SMTL ID : 8x9e.1

Crystal structure of CO dehydrogenase mutant with increased affinity for electron mediators in low PEG concentration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.68, H.70, C.71, Q.73, G.74, C.76, G.88, I.89, C.90, 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 SF4.6: 12 residues within 4Å: Chain B: C.68, H.70, C.71, Q.73, G.74, C.76, G.88, I.89, C.90, 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: 8 residues within 4Å: Chain A: C.59, F.61, G.62, C.67 Chain B: R.69 Ligands: EDO.5, FES.7, EDO.10 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.59, A:C.67 FES.7: 8 residues within 4Å: Chain A: R.69 Chain B: C.59, F.61, G.62, C.67 Ligands: FES.2, EDO.5, EDO.10 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.59, B:C.67

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

XCC.3: 13 residues within 4Å: Chain A: H.281, C.314, C.315, S.332, C.353, G.465, C.466, C.496, C.546, M.580, H.581, K.583 Ligands: FE.4 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.281, A:C.315, A:C.353, A:C.466, A:C.496, A:C.546, H2O.5, H2O.5 XCC.8: 13 residues within 4Å: Chain B: H.281, C.314, C.315, S.332, C.353, G.465, C.466, C.496, C.546, M.580, H.581, K.583 Ligands: FE.9 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.281, B:C.315, B:C.353, B:C.466, B:C.496, B:C.546, H2O.9, H2O.9

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

FE.4: 4 residues within 4Å: Chain A: C.314, C.353, C.496 Ligands: XCC.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.314, A:C.496 FE.9: 4 residues within 4Å: Chain B: C.314, C.353, C.496 Ligands: XCC.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.314, B:C.496

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: F.61 Chain B: C.59 Ligands: FES.2, FES.7, EDO.10 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: C.59 Chain B: F.61 Ligands: FES.2, EDO.5, FES.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S.M. et al., Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Carbon monoxide dehydrogenase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Carbon monoxide dehydrogenase 2

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