SMTL ID : 4u9i.1

High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

hetero-oligomer

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: E.14, C.15, T.16, G.17, C.18, E.73, G.110, T.111, C.112, V.118, G.147, C.148, P.149 Chain B: R.60, H.216 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.73 Metal complexes: A:C.15, A:C.18, A:C.112, A:C.148 SF4.2: 14 residues within 4Å: Chain A: V.185, H.186, C.189, R.191, L.192, F.195, C.214, L.215, Y.216, C.220, G.222, P.223, W.239, V.241 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.186, A:C.189, A:C.214, A:C.220

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

F3S.3: 14 residues within 4Å: Chain A: V.185, T.225, N.227, C.229, F.234, W.239, P.240, C.247, I.248, G.249, C.250, S.251 Chain B: K.213, Q.218 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.229, A:C.247, A:C.250

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

MPD.4: 8 residues within 4Å: Chain A: T.114, F.115, N.132, D.133, K.136, N.144, L.174, N.175 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.115, A:N.132, A:L.174, A:N.175 Hydrogen bonds: A:N.132, A:N.144 Water bridges: A:N.132, A:N.132 MPD.5: 5 residues within 4Å: Chain A: H.186, F.195, Y.216, P.223, V.224 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.195, A:P.223 Hydrogen bonds: A:P.223 MPD.6: 8 residues within 4Å: Chain A: R.191, A.209, R.210, K.211, G.212, D.242 Chain B: Y.228, D.229 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.210 Water bridges: A:R.191 Hydrophobic interactions: B:Y.228 MPD.7: 2 residues within 4Å: Chain A: P.65, H.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.65 MPD.8: 6 residues within 4Å: Chain A: D.31 Chain B: A.150, V.151, K.154, L.194, R.198 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.31 Hydrophobic interactions: B:L.194 MPD.9: 10 residues within 4Å: Chain A: P.5, S.6, H.66, G.67, F.68, I.69, Q.104, Y.162, L.163, K.166 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.5, A:I.69, A:I.69, A:Y.162, A:L.163 Water bridges: A:S.6, A:H.66 MPD.12: 2 residues within 4Å: Chain B: K.341, D.348 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.341 MPD.13: 9 residues within 4Å: Chain B: F.305, L.373, Y.376, S.377, T.387, L.391, P.398, L.401, F.402 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.305, B:Y.376, B:L.391, B:L.401, B:F.402 Hydrogen bonds: B:S.377 Water bridges: B:Y.376

1 x NWN: hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron(Non-covalent)

NWN.10: 14 residues within 4Å: Chain B: C.62, V.64, C.65, T.68, H.69, A.458, P.459, R.460, L.463, V.481, P.482, S.483, C.527, C.530 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.460, B:R.460, B:S.483, B:S.483 Metal complexes: B:C.62, B:C.65, B:C.65, B:C.527, B:C.530, B:C.530

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain B: E.43, K.355, L.479, H.533 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.43, B:L.479, B:H.533, H2O.12, H2O.12, H2O.13

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 3 residues within 4Å: Chain B: Y.180, D.182, A.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.182, B:D.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogata, H. et al., Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase. Nature (2015)

Release Date

2015-01-21

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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