SMTL ID : 1wpn.1

Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.9, D.13, D.75 Ligands: MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.9, A:D.13, A:D.75, H2O.1, H2O.3 MN.2: 6 residues within 4Å: Chain A: D.15, D.75, H.97, T.119, D.149 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.15, A:D.75, A:H.97, A:D.149, H2O.1 MN.6: 4 residues within 4Å: Chain B: H.9, D.13, D.75 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.9, B:D.13, B:D.75, H2O.9, H2O.12 MN.7: 7 residues within 4Å: Chain B: D.15, D.75, H.97, H.98, T.119, D.149 Ligands: MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.15, B:D.75, B:H.97, B:D.149, H2O.9

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

SO4.3: 6 residues within 4Å: Chain A: V.89, Q.90, V.91, T.105, A.106, E.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.91, A:A.106, A:E.107, A:E.107 Water bridges: A:V.89 SO4.4: 4 residues within 4Å: Chain A: Q.47, L.50, E.56, S.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.47, A:Q.47, A:S.57 Water bridges: A:D.51 SO4.5: 3 residues within 4Å: Chain A: R.38, Q.41, L.60 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.42 Salt bridges: A:R.38

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

Manganese-dependent inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Manganese-dependent inorganic pyrophosphatase