SMTL ID : 3ze6.1

3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the as-isolated oxidized state at 1.50 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.207, H.208, C.211, Y.213, L.214, Y.217, C.232, R.233, Y.234, C.238, G.240, P.241, V.260 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.232, A:C.238 SF4.2: 16 residues within 4Å: Chain A: W.165, I.207, T.243, A.245, C.247, W.252, W.258, C.259, V.260, C.265, I.266, G.267, C.268, V.269 Chain B: R.171, Q.176 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.247, A:C.259, A:C.265, A:C.268 SF4.3: 17 residues within 4Å: Chain A: Q.14, G.17, C.18, T.19, G.20, C.21, E.77, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.62, H.174 Ligands: FSX.4 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.121, A:C.159

1 x FSX: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)(Covalent)

FSX.4: 18 residues within 4Å: Chain A: Q.14, G.17, C.18, T.19, G.20, C.21, E.77, G.78, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.62, H.174 Ligands: SF4.3 9 PLIP interactions: 9 interactions with chain A, Hydrogen bonds: A:C.18, A:G.20, A:G.78 Water bridges: A:C.121, A:C.121 Metal complexes: A:C.18, A:E.77, A:C.121, A:C.159

5 x SBY: 3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE(Non-covalent)

SBY.5: 14 residues within 4Å: Chain A: W.12, S.22, L.25, L.26, S.28, I.33, A.34, L.37, L.43, H.46, V.49 Chain B: L.155, E.156 Ligands: SBY.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.33, A:I.33, A:L.37 SBY.6: 11 residues within 4Å: Chain A: P.8, V.10, V.40, I.41, F.73, V.75, L.116, V.170, A.173, L.174, I.177 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.8, A:V.10, A:I.41, A:F.73, A:F.73, A:L.116, A:V.170, A:L.174, A:I.177 SBY.12: 14 residues within 4Å: Chain A: L.38 Chain B: A.116, Q.117, V.120, Q.121, G.122, P.123, T.125, F.128, G.147, V.148, Y.151, I.152 Ligands: SBY.13 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.117, B:V.120, B:P.123, B:F.128, B:F.128, B:F.128, B:Y.151, B:Y.151, B:Y.151, B:I.152, A:L.38 SBY.13: 13 residues within 4Å: Chain A: L.26, A.34, L.37, L.38, L.43, V.49 Chain B: P.127, F.128, Y.151, I.152, L.155 Ligands: SBY.5, SBY.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.155 SBY.14: 11 residues within 4Å: Chain B: Y.215, K.222, F.225, K.226, L.338, F.342, I.344, L.352, A.356, G.362, V.365 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.225, B:F.225, B:L.338, B:I.344, B:L.352, B:A.356, B:V.365

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

FCO.7: 12 residues within 4Å: Chain B: C.67, H.71, A.409, P.410, R.411, L.414, S.432, A.433, S.434, U.478, C.481 Ligands: NI.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.411, B:R.411, B:A.433, B:S.434 Metal complexes: B:C.67, B:C.481

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

NI.8: 6 residues within 4Å: Chain B: C.64, C.67, R.411, U.478, C.481 Ligands: FCO.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.67, B:C.481

1 x FE2: FE (II) ION(Non-covalent)

FE2.9: 4 residues within 4Å: Chain B: E.45, K.306, I.430, H.484 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.45, B:I.430, B:H.484, H2O.13, H2O.13, H2O.22

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

CL.10: 6 residues within 4Å: Chain B: C.67, T.69, A.70, F.99, N.102, P.410 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain B: S.219, K.220, K.222, L.341 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.219, B:S.219, B:K.220, B:K.222, B:L.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques, M.C. et al., Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough. Int.J.Hydrogen Energy (2013)

Release Date

2013-06-12

Peptides

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT: A
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYS SELENOCYSTEINE-CONTAINING: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT

PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYS SELENOCYSTEINE-CONTAINING

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