87, C.88, A.90, R.98, I.219 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.67, A:C.70, A:C.75, A:C.88 SF4.9: 9 residues within 4Å: Chain A: C.58, C.66, R.68 Chain B: C.58, F.60, G.61, C.66, R.76 Ligands: SF4.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.58, B:C.66 SF4.10: 11 residues within 4Å: Chain B: C.67, F.69, C.70, G.73, C.75, G.86, I.87, C.88, A.90, R.98, I.219 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.67, B:C.70, B:C.75, B:C.88 SF4.16: 11 residues within 4Å: Chain C: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.17 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.505, C:C.508, C:C.517, C:C.527 SF4.21: 11 residues within 4Å: Chain D: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, I.530, C.596 Ligands: NI.22 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.505, D:C.508, D:C.517, D:C.527

4 x OH: HYDROXIDE ION(Non-covalent)

OH.4: 4 residues within 4Å: Chain A: G.465, C.466, C.545 Ligands: RQM.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.548 OH.5: 6 residues within 4Å: Chain A: H.111, H.281, C.315, C.545, K.582 Ligands: RQM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.111 Water bridges: A:V.546 OH.11: 4 residues within 4Å: Chain B: G.465, C.466, C.545 Ligands: RQM.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.548 OH.12: 6 residues within 4Å: Chain B: H.111, H.281, C.315, C.545, K.582 Ligands: RQM.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.546

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 9 residues within 4Å: Chain A: V.100, I.104, T.229, L.233, T.588, F.611, I.614, T.615, F.627 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.100, A:L.233, A:F.611, A:F.611, A:F.627 MRD.7: 8 residues within 4Å: Chain A: V.226, T.229, A.230, L.233, I.614, Y.623 Chain C: Y.34, I.37 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.226, A:A.230, A:L.233, A:Y.623, C:Y.34, C:I.37 Hydrogen bonds: A:Y.623, A:Y.623 MRD.13: 9 residues within 4Å: Chain B: V.100, I.104, T.229, L.233, T.588, F.611, I.614, T.615, F.627 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.100, B:L.233, B:F.611, B:F.611, B:F.627 MRD.14: 8 residues within 4Å: Chain B: V.226, T.229, A.230, L.233, I.614, Y.623 Chain D: Y.34, I.37 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:V.226, B:A.230, B:L.233, B:Y.623, D:Y.34, D:I.37 Hydrogen bonds: B:Y.623

4 x NI: NICKEL (II) ION(Non-covalent)

NI.15: 7 residues within 4Å: Chain C: L.526, C.594, G.595, C.596, F.597 Ligands: NI.17, ACT.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.594, C:C.596 NI.17: 6 residues within 4Å: Chain C: C.508, C.594, C.596 Ligands: NI.15, SF4.16, ACT.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.508, C:C.594, C:C.596, ACT.18 NI.20: 7 residues within 4Å: Chain D: L.526, C.594, G.595, C.596, F.597 Ligands: NI.22, ACT.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.594, D:C.596 NI.22: 6 residues within 4Å: Chain D: C.508, C.594, C.596 Ligands: NI.20, SF4.21, ACT.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.508, D:C.594, D:C.596, ACT.23

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.18: 10 residues within 4Å: Chain C: G.144, I.145, V.148, F.228, C.508, F.511, C.594, C.596 Ligands: NI.15, NI.17 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.148, C:F.228, C:F.511 ACT.23: 10 residues within 4Å: Chain D: G.144, I.145, V.148, F.228, C.508, F.511, C.594, C.596 Ligands: NI.20, NI.22 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.148, D:F.228, D:F.511

2 x NA: SODIUM ION(Non-functional Binders)

NA.19: 5 residues within 4Å: Chain C: F.327, E.330, N.411, G.413, F.416 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.413, C:F.416 NA.24: 5 residues within 4Å: Chain D: F.327, E.330, N.411, G.413, F.416 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.327, D:E.330, D:F.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruickoldt, J. et al., On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases. ACS Catal. (2022)

Release Date

2022-11-02

Peptides

Carbon monoxide dehydrogenase: AB
CO-methylating acetyl-CoA synthase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Carbon monoxide dehydrogenase

CO-methylating acetyl-CoA synthase

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