SMTL ID : 2iw4.1

CRYSTAL STRUCTURE OF BASILLUS SUBTILIS FAMILY II INORGANIC PYROPHOSPHATASE MUTANT, H98Q, IN COMPLEX WITH PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 9 residues within 4Å: Chain A: H.9, D.13, T.16, D.75 Ligands: FE.2, MG.4, MN.5, MN.6, 2PN.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:D.13, A:D.13, A:D.75, H2O.8 FE.2: 11 residues within 4Å: Chain A: D.15, D.75, H.97, Q.98, T.119, D.149 Ligands: FE.1, MG.4, MN.5, MN.6, 2PN.7 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.8 FE.11: 8 residues within 4Å: Chain B: H.9, D.13, T.16, D.75 Ligands: FE.12, MG.14, MN.17, 2PN.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.9, B:D.13, B:D.13, B:D.75, H2O.19 FE.12: 10 residues within 4Å: Chain B: D.15, D.75, H.97, Q.98, T.119, D.149 Ligands: FE.11, MG.14, MN.17, 2PN.18 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.19

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.13, R.295 Ligands: MG.4, 2PN.7 No protein-ligand interaction detected (PLIP) MG.4: 8 residues within 4Å: Chain A: D.13, D.149 Ligands: FE.1, FE.2, MG.3, MN.5, MN.6, 2PN.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.13, A:D.149, H2O.5, H2O.8, H2O.8 MG.13: 4 residues within 4Å: Chain B: D.13, R.295 Ligands: MG.14, 2PN.18 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain B: D.13, D.149 Ligands: FE.11, FE.12, MG.13, MN.17, 2PN.18 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.13, B:D.149, H2O.15, H2O.19, H2O.19

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

MN.5: 9 residues within 4Å: Chain A: H.9, D.13, T.16, D.75 Ligands: FE.1, FE.2, MG.4, MN.6, 2PN.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.9, A:D.13, A:D.13, A:D.75, H2O.8 MN.6: 11 residues within 4Å: Chain A: D.15, D.75, H.97, Q.98, T.119, D.149 Ligands: FE.1, FE.2, MG.4, MN.5, 2PN.7 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.8 MN.17: 10 residues within 4Å: Chain B: D.15, D.75, H.97, Q.98, T.119, D.149 Ligands: FE.11, FE.12, MG.14, 2PN.18 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.19

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.7: 15 residues within 4Å: Chain A: H.9, D.13, D.75, H.97, Q.98, D.149, K.205, R.295, K.296 Ligands: FE.1, FE.2, MG.3, MG.4, MN.5, MN.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.98, A:Q.98, A:K.205, A:R.295, A:R.295, A:K.296, A:K.296, A:K.296 2PN.18: 14 residues within 4Å: Chain B: H.9, D.13, D.75, H.97, Q.98, D.149, K.205, R.295, K.296 Ligands: FE.11, FE.12, MG.13, MG.14, MN.17 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.75, B:Q.98, B:Q.98, B:D.149, B:K.205, B:R.295, B:R.295, B:K.296, B:K.296, B:K.296 Water bridges: B:D.13, B:D.149

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

SO4.8: 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 SO4.19: 3 residues within 4Å: Chain B: R.38, Q.41, L.60 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.38, B:Q.41, B:V.42 Salt bridges: B:R.38

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain B: Y.23, K.27, L.30, F.32, E.93, Y.110, N.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.27, B:E.93, B:E.93 PG4.10: 3 residues within 4Å: Chain B: M.1, E.2, N.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.1, B:N.33 Water bridges: B:K.3

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain B: K.133, E.135, K.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.136, B:E.137 Water bridges: B:E.135, B:E.135 GOL.16: 5 residues within 4Å: Chain B: T.195, V.196, E.197, R.230, E.233 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.196, B:E.197, B:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabrichniy, I.P. et al., A Trimetal Site and Substrate Distortion in a Family II Inorganic Pyrophosphatase. J.Biol.Chem. (2007)

Release Date

2006-11-07

Peptides

MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE