SMTL ID : 9f47.1

crystal structure of [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 402: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)(Non-covalent)

402.1: 20 residues within 4Å: Chain A: A.292, P.293, A.294, T.330, A.334, C.367, C.368, S.391, P.392, M.393, M.421, P.422, C.423, K.426, F.485, G.486, V.491, M.565, C.571 Ligands: SF4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.294, A:C.367, A:M.393, A:K.426 Metal complexes: A:C.571 402.12: 20 residues within 4Å: Chain B: A.292, P.293, A.294, T.330, A.334, C.367, C.368, S.391, P.392, M.393, M.421, P.422, C.423, K.426, F.485, G.486, V.491, M.565, C.571 Ligands: SF4.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.294, B:C.367, B:M.393, B:K.426 Metal complexes: B:C.367, B:C.571

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

SF4.2: 13 residues within 4Å: Chain A: C.368, P.369, P.422, C.423, A.425, K.426, M.565, A.566, C.567, G.570, C.571, G.574 Ligands: 402.1 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.368, A:C.423, A:C.567, A:C.571 SF4.3: 14 residues within 4Å: Chain A: I.218, C.222, I.223, G.224, C.225, G.226, A.227, C.228, H.245, C.262, P.263, V.264, A.266, I.267 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.222, A:C.225, A:C.228, A:C.262 SF4.4: 14 residues within 4Å: Chain A: L.216, C.232, P.233, V.234, C.236, I.237, I.247, C.252, T.253, H.254, C.255, G.256, A.257, C.258 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.232, A:C.252, A:C.255, A:C.258 SF4.13: 14 residues within 4Å: Chain B: C.255, C.368, P.369, S.370, P.422, C.423, A.425, K.426, M.565, A.566, C.567, C.571, G.574 Ligands: 402.12 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.368, B:C.423, B:C.567, B:C.571 SF4.14: 13 residues within 4Å: Chain B: I.218, C.222, I.223, G.224, C.225, G.226, A.227, C.228, H.245, C.262, P.263, A.266, I.267 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.222, B:C.225, B:C.228, B:H.245, B:C.262 SF4.15: 14 residues within 4Å: Chain B: L.216, C.232, P.233, V.234, C.236, I.237, I.247, C.252, T.253, H.254, C.255, G.256, A.257, C.258 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.232, B:C.252, B:C.255, B:C.258

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.113, I.115, Q.116, H.199, C.205, C.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.113, A:H.199, A:C.205, A:C.210 ZN.16: 6 residues within 4Å: Chain B: C.113, I.115, Q.116, H.199, C.205, C.210 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.113, B:H.199, B:C.205, B:C.210

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

CL.6: 3 residues within 4Å: Chain A: E.470, I.471, E.477 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: L.280, K.285, G.323, D.325 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: Y.121, M.147, V.174, N.183, I.184 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: I.403, W.404, E.407, V.474 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: R.450, Q.577, P.578, K.579, T.580 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: L.216, Y.249, H.254, A.269 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: K.619, Y.620, D.622, K.628 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: E.470, E.477 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: L.280, K.285, G.323, D.325 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: G.574, Q.577, P.578, K.579, T.580, R.591 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, J. et al., A Zinc Binding Four-Helix Domain Stabilizes the Dimeric Structure of O2-stable [FeFe]-Hydrogenase CbA5H from Clostridium beijerinckii. To Be Published

Release Date

2024-12-18

Peptides

[FeFe]-hydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[FeFe]-hydrogenase

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