SMTL ID : 1mns.1

ON THE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE FROM PSEUDOMONAS PUTIDA: MECHANISTIC AND CRYSTALLOGRAPHIC EVIDENCE FOR STEREOSPECIFIC ALKYLATION BY (R)-ALPHA-PHENYLGLYCIDATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: K.162, K.164, D.193, E.219, E.245 Ligands: APG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.193, A:E.219, A:E.245, H2O.14 MG.3: 6 residues within 4Å: Chain B: K.162, K.164, D.193, E.219, E.245 Ligands: APG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.193, B:E.219, B:E.245, H2O.223 MG.5: 6 residues within 4Å: Chain C: K.162, K.164, D.193, E.219, E.245 Ligands: APG.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.193, C:E.219, C:E.245, H2O.432 MG.7: 6 residues within 4Å: Chain D: K.162, K.164, D.193, E.219, E.245 Ligands: APG.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.193, D:E.219, D:E.245, H2O.641 MG.9: 6 residues within 4Å: Chain E: K.162, K.164, D.193, E.219, E.245 Ligands: APG.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.193, E:E.219, E:E.245, H2O.850 MG.11: 6 residues within 4Å: Chain F: K.162, K.164, D.193, E.219, E.245 Ligands: APG.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.193, F:E.219, F:E.245, H2O.1059 MG.13: 6 residues within 4Å: Chain G: K.162, K.164, D.193, E.219, E.245 Ligands: APG.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.193, G:E.219, G:E.245, H2O.1268 MG.15: 6 residues within 4Å: Chain H: K.162, K.164, D.193, E.219, E.245 Ligands: APG.16 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.193, H:E.219, H:E.245, H2O.1477

8 x APG: ATROLACTIC ACID (2-PHENYL-LACTIC ACID)(Covalent)

APG.2: 13 residues within 4Å: Chain A: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.50, A:Y.52, A:K.164, A:L.317 Hydrogen bonds: A:S.137, A:K.164, A:N.195, A:E.245, A:E.245 Salt bridges: A:K.162, A:K.164, A:H.295 pi-Stacking: A:H.295 APG.4: 13 residues within 4Å: Chain B: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.50, B:Y.52, B:K.164, B:L.317 Hydrogen bonds: B:S.137, B:K.164, B:N.195, B:E.245, B:E.245 Salt bridges: B:K.162, B:K.164, B:H.295 pi-Stacking: B:H.295 APG.6: 13 residues within 4Å: Chain C: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.50, C:Y.52, C:K.164, C:L.317 Hydrogen bonds: C:S.137, C:K.164, C:N.195, C:E.245, C:E.245 Salt bridges: C:K.162, C:K.164, C:H.295 pi-Stacking: C:H.295 APG.8: 13 residues within 4Å: Chain D: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.50, D:Y.52, D:K.164, D:L.317 Hydrogen bonds: D:S.137, D:K.164, D:N.195, D:E.245, D:E.245 Salt bridges: D:K.162, D:K.164, D:H.295 pi-Stacking: D:H.295 APG.10: 13 residues within 4Å: Chain E: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:F.50, E:Y.52, E:K.164, E:L.317 Hydrogen bonds: E:S.137, E:N.195, E:E.245, E:E.245 Water bridges: E:K.164, E:E.219 Salt bridges: E:K.162, E:K.164, E:H.295 pi-Stacking: E:H.295 APG.12: 13 residues within 4Å: Chain F: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.11 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.50, F:Y.52, F:K.164, F:L.317 Hydrogen bonds: F:S.137, F:N.195, F:E.245, F:E.245 Water bridges: F:K.164, F:E.219 Salt bridges: F:K.162, F:K.164, F:H.295 pi-Stacking: F:H.295 APG.14: 13 residues within 4Å: Chain G: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.13 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:F.50, G:Y.52, G:K.164, G:L.317 Hydrogen bonds: G:S.137, G:N.195, G:E.245, G:E.245 Water bridges: G:K.164, G:E.219 Salt bridges: G:K.162, G:K.164, G:H.295 pi-Stacking: G:H.295 APG.16: 13 residues within 4Å: Chain H: F.50, Y.52, S.137, K.162, K.164, D.193, N.195, E.219, E.245, H.295, E.315, L.317 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:F.50, H:Y.52, H:K.164, H:L.317 Hydrogen bonds: H:S.137, H:N.195, H:E.245, H:E.245 Water bridges: H:K.164, H:E.219 Salt bridges: H:K.162, H:K.164, H:H.295 pi-Stacking: H:H.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Landro, J.A. et al., The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate. Biochemistry (1994)

Release Date

1993-10-31

Peptides

MANDELATE RACEMASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

MANDELATE RACEMASE

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