SMTL ID : 6b6w.1

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 2), oxidized C-cluster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.59, A:C.62, A:C.67, A:C.82 SF4.7: 12 residues within 4Å: Chain B: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.59, B:C.62, B:C.67, B:C.82

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: GOL.11 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

XCC.4: 14 residues within 4Å: Chain A: H.274, C.309, C.310, H.327, C.348, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564 Ligands: CUV.5 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:H.274, A:C.310, A:C.348, A:C.456, A:C.486 XCC.16: 14 residues within 4Å: Chain B: H.274, C.309, C.310, H.327, C.348, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564 Ligands: CUV.17 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:H.274, B:C.310, B:C.348, B:C.456, B:C.486

2 x CUV: Fe(4)-Ni(1)-S(4) cluster, oxidized(Non-covalent)(Covalent)

CUV.5: 14 residues within 4Å: Chain A: H.274, C.309, C.310, C.348, V.454, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564 Ligands: XCC.4 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:H.274, A:C.309, A:C.310, A:C.310, A:C.348, A:C.456, A:C.486 CUV.17: 14 residues within 4Å: Chain B: H.274, C.309, C.310, C.348, V.454, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564 Ligands: XCC.16 7 PLIP interactions: 7 interactions with chain B, Metal complexes: B:H.274, B:C.309, B:C.310, B:C.310, B:C.348, B:C.456, B:C.486

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

FES.6: 11 residues within 4Å: Chain A: C.50, F.52, C.53, T.58, R.68 Chain B: C.50, F.52, C.53, T.58, R.68 Ligands: GOL.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.50, B:C.53, A:C.50, A:C.53

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: C.50, R.68 Chain B: C.50, F.52, R.68 Ligands: FES.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.68, B:R.68, A:R.68, A:R.68 GOL.9: 6 residues within 4Å: Chain B: A.86, D.87, G.589, S.590, E.591, N.592 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.591, B:N.592, B:N.592 Water bridges: B:A.86, B:A.86, B:D.87 GOL.10: 6 residues within 4Å: Chain B: G.35, I.36, S.37, Q.355, I.356, C.359 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.37 GOL.11: 9 residues within 4Å: Chain A: P.369 Chain B: L.191, G.192, R.208, S.219, V.222, H.223, R.226 Ligands: MG.2 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.192, B:R.208, B:S.219, B:H.223, B:R.226, A:P.369 Water bridges: B:R.226, B:R.226

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain B: P.151, A.152 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: R.171, N.172, A.173 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wittenborn, E.C. et al., Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase. Elife (2018)

Release Date

2018-10-03

Peptides

Carbon monoxide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carbon monoxide dehydrogenase

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