SMTL ID : 1h2r.1

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, E.75, G.112, T.113, C.114, G.149, C.150, P.151 Chain B: R.61, H.217 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.75 Metal complexes: A:C.17, A:C.20, A:C.114, A:C.150 SF4.2: 11 residues within 4Å: Chain A: H.188, C.191, R.193, L.194, F.197, C.216, L.217, Y.218, C.222, G.224, P.225 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.188, A:C.191, A:C.216, A:C.222

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

F3S.3: 12 residues within 4Å: Chain A: T.227, N.229, C.231, F.236, W.241, P.242, C.249, I.250, G.251, C.252 Chain B: K.214, Q.219 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.231, A:C.249, A:C.252, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: E.44, L.480, H.534 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.44, B:L.480, B:H.534, H2O.8, H2O.8, H2O.8

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

NFE.5: 13 residues within 4Å: Chain B: C.63, C.66, T.69, H.70, A.459, P.460, R.461, L.464, V.482, P.483, S.484, C.528, C.531 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.461, B:R.461, B:S.484 Metal complexes: B:C.63, B:C.66, B:C.66, B:C.528, B:C.531, B:C.531

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higuchi, Y. et al., Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des. (1999)

Release Date

2000-01-05

Peptides

PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT): A
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)

PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)

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