SMTL ID : 4udy.1

NCO- bound to cluster C of Ni,Fe-CO dehydrogenase at true-atomic resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: C.48, R.49, H.50, C.51, Q.53, G.54, C.56, G.68, I.69, C.70, A.72, I.77, R.80, M.199 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.48, A:C.51, A:C.56, A:C.70 SF4.6: 14 residues within 4Å: Chain B: C.48, R.49, H.50, C.51, Q.53, G.54, C.56, G.68, I.69, C.70, A.72, I.77, R.80, M.199 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.48, B:C.51, B:C.56, B:C.70

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

FES.2: 10 residues within 4Å: Chain A: C.39, F.41, G.42, C.47, R.57 Chain B: C.39, C.47, R.49, P.55 Ligands: FES.7 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.39, A:C.47 FES.7: 10 residues within 4Å: Chain A: C.39, C.47, R.49, P.55 Chain B: C.39, F.41, G.42, C.47, R.57 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.39, B:C.47

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

WCC.3: 15 residues within 4Å: Chain A: H.261, C.294, C.295, S.312, C.333, G.445, C.446, G.475, C.476, C.526, M.560, H.561, K.563 Ligands: FE2.4, 0NM.5 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:C.333, A:C.446, A:C.476, A:C.526, 0NM.5, H2O.27 WCC.8: 15 residues within 4Å: Chain B: H.261, C.294, C.295, S.312, C.333, G.445, C.446, G.475, C.476, C.526, M.560, H.561, K.563 Ligands: FE2.9, 0NM.10 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:C.333, B:C.446, B:C.476, B:C.526, 0NM.10, H2O.56

2 x FE2: FE (II) ION(Non-covalent)

FE2.4: 6 residues within 4Å: Chain A: H.261, C.295, G.475, C.526 Ligands: WCC.3, 0NM.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.295, A:C.526, 0NM.5 FE2.9: 6 residues within 4Å: Chain B: H.261, C.295, G.475, C.526 Ligands: WCC.8, 0NM.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.295, B:C.526, 0NM.10

2 x 0NM: cyanic acid(Non-covalent)

0NM.5: 8 residues within 4Å: Chain A: H.93, H.261, C.295, C.526, K.563, I.567 Ligands: WCC.3, FE2.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.563 Water bridges: A:V.527, A:V.527, A:V.527 0NM.10: 8 residues within 4Å: Chain B: H.93, H.261, C.295, C.526, K.563, I.567 Ligands: WCC.8, FE2.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.563 Water bridges: B:V.527, B:V.527, B:V.527

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fesseler, J. et al., How the [Nife4 S4 ] Cluster of Co Dehydrogenase Activates Co2 and Nco(.). Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-05-13

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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