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

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, reduced

Coordinates

PDB Format

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 SF4.9: 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 XCC: FE(4)-NI(1)-S(4) CLUSTER(Non-covalent)

XCC.2: 13 residues within 4Å: Chain A: H.274, C.309, C.310, H.327, C.348, G.455, C.456, C.486, C.527, Y.561, S.562, K.564 Ligands: FE.3 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.10: 13 residues within 4Å: Chain B: H.274, C.309, C.310, H.327, C.348, G.455, C.456, C.486, C.527, Y.561, S.562, K.564 Ligands: FE.11 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 FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: H.274, C.310, C.527 Ligands: XCC.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.527 FE.11: 3 residues within 4Å: Chain B: C.310, C.527 Ligands: XCC.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.527

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

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.6: 4 residues within 4Å: Chain A: R.184, S.549, V.605, G.606 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: P.578, Q.602, G.606, H.625, R.629 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: S.417 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: R.184, S.549, V.605, G.606 Ligand excluded by PLIP

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

FES.8: 10 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 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wittenborn, E.C. et al., Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase. J.Biol.Chem. (2019)

Release Date

2019-07-24

Peptides

Carbon monoxide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carbon monoxide dehydrogenase

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