SMTL ID : 1yq9.1 (1 other biounit)

Structure of the unready oxidized form of [NiFe] hydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.185, C.188, R.190, L.191, F.194, C.213, L.214, Y.215, C.219, G.221, P.222, V.240 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.185, A:C.188, A:C.213, A:C.219 SF4.3: 12 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, G.110, T.111, C.112, G.147, C.148, P.149 Chain B: R.63, H.219 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.73 Metal complexes: A:C.17, A:C.20, A:C.112, A:C.148

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

F3S.2: 12 residues within 4Å: Chain A: T.224, N.226, C.228, F.233, W.238, P.239, C.246, I.247, A.248, C.249 Chain B: K.216, Q.221 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.228, A:C.246, A:C.249

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 4 residues within 4Å: Chain A: T.111, Y.115, G.117, N.253 No protein-ligand interaction detected (PLIP) H2S.13: 4 residues within 4Å: Chain A: Y.262 Chain B: R.55, V.224, V.225 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: H.54, G.88, R.90 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.54 Water bridges: A:E.57 GOL.6: 7 residues within 4Å: Chain A: E.57, L.60, H.61, I.64, R.90, E.98 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.57, A:H.61, A:H.61 GOL.7: 1 residues within 4Å: Chain A: K.102 No protein-ligand interaction detected (PLIP) GOL.8: 7 residues within 4Å: Chain A: A.208, K.209, K.210, G.211 Chain B: Y.231, D.232, R.235 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.232, A:A.208 GOL.14: 3 residues within 4Å: Chain A: G.89 Chain B: E.347, F.348 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.347, B:F.348, A:G.89 GOL.15: 6 residues within 4Å: Chain B: V.84, G.85, V.86, D.446, W.447, Q.448 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.448, B:Q.448 Water bridges: B:V.84

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

NI.9: 6 residues within 4Å: Chain B: C.65, C.68, C.530, C.533 Ligands: FCO.11, PER.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.68, B:C.530, B:C.533

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain B: E.46, L.482, H.536 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.46, B:L.482, B:H.536, H2O.5, H2O.5, H2O.5

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

FCO.11: 14 residues within 4Å: Chain B: C.68, V.71, H.72, A.461, P.462, R.463, L.466, V.484, P.485, S.486, C.530, C.533 Ligands: NI.9, PER.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.463, B:R.463, B:S.486 Metal complexes: B:C.68, B:C.533

1 x PER: PEROXIDE ION(Non-covalent)

PER.12: 8 residues within 4Å: Chain B: C.65, V.67, C.68, R.463, C.530, C.533 Ligands: NI.9, FCO.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.68, B:R.463, B:R.463

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases. J.Biol.Inorg.Chem. (2005)

Release Date

2005-04-19

Peptides

Periplasmic [NiFe] hydrogenase small subunit: A
Periplasmic [NiFe] hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Periplasmic [NiFe] hydrogenase small subunit

Periplasmic [NiFe] hydrogenase large subunit

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