SMTL ID : 1oao.1

NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: C.68, F.70, C.71, A.73, G.74, C.76, G.88, I.89, C.90, I.97, R.100, M.221 Chain B: M.584 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.68, A:C.71, A:C.76, A:C.90 SF4.17: 8 residues within 4Å: Chain A: C.59, G.62, C.67, R.69 Chain B: C.59, G.62, C.67, R.69 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.59, B:C.67, A:C.59, A:C.67 SF4.18: 12 residues within 4Å: Chain A: M.584 Chain B: C.68, F.70, C.71, A.73, G.74, C.76, G.88, I.89, C.90, R.100, M.221 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.90 SF4.35: 12 residues within 4Å: Chain C: I.146, C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: ZN.36 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.506, C:C.509, C:C.518, C:C.528 SF4.49: 12 residues within 4Å: Chain D: C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: NI.50, ACT.52 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.506, D:C.509, D:C.518, D:C.528

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

XCC.2: 13 residues within 4Å: Chain A: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 Ligands: FOR.3, FE2.16 10 PLIP interactions: 5 interactions with chain A, 5 Ligand-Ligand interactions Metal complexes: A:H.283, A:C.317, A:C.355, A:C.470, A:C.500, XCC.2, XCC.2, XCC.2, XCC.2, FOR.3 XCC.19: 13 residues within 4Å: Chain B: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 Ligands: FOR.20, FE2.34 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.283, B:C.317, B:C.355, B:C.470, B:C.500, FOR.20

2 x FOR: FORMYL GROUP(Non-covalent)

FOR.3: 5 residues within 4Å: Chain A: G.469, C.470, A.588, I.591 Ligands: XCC.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.553 FOR.20: 5 residues within 4Å: Chain B: G.469, S.585, A.588, I.591 Ligands: XCC.19 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.553

31 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: P.273, R.411, K.412, P.417, V.418 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: A.94, W.95, G.612, S.613, D.614, L.615 Chain D: H.27 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: P.17, R.18, V.19 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.148, E.153, V.154, E.155 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: S.414, N.415 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: K.195, R.199 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: T.399, R.402 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: K.398, R.402 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: K.144, R.148 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: R.176, E.180 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: H.119, H.122, Q.389, T.390 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain B: A.94, W.95, G.612, S.613, D.614, L.615 Chain C: H.27 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: R.25, D.26, K.41 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: P.17, R.18, V.19 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain B: T.399, R.402 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: K.195, R.199 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: K.398, R.402 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: H.119, H.122, Q.389, T.390 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: K.144, R.148 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain B: R.450 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain B: K.44, V.45, I.46, A.362, V.363, C.366 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain C: D.617, H.618, A.619, G.620 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain C: R.143, R.616, D.617, R.649 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain C: Y.572, R.577 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain C: S.69, R.85, K.86, Q.89, R.237 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain C: N.95, F.96, E.97 Ligands: GOL.46 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain C: R.334, K.335, R.429 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain D: D.617, H.618, A.619, G.620 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain D: S.69, R.85, K.86, Q.89, R.237 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain D: T.615, D.617, R.649, S.673, L.674 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain D: V.500, D.501, T.502, W.533, K.537 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: K.44, V.45, I.46, R.51, A.362, V.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.44, A:I.46, A:R.51 GOL.31: 4 residues within 4Å: Chain B: N.479, L.482, T.483, K.486 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.483, B:K.486 GOL.32: 5 residues within 4Å: Chain B: S.40, K.41, K.44, V.45, D.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.25, B:V.45 Water bridges: B:R.25 GOL.42: 3 residues within 4Å: Chain C: E.554, G.555, E.556 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.555, C:E.556 GOL.44: 6 residues within 4Å: Chain C: A.59, Y.60, Y.61, R.66, G.633, M.634 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.66, C:G.633 Water bridges: C:E.72 GOL.46: 8 residues within 4Å: Chain C: M.1, D.5, F.8, E.9, F.96, E.97, R.100 Ligands: SO4.45 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.97, C:E.97, C:E.97, C:R.100, C:R.100 GOL.48: 7 residues within 4Å: Chain C: T.499, V.500, D.501, T.502, Y.504, W.533, K.537 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.499, C:D.501, C:T.502, C:Y.504 GOL.55: 6 residues within 4Å: Chain B: I.386, T.399, M.403 Chain D: P.80, P.81, N.84 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Water bridges: B:D.387 Hydrogen bonds: D:N.84

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

FE2.16: 5 residues within 4Å: Chain A: H.283, C.317, C.550, K.587 Ligands: XCC.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.283, A:C.317, A:C.550 FE2.34: 5 residues within 4Å: Chain B: H.283, C.317, C.550, K.587 Ligands: XCC.19 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.283, B:C.317, B:C.550

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.33: 4 residues within 4Å: Chain B: R.148, E.153, V.154, E.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.154, B:E.155, B:E.155

1 x ZN: ZINC ION(Non-covalent)

ZN.36: 6 residues within 4Å: Chain C: C.509, C.595, C.597 Ligands: SF4.35, NI.37, SX.38 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.509, C:C.595, C:C.597

3 x NI: NICKEL (II) ION(Non-covalent)

NI.37: 7 residues within 4Å: Chain C: L.527, C.595, G.596, C.597, F.598 Ligands: ZN.36, SX.38 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.595, C:C.597 NI.50: 7 residues within 4Å: Chain D: C.509, F.512, C.595, C.597 Ligands: SF4.49, NI.51, ACT.52 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.509, D:C.595, D:C.597 NI.51: 6 residues within 4Å: Chain D: L.527, C.595, G.596, C.597, F.598 Ligands: NI.50 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.595, D:C.597

1 x SX: SULFUR OXIDE(Non-covalent)

SX.38: 8 residues within 4Å: Chain C: G.145, V.149, F.229, C.509, C.595, C.597 Ligands: ZN.36, NI.37 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.52: 6 residues within 4Å: Chain D: C.509, F.512, C.528, C.597 Ligands: SF4.49, NI.50 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Darnault, C. et al., Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase. Nat.Struct.Biol. (2003)

Release Date

2003-04-11

Peptides

CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA: AB
CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT BETA

CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ALPHA

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