SMTL ID : 1wpp.1

Structure of Streptococcus gordonii inorganic pyrophosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.9, D.13, D.77 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.9, A:D.13, A:D.77, H2O.1, H2O.2 ZN.2: 6 residues within 4Å: Chain A: D.15, D.77, H.99, H.100, D.151 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.15, A:D.77, A:H.99, A:D.151, H2O.1 ZN.6: 4 residues within 4Å: Chain B: H.9, D.13, D.77 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.9, B:D.13, B:D.77, H2O.11, H2O.15 ZN.7: 6 residues within 4Å: Chain B: D.15, D.77, H.99, H.100, D.151 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.15, B:D.77, B:H.99, B:D.151, H2O.11

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: R.297, K.298 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.297, A:K.298 Water bridges: A:D.205, A:K.298 Salt bridges: A:R.297, A:K.298 SO4.4: 5 residues within 4Å: Chain A: E.92, V.93, T.107, A.108, S.109 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.93, A:V.93, A:A.108, A:S.109 Water bridges: A:E.92, A:S.109 SO4.5: 3 residues within 4Å: Chain A: Q.82, Q.83, K.207 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.82, A:Q.83 Water bridges: A:K.207, A:R.217 Salt bridges: A:K.207 SO4.8: 2 residues within 4Å: Chain B: R.297, K.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.297, B:K.298 Salt bridges: B:K.207, B:R.297 SO4.9: 5 residues within 4Å: Chain B: E.92, V.93, T.107, A.108, S.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.93, B:A.108, B:S.109 SO4.10: 3 residues within 4Å: Chain B: Q.82, Q.83, K.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.82, B:Q.83 Salt bridges: B:K.207

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

CL.11: 4 residues within 4Å: Chain A: P.110 Chain B: H.100, R.101, K.298 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabrichniy, I.P. et al., Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion. Biochemistry (2004)

Release Date

2004-11-23

Peptides

Probable manganese-dependent inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable manganese-dependent inorganic pyrophosphatase