SMTL ID : 6b6y.1

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, dithionite-reduced then oxygen-exposed (protein batch 2), oxidized C-cluster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 SF4.5: 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

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

CUV.2: 14 residues within 4Å: Chain A: H.274, C.309, C.310, N.313, C.348, V.454, G.455, C.456, G.485, C.486, C.527, Y.561, S.562, K.564 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.6: 13 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 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 GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: E.429, A.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.430

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

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

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

Related Entries With Identical Sequence