SMTL ID : 6onc.2 (1 other biounit)

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, as-isolated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.274, A:C.310, A:C.348, A:C.456, A:C.486, H2O.7 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 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.274, B:C.310, B:C.348, B:C.456, B:C.486, H2O.29

2 x FE: FE (III) ION(Non-covalent)

FE.3: 3 residues within 4Å: Chain A: C.310, C.527 Ligands: XCC.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.527, H2O.7 FE.11: 3 residues within 4Å: Chain B: C.310, C.527 Ligands: XCC.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.527, H2O.29

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: A.86, D.87, G.589, S.590, E.591, N.592 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.591, A:N.592, A:N.592 Water bridges: A:A.86, A:A.86, A:D.87, A:N.592 GOL.12: 6 residues within 4Å: Chain B: A.86, D.87, G.589, S.590, E.591, N.592 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.589, B:E.591, B:N.592, B:N.592 Water bridges: B:A.86, B:A.86, B:D.87, B:E.591, B:N.592

5 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: Q.414 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: R.171, N.172, A.173 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
C

B
D

Carbon monoxide dehydrogenase

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