SMTL ID : 1w54.1

Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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.9: 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.13: 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.17: 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.21: 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.25: 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.29: 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

8 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: D.37, D.319 Chain D: L.27, R.29 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.37, A:D.319, H2O.20, H2O.20 K.6: 5 residues within 4Å: Chain B: D.36, D.37, D.319 Chain E: L.27, R.29 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.37, B:D.319, H2O.24 K.10: 4 residues within 4Å: Chain C: D.37, D.319 Chain H: L.27, R.29 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.37, C:D.319, H2O.43, H2O.44 K.14: 5 residues within 4Å: Chain A: L.27, R.29 Chain D: D.36, D.37, D.319 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.37, D:D.319, H2O.1 K.18: 4 residues within 4Å: Chain B: L.27, R.29 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.8, H2O.8 K.22: 5 residues within 4Å: Chain F: D.36, D.37, D.319 Chain G: L.27, R.29 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.37, F:D.319, H2O.36 K.26: 4 residues within 4Å: Chain F: L.27, R.29 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.32, H2O.32 K.30: 5 residues within 4Å: Chain C: L.27, R.29 Chain H: D.36, D.37, D.319 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.37, H:D.319, H2O.13

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.5, H2O.6, H2O.6, H2O.6, H2O.6 MG.7: 5 residues within 4Å: Chain B: M.178, D.179, R.181, E.245, D.249 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.245, H2O.11, H2O.11 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.16, H2O.17, H2O.17, H2O.17, H2O.17 MG.15: 5 residues within 4Å: Chain D: M.178, D.179, R.181, E.245, D.249 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.245, H2O.23, H2O.23 MG.19: 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.28, H2O.29, H2O.29, H2O.29, H2O.29 MG.23: 5 residues within 4Å: Chain F: M.178, D.179, R.181, E.245, D.249 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.245, H2O.35, H2O.35 MG.27: 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.40, H2O.41, H2O.41, H2O.41, H2O.41 MG.31: 5 residues within 4Å: Chain H: M.178, D.179, R.181, E.245, D.249 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.245, H2O.46, H2O.46

8 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: A.129, D.131, C.139 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:C.139, H2O.7, H2O.7 ZN.8: 4 residues within 4Å: Chain B: A.129, D.131, C.139, S.175 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.131 ZN.12: 3 residues within 4Å: Chain C: A.129, D.131, C.139 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.131, C:C.139, H2O.19, H2O.19 ZN.16: 4 residues within 4Å: Chain D: A.129, D.131, C.139, S.175 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.131 ZN.20: 3 residues within 4Å: Chain E: A.129, D.131, C.139 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:C.139, H2O.31, H2O.31 ZN.24: 4 residues within 4Å: Chain F: A.129, D.131, C.139, S.175 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.131 ZN.28: 3 residues within 4Å: Chain G: A.129, D.131, C.139 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.131, G:C.139, H2O.42, H2O.42 ZN.32: 4 residues within 4Å: Chain H: A.129, D.131, C.139, S.175 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.131

Links

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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