SMTL ID : 1ubm.1

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

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: 14 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, E.75, G.112, T.113, C.114, V.120, 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: 12 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, V.243 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 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.231, A:C.249, A:C.252

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 3 residues within 4Å: Chain A: L.194, P.195, D.198 No protein-ligand interaction detected (PLIP) MPD.5: 7 residues within 4Å: Chain A: T.116, F.117, N.134, D.135, N.146, L.176, N.177 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.117, A:N.134 Hydrogen bonds: A:N.134, A:N.146, A:L.176 MPD.6: 7 residues within 4Å: Chain A: P.7, H.68, G.69, F.70, I.71, Q.106, Y.164 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.106, A:Y.164 Water bridges: A:H.68, A:G.69 MPD.9: 8 residues within 4Å: Chain B: F.306, L.374, Y.377, S.378, L.392, P.399, L.402, F.403 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.306, B:F.306, B:L.392, B:P.399, B:F.403 MPD.10: 3 residues within 4Å: Chain B: R.53, W.445, M.447 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.445, B:W.445 Hydrogen bonds: B:W.445 Water bridges: B:R.53, B:W.445, B:M.447

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 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.11, H2O.11, H2O.11

1 x FNE: (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)(Non-covalent)

FNE.8: 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

Ogata, H. et al., Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen. J.Am.Chem.Soc. (2002)

Release Date

2003-04-29

Peptides

Periplasmic [NiFe] hydrogenase Small subunit: A
Periplasmic [NiFe] hydrogenase Large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

Periplasmic [NiFe] hydrogenase Small subunit

Periplasmic [NiFe] hydrogenase Large subunit

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