SMTL ID : 6x5k.1 (1 other biounit)

Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: C.59, G.62, C.67, R.69 Chain B: C.59, G.62, C.67, R.69 Ligands: PGE.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.59, A:C.67, B:C.59, B:C.67 SF4.2: 12 residues within 4Å: Chain A: C.68, F.70, C.71, A.73, G.74, C.76, G.88, I.89, C.90, R.100, M.221 Chain B: M.584 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.68, A:C.71, A:C.76, A:C.90 SF4.5: 10 residues within 4Å: Chain A: M.584 Chain B: C.68, C.71, A.73, G.74, C.76, G.88, C.90, R.100, M.221 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.90 SF4.7: 12 residues within 4Å: Chain C: I.146, C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: NI.8 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.506, C:C.509, C:C.518, C:C.528 SF4.11: 12 residues within 4Å: Chain D: I.146, C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: NI.12 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.506, D:C.509, D:C.518, D:C.528

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

XCC.3: 11 residues within 4Å: Chain A: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.283, A:C.317, A:C.355, A:C.470, A:C.500, A:C.550, A:C.550, H2O.4 XCC.6: 11 residues within 4Å: Chain B: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.283, B:C.317, B:C.355, B:C.470, B:C.500, B:C.550, B:C.550, H2O.7

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain A: C.59, K.60, I.61 Chain B: C.59, K.60, I.61 Ligands: SF4.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.60, B:K.60

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

NI.8: 6 residues within 4Å: Chain C: C.509, C.595, C.597 Ligands: SF4.7, NI.9, CMO.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.509, C:C.595, C:C.597, CMO.10 NI.9: 7 residues within 4Å: Chain C: L.527, C.595, G.596, C.597, F.598 Ligands: NI.8, CMO.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.595, C:C.597 NI.12: 6 residues within 4Å: Chain D: C.509, C.595, C.597 Ligands: SF4.11, NI.13, CMO.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.509, D:C.595, D:C.597, CMO.14 NI.13: 7 residues within 4Å: Chain D: L.527, C.595, G.596, C.597, F.598 Ligands: NI.12, CMO.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.595, D:C.597

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.10: 8 residues within 4Å: Chain C: G.145, V.149, F.229, C.509, C.595, C.597 Ligands: NI.8, NI.9 No protein-ligand interaction detected (PLIP) CMO.14: 8 residues within 4Å: Chain D: G.145, V.149, F.229, C.509, C.595, C.597 Ligands: NI.12, NI.13 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 5 residues within 4Å: Chain D: F.328, E.331, N.412, G.414, L.417 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.331, D:N.412, D:G.414, D:L.417, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cohen, S.E. et al., Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase. Acs Catalysis (2020)

Release Date

2020-10-07

Peptides

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta: AB
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
M

D
N

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

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