SMTL ID : 1h2a.1

SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: E.66, C.67, G.69, C.70, E.125, T.163, C.164, G.199, C.200, P.201 Chain B: R.79, H.235 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.125 Metal complexes: A:C.67, A:C.70, A:C.164, A:C.200 SF4.2: 9 residues within 4Å: Chain A: H.238, C.241, R.243, L.244, F.247, C.266, L.267, Y.268, C.272 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.238, A:C.241, A:C.266, A:C.272

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

F3S.3: 12 residues within 4Å: Chain A: T.277, N.279, C.281, F.286, W.291, P.292, C.299, I.300, G.301, C.302 Chain B: K.232, Q.237 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.281, A:C.299, A:C.302

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: E.62, L.498, H.552 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.62, B:L.498, B:H.552, H2O.10, H2O.10, H2O.10

1 x NFE: NI-FE ACTIVE CENTER(Non-covalent)

NFE.5: 12 residues within 4Å: Chain B: C.81, C.84, T.87, H.88, A.477, P.478, R.479, L.482, P.501, S.502, C.546, C.549 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.479, B:R.479, B:S.502 Metal complexes: B:C.81, B:C.84, B:C.84, B:C.546, B:C.549, B:C.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higuchi, Y. et al., Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis. Structure (1997)

Release Date

1999-02-09

Peptides

HYDROGENASE: A
HYDROGENASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

HYDROGENASE

HYDROGENASE