SMTL ID : 4lps.1 (1 other biounit)

Crystal structure of HypB from Helicobacter pylori in complex with nickel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.60, D.86, E.135 Ligands: GDP.2, PO4.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.60, A:D.86, A:E.135, H2O.6

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 15 residues within 4Å: Chain A: G.56, S.57, G.58, K.59, T.60, T.61, R.89, E.135, K.183, D.185, M.186, S.214, S.215 Ligands: MG.1, PO4.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.56, A:S.57, A:G.58, A:K.59, A:T.60, A:T.61, A:T.61, A:K.183, A:K.183, A:S.215, A:S.215, A:K.216 Water bridges: A:T.61, A:R.89, A:R.89 Salt bridges: A:K.59, A:R.89, A:D.185

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 11 residues within 4Å: Chain A: S.54, P.55, G.56, K.59, D.80, D.86, E.135, N.136, G.138 Ligands: MG.1, GDP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.56, A:E.135, A:G.138 Water bridges: A:T.60 Salt bridges: A:K.59 PO4.7: 5 residues within 4Å: Chain A: R.40, K.43, E.44, F.117, K.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.44 Salt bridges: A:R.40, A:K.43, A:K.121

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

NI.4: 3 residues within 4Å: Chain A: C.106, N.139, C.142 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.106, A:C.142

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: F.74, C.75, V.95, S.96, K.128, S.129 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.96 GOL.6: 9 residues within 4Å: Chain A: L.66, A.67, F.69, K.70, F.72, K.73, F.74, G.94 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.69, A:K.70, A:F.74, A:F.74 GOL.10: 3 residues within 4Å: Chain A: I.32, K.33, E.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.33, A:K.33

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.8: 1 residues within 4Å: Chain A: R.85 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.84 Salt bridges: A:R.85 MLI.9: 4 residues within 4Å: Chain A: M.174, K.205, T.239, H.240 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.239, A:T.239 Water bridges: A:H.240, A:S.241 Salt bridges: A:K.205, A:K.205, A:H.240, A:H.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sydor, A.M. et al., Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB. J.Biol.Chem. (2014)

Release Date

2013-12-18

Peptides

Hydrogenase/urease nickel incorporation protein HypB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hydrogenase/urease nickel incorporation protein HypB

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