SMTL ID : 1w56.1

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C and D131C)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-octamer

Ligands

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 6 residues within 4Å: Chain A: Y.211, F.214, Y.283, V.285, S.286, Y.324 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.283, A:Y.283, A:S.286, A:Y.324 FMT.5: 6 residues within 4Å: Chain B: Y.211, F.214, Y.283, V.285, S.286, Y.324 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.211, B:S.286 FMT.10: 6 residues within 4Å: Chain C: Y.211, F.214, Y.283, V.285, S.286, Y.324 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.283, C:Y.283, C:S.286, C:Y.324 FMT.14: 6 residues within 4Å: Chain D: Y.211, F.214, Y.283, V.285, S.286, Y.324 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.211, D:S.286 FMT.19: 6 residues within 4Å: Chain E: Y.211, F.214, Y.283, V.285, S.286, Y.324 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.283, E:Y.283, E:S.286, E:Y.324 FMT.23: 6 residues within 4Å: Chain F: Y.211, F.214, Y.283, V.285, S.286, Y.324 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.211, F:S.286 FMT.28: 6 residues within 4Å: Chain G: Y.211, F.214, Y.283, V.285, S.286, Y.324 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.283, G:Y.283, G:S.286, G:Y.324 FMT.32: 6 residues within 4Å: Chain H: Y.211, F.214, Y.283, V.285, S.286, Y.324 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.211, H:S.286

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.245, H2O.10, H2O.12, H2O.12, H2O.12, H2O.12 MG.6: 3 residues within 4Å: Chain B: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.245, H2O.23, H2O.23, H2O.25, H2O.25, H2O.25 MG.7: 1 residues within 4Å: Chain B: N.49 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.245, H2O.37, H2O.39, H2O.39, H2O.39, H2O.39 MG.15: 3 residues within 4Å: Chain D: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.245, H2O.50, H2O.50, H2O.52, H2O.52, H2O.52 MG.16: 1 residues within 4Å: Chain D: N.49 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain E: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.245, H2O.63, H2O.65, H2O.65, H2O.65, H2O.65 MG.24: 3 residues within 4Å: Chain F: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.245, H2O.77, H2O.77, H2O.78, H2O.78, H2O.78 MG.25: 1 residues within 4Å: Chain F: N.49 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain G: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.245, H2O.90, H2O.92, H2O.92, H2O.92, H2O.92 MG.33: 3 residues within 4Å: Chain H: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.245, H2O.103, H2O.103, H2O.105, H2O.105, H2O.105 MG.34: 1 residues within 4Å: Chain H: N.49 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.129, C.131, D.139, S.175 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.129, A:C.131, H2O.14, H2O.14 ZN.8: 4 residues within 4Å: Chain B: C.129, C.131, D.139, S.175 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.129, B:C.131, B:D.139, H2O.27 ZN.12: 4 residues within 4Å: Chain C: C.129, C.131, D.139, S.175 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.129, C:C.131, H2O.41, H2O.41 ZN.17: 4 residues within 4Å: Chain D: C.129, C.131, D.139, S.175 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.129, D:C.131, D:D.139, H2O.54 ZN.21: 4 residues within 4Å: Chain E: C.129, C.131, D.139, S.175 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:C.129, E:C.131, H2O.67, H2O.67 ZN.26: 4 residues within 4Å: Chain F: C.129, C.131, D.139, S.175 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.129, F:C.131, F:D.139, H2O.80 ZN.30: 4 residues within 4Å: Chain G: C.129, C.131, D.139, S.175 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:C.129, G:C.131, H2O.94, H2O.94 ZN.35: 4 residues within 4Å: Chain H: C.129, C.131, D.139, S.175 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.129, H:C.131, H:D.139, H2O.107

8 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: L.27 Chain D: D.37, D.319 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.37, D:D.319, H2O.2, H2O.2 K.9: 3 residues within 4Å: Chain B: L.27 Chain E: D.37, D.319 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.37, E:D.319, H2O.16, H2O.17 K.13: 3 residues within 4Å: Chain C: L.27 Chain H: D.37, D.319 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.37, H:D.319, H2O.29, H2O.29 K.18: 3 residues within 4Å: Chain A: D.37, D.319 Chain D: L.27 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.37, A:D.319, H2O.43, H2O.43 K.22: 3 residues within 4Å: Chain B: D.37, D.319 Chain E: L.27 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.37, B:D.319, H2O.55, H2O.56 K.27: 3 residues within 4Å: Chain F: L.27 Chain G: D.37, D.319 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.37, G:D.319, H2O.70, H2O.70 K.31: 3 residues within 4Å: Chain F: D.37, D.319 Chain G: L.27 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.37, F:D.319, H2O.82, H2O.82 K.36: 3 residues within 4Å: Chain C: D.37, D.319 Chain H: L.27 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.37, C:D.319, H2O.96, H2O.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frere, F. et al., Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro. J.Mol.Biol. (2005)

Release Date

2005-01-19

Peptides

DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

DELTA-AMINOLEVULINIC ACID DEHYDRATASE