SMTL ID : 2yiv.1

NI,FE-CODH with n-butylisocyanate state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: C.68, R.69, H.70, C.71, Q.73, G.74, C.76, G.88, I.89, C.90, A.92, I.97, R.100, M.219 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.68, A:C.71, A:C.76, A:C.90 SF4.7: 14 residues within 4Å: Chain B: C.68, R.69, H.70, C.71, Q.73, G.74, C.76, G.88, I.89, C.90, A.92, I.97, R.100, M.219 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.90

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

FES.2: 10 residues within 4Å: Chain A: C.59, F.61, G.62, C.67, R.77 Chain B: C.59, C.67, R.69, P.75 Ligands: FES.8 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.59, A:C.67 FES.8: 10 residues within 4Å: Chain A: C.59, C.67, R.69, P.75 Chain B: C.59, F.61, G.62, C.67, R.77 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.59, B:C.67

2 x WCC: FE(3)-NI(1)-S(4) CLUSTER(Non-covalent)

WCC.3: 15 residues within 4Å: Chain A: H.281, C.314, C.315, S.332, C.353, G.465, C.466, G.495, C.496, C.546, M.580, H.581, K.583 Ligands: YIV.4, FE.5 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.353, A:C.466, A:C.496, A:C.546 WCC.9: 15 residues within 4Å: Chain B: H.281, C.314, C.315, S.332, C.353, G.465, C.466, G.495, C.496, C.546, M.580, H.581, K.583 Ligands: YIV.10, FE.11 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.353, B:C.466, B:C.496, B:C.546

2 x YIV: N-butylformamide(Non-covalent)

YIV.4: 12 residues within 4Å: Chain A: H.113, A.464, G.465, C.466, C.546, N.549, A.576, K.583, A.584, I.587, G.588 Ligands: WCC.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.464, A:A.576, A:A.584, A:I.587, A:I.587 Hydrogen bonds: A:H.113, A:K.583, A:K.583 Water bridges: A:V.547 YIV.10: 12 residues within 4Å: Chain B: H.113, A.464, G.465, C.466, C.546, N.549, A.576, K.583, A.584, I.587, G.588 Ligands: WCC.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.464, B:A.576, B:A.584, B:I.587, B:I.587 Hydrogen bonds: B:H.113, B:K.583, B:K.583 Water bridges: B:V.547

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

FE.5: 5 residues within 4Å: Chain A: H.281, C.315, C.546, K.583 Ligands: WCC.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.281, A:C.315, H2O.32 FE.11: 5 residues within 4Å: Chain B: H.281, C.315, C.546, K.583 Ligands: WCC.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.281, B:C.315, H2O.64

2 x NBN: N-BUTYL ISOCYANIDE(Non-covalent)

NBN.6: 12 residues within 4Å: Chain A: L.102, V.585, T.589, I.600, P.604, P.605, I.606, L.616, T.617, F.628, V.630 Chain B: L.72 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.600, A:P.604, A:I.606, A:F.628, A:F.628, A:F.628, A:V.630 NBN.12: 12 residues within 4Å: Chain A: L.72 Chain B: L.102, V.585, T.589, I.600, P.604, P.605, I.606, L.616, T.617, F.628, V.630 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.600, B:P.604, B:I.606, B:F.628, B:F.628, B:F.628, B:V.630

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeoung, J.H. et al., N-Butyl Isocyanide Oxidation at the [Nife4S4Oh(X)] Cluster of Co Dehydrogenase. J.Biol.Inorg.Chem. (2012)

Release Date

2012-03-28

Peptides

CARBON MONOXIDE DEHYDROGENASE 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

CARBON MONOXIDE DEHYDROGENASE 2

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