SMTL ID : 2zo9.1 (1 other biounit)

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

FE2.1: 6 residues within 4Å: Chain A: D.8, H.10, D.50, H.197 Ligands: FE2.2, MLI.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:H.10, A:D.50, A:H.197 FE2.2: 6 residues within 4Å: Chain A: D.50, N.80, H.156, H.195 Ligands: FE2.1, MLI.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.50, A:H.156, A:H.195 FE2.4: 6 residues within 4Å: Chain B: D.8, H.10, D.50, H.197 Ligands: FE2.5, MLI.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:H.10, B:D.50, B:H.197 FE2.5: 6 residues within 4Å: Chain B: D.50, N.80, H.156, H.195 Ligands: FE2.4, MLI.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.50, B:H.156, B:H.195 FE2.7: 6 residues within 4Å: Chain C: D.8, H.10, D.50, H.197 Ligands: FE2.8, MLI.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:H.10, C:D.50, C:H.197 FE2.8: 6 residues within 4Å: Chain C: D.50, N.80, H.156, H.195 Ligands: FE2.7, MLI.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.50, C:H.156, C:H.195 FE2.10: 6 residues within 4Å: Chain D: D.8, H.10, D.50, H.197 Ligands: FE2.11, MLI.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.8, D:H.10, D:D.50, D:H.197 FE2.11: 6 residues within 4Å: Chain D: D.50, N.80, H.156, H.195 Ligands: FE2.10, MLI.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.50, D:H.156, D:H.195 FE2.13: 6 residues within 4Å: Chain E: D.8, H.10, D.50, H.197 Ligands: FE2.14, MLI.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.8, E:H.10, E:D.50, E:H.197 FE2.14: 6 residues within 4Å: Chain E: D.50, N.80, H.156, H.195 Ligands: FE2.13, MLI.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.50, E:H.156, E:H.195 FE2.16: 6 residues within 4Å: Chain F: D.8, H.10, D.50, H.197 Ligands: FE2.17, MLI.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.8, F:H.10, F:D.50, F:H.197 FE2.17: 6 residues within 4Å: Chain F: D.50, N.80, H.156, H.195 Ligands: FE2.16, MLI.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.50, F:H.156, F:H.195

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

MLI.3: 10 residues within 4Å: Chain A: D.8, H.10, D.50, N.80, H.81, I.170, H.195, H.197 Ligands: FE2.1, FE2.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.80, A:N.80 Salt bridges: A:H.10, A:H.81, A:H.81, A:H.195, A:H.195, A:H.197 MLI.6: 11 residues within 4Å: Chain B: D.8, H.10, D.50, N.80, H.81, M.167, I.170, H.195, H.197 Ligands: FE2.4, FE2.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.80 Salt bridges: B:H.10, B:H.81, B:H.81, B:H.195, B:H.195, B:H.197 MLI.9: 10 residues within 4Å: Chain C: D.8, H.10, D.50, N.80, H.81, I.170, H.195, H.197 Ligands: FE2.7, FE2.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.80, C:N.80 Salt bridges: C:H.10, C:H.81, C:H.81, C:H.195, C:H.195, C:H.197 MLI.12: 11 residues within 4Å: Chain D: D.8, H.10, D.50, N.80, H.81, M.167, I.170, H.195, H.197 Ligands: FE2.10, FE2.11 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.80 Salt bridges: D:H.10, D:H.81, D:H.81, D:H.195, D:H.195, D:H.197 MLI.15: 10 residues within 4Å: Chain E: D.8, H.10, D.50, N.80, H.81, I.170, H.195, H.197 Ligands: FE2.13, FE2.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:N.80, E:N.80 Salt bridges: E:H.10, E:H.81, E:H.81, E:H.195, E:H.195, E:H.197 MLI.18: 11 residues within 4Å: Chain F: D.8, H.10, D.50, N.80, H.81, M.167, I.170, H.195, H.197 Ligands: FE2.16, FE2.17 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.80 Salt bridges: F:H.10, F:H.81, F:H.81, F:H.195, F:H.195, F:H.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, C.J. et al., Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr.,Sect.F (2008)

Release Date

2008-10-07

Peptides

Phosphohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
B

D
C

E
B

F
C

Phosphohydrolase

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