SMTL ID : 2mnr.1

MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: K.162, D.193, E.219, E.245 Ligands: SO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.193, A:E.219, A:E.245, H2O.1, H2O.3 MN.3: 5 residues within 4Å: Chain B: K.162, D.193, E.219, E.245 Ligands: SO4.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.193, B:E.219, B:E.245, H2O.9, H2O.11 MN.5: 5 residues within 4Å: Chain C: K.162, D.193, E.219, E.245 Ligands: SO4.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.193, C:E.219, C:E.245, H2O.17, H2O.19 MN.7: 5 residues within 4Å: Chain D: K.162, D.193, E.219, E.245 Ligands: SO4.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.193, D:E.219, D:E.245, H2O.25, H2O.27 MN.9: 5 residues within 4Å: Chain E: K.162, D.193, E.219, E.245 Ligands: SO4.10 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.193, E:E.219, E:E.245, H2O.33, H2O.35 MN.11: 5 residues within 4Å: Chain F: K.162, D.193, E.219, E.245 Ligands: SO4.12 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.193, F:E.219, F:E.245, H2O.42, H2O.43 MN.13: 5 residues within 4Å: Chain G: K.162, D.193, E.219, E.245 Ligands: SO4.14 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.193, G:E.219, G:E.245, H2O.50, H2O.51 MN.15: 5 residues within 4Å: Chain H: K.162, D.193, E.219, E.245 Ligands: SO4.16 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.193, H:E.219, H:E.245, H2O.58, H2O.59

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

SO4.2: 10 residues within 4Å: Chain A: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.137 Water bridges: A:S.137, A:K.164, A:K.164, A:N.195, A:E.245 Salt bridges: A:K.162, A:K.164, A:H.295 SO4.4: 10 residues within 4Å: Chain B: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.137 Water bridges: B:S.137, B:K.164, B:K.164, B:N.195, B:E.245 Salt bridges: B:K.162, B:K.164, B:H.295 SO4.6: 10 residues within 4Å: Chain C: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.5 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.137 Water bridges: C:S.137, C:K.164, C:K.164, C:N.195, C:E.245 Salt bridges: C:K.162, C:K.164, C:H.295 SO4.8: 10 residues within 4Å: Chain D: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.7 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.137 Water bridges: D:S.137, D:K.164, D:K.164, D:N.195, D:E.245 Salt bridges: D:K.162, D:K.164, D:H.295 SO4.10: 10 residues within 4Å: Chain E: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.9 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.137 Water bridges: E:S.137, E:K.164, E:K.164, E:N.195, E:E.245 Salt bridges: E:K.162, E:K.164, E:H.295 SO4.12: 10 residues within 4Å: Chain F: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.11 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.137 Water bridges: F:S.137, F:K.164, F:K.164, F:N.195, F:E.245 Salt bridges: F:K.162, F:K.164, F:H.295 SO4.14: 10 residues within 4Å: Chain G: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.13 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:S.137 Water bridges: G:S.137, G:K.164, G:K.164, G:N.195, G:E.245 Salt bridges: G:K.162, G:K.164, G:H.295 SO4.16: 10 residues within 4Å: Chain H: S.137, K.162, K.164, D.193, E.219, E.245, H.295, E.315, L.317 Ligands: MN.15 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:S.137, H:D.193 Water bridges: H:K.164, H:K.164, H:N.195, H:E.245 Salt bridges: H:K.162, H:K.164, H:H.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neidhart, D.J. et al., Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues. Biochemistry (1991)

Release Date

1994-01-31

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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