SMTL ID : 6g94.1

Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-4-4-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.8: 12 residues within 4Å: Chain C: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221 SF4.15: 12 residues within 4Å: Chain E: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:H.187, E:C.190, E:C.215, E:C.221 SF4.22: 11 residues within 4Å: Chain G: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, I.243 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:H.187, G:C.190, G:C.215, G:C.221

4 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 11 residues within 4Å: Chain A: I.186, T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.249, A:C.252 F3S.9: 11 residues within 4Å: Chain C: I.186, T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252 F3S.16: 10 residues within 4Å: Chain E: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain F: K.226 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.230, E:C.249, E:C.252 F3S.23: 11 residues within 4Å: Chain G: I.186, T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain H: K.226 3 PLIP interactions: 3 interactions with chain G, Metal complexes: G:C.230, G:C.249, G:C.252

4 x ER2: Fe4S4(Non-covalent)

ER2.3: 14 residues within 4Å: Chain A: E.16, C.17, T.18, G.19, C.20, G.113, T.114, C.115, C.120, G.148, C.149, P.150 Chain B: R.74, H.229 7 PLIP interactions: 7 interactions with chain A, Salt bridges: A:E.16, A:E.76 Metal complexes: A:C.17, A:C.20, A:C.115, A:C.120, A:C.149 ER2.10: 12 residues within 4Å: Chain C: C.17, T.18, G.19, C.20, T.114, C.115, C.120, G.148, C.149, P.150 Chain D: R.74, H.229 6 PLIP interactions: 6 interactions with chain C, Salt bridges: C:E.76 Metal complexes: C:C.17, C:C.20, C:C.115, C:C.120, C:C.149 ER2.17: 15 residues within 4Å: Chain E: E.16, C.17, T.18, G.19, C.20, E.76, G.113, T.114, C.115, C.120, G.148, C.149, P.150 Chain F: R.74, H.229 7 PLIP interactions: 7 interactions with chain E, Salt bridges: E:E.16, E:E.76 Metal complexes: E:C.17, E:C.20, E:C.115, E:C.120, E:C.149 ER2.24: 12 residues within 4Å: Chain G: C.17, T.18, G.19, C.20, T.114, C.115, C.120, G.148, C.149, P.150 Chain H: R.74, H.229 6 PLIP interactions: 6 interactions with chain G, Salt bridges: G:E.76 Metal complexes: G:C.17, G:C.20, G:C.115, G:C.120, G:C.149

4 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.4: 13 residues within 4Å: Chain B: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.5 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.509, B:R.509, B:T.532, B:T.532 Metal complexes: B:C.79, B:C.579, H2O.7 FCO.11: 13 residues within 4Å: Chain D: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.12 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Water interactions Hydrogen bonds: D:R.509, D:R.509, D:T.532, D:T.532 Metal complexes: D:C.79, D:C.579, H2O.14 FCO.18: 13 residues within 4Å: Chain F: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.19 7 PLIP interactions: 6 interactions with chain F, 1 Ligand-Water interactions Hydrogen bonds: F:R.509, F:R.509, F:T.532, F:T.532 Metal complexes: F:C.79, F:C.579, H2O.20 FCO.25: 13 residues within 4Å: Chain H: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.26 6 PLIP interactions: 5 interactions with chain H, 1 Ligand-Water interactions Hydrogen bonds: H:R.509, H:R.509, H:T.532 Metal complexes: H:C.79, H:C.579, H2O.27

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

NI.5: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:C.79, B:C.576, B:C.579, H2O.7 NI.12: 5 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.11 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.76, D:C.79, D:C.576, D:C.579, H2O.14 NI.19: 5 residues within 4Å: Chain F: C.76, C.79, C.576, C.579 Ligands: FCO.18 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.76, F:C.79, F:C.576, F:C.579, H2O.20 NI.26: 5 residues within 4Å: Chain H: C.76, C.79, C.576, C.579 Ligands: FCO.25 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.76, H:C.79, H:C.576, H:C.579, H2O.27

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.57, B:C.528, B:H.582, H2O.5, H2O.6, H2O.7 MG.13: 3 residues within 4Å: Chain D: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.57, D:C.528, D:H.582, H2O.12, H2O.12, H2O.13 MG.20: 3 residues within 4Å: Chain F: E.57, C.528, H.582 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.57, F:C.528, F:H.582, H2O.18, H2O.20 MG.27: 3 residues within 4Å: Chain H: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:E.57, H:C.528, H:H.582, H2O.24, H2O.26, H2O.27

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

CL.7: 2 residues within 4Å: Chain B: F.212, R.266 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: F.212, R.266 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain F: F.212, R.266 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain H: F.212, R.266 Ligand excluded by PLIP

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.29: 22 residues within 4Å: Chain I: M.29, L.32, M.33, G.36, Y.37, I.39, G.40, R.60, H.63, F.64, G.67, T.71, M.143, I.144, G.147, F.148, L.150, Y.151, H.181, H.184, R.185, M.188 17 PLIP interactions: 17 interactions with chain I, Hydrophobic interactions: I:L.32, I:L.32, I:L.32, I:F.64, I:M.143, I:I.144, I:F.148, I:L.150, I:L.150, I:R.185 Water bridges: I:R.60 Salt bridges: I:R.60, I:H.181, I:H.181, I:R.185 Metal complexes: I:H.63, I:H.184 HEM.30: 23 residues within 4Å: Chain J: M.29, L.32, M.33, G.36, Y.37, I.39, G.40, R.60, H.63, F.64, G.67, T.71, M.143, I.144, G.147, F.148, L.150, Y.151, H.181, H.184, R.185, M.188, I.191 17 PLIP interactions: 17 interactions with chain J, Hydrophobic interactions: J:L.32, J:L.32, J:L.32, J:I.39, J:F.64, J:I.144, J:F.148, J:L.150, J:L.150, J:I.191 Water bridges: J:R.60 Salt bridges: J:R.60, J:H.181, J:H.181, J:R.185 Metal complexes: J:H.63, J:H.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster. Chem. Commun. (Camb.) (2018)

Release Date

2018-06-13

Peptides

Hydrogenase-1 small chain: ACEG
Hydrogenase-1 large chain: BDFH
Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

E
Q

G
R

B
L

D
M

F
J

H
K

I
A

J
B

Membrane

We predict this structure to be a membrane protein.
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Hydrogenase-1 small chain

Hydrogenase-1 large chain

Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit

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