SMTL ID : 3ekg.1 (1 other biounit)

CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 12 residues within 4Å: Chain A: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.216, A:E.270 Water bridges: A:D.216, A:D.216 Salt bridges: A:H.24, A:R.50, A:K.179, A:H.320 TLA.3: 12 residues within 4Å: Chain B: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.270 Water bridges: B:Y.161, B:E.270 Salt bridges: B:H.24, B:R.50, B:K.179, B:H.320 TLA.5: 12 residues within 4Å: Chain C: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.216, C:E.270 Water bridges: C:D.216, C:D.216 Salt bridges: C:H.24, C:R.50, C:K.179, C:H.320 TLA.7: 12 residues within 4Å: Chain D: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.270 Water bridges: D:Y.161, D:E.270 Salt bridges: D:H.24, D:R.50, D:K.179, D:H.320 TLA.9: 12 residues within 4Å: Chain E: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.216, E:E.270 Water bridges: E:D.216, E:D.216 Salt bridges: E:H.24, E:R.50, E:K.179, E:H.320 TLA.11: 12 residues within 4Å: Chain F: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.12 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:E.270 Water bridges: F:Y.161, F:E.270 Salt bridges: F:H.24, F:R.50, F:K.179, F:H.320 TLA.13: 12 residues within 4Å: Chain G: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.14 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:D.216, G:E.270 Water bridges: G:D.216, G:D.216 Salt bridges: G:H.24, G:R.50, G:K.179, G:H.320 TLA.15: 12 residues within 4Å: Chain H: H.24, R.50, T.163, K.179, D.216, W.218, E.242, E.270, H.320, E.340, L.342 Ligands: MG.16 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:D.216, H:E.270 Water bridges: H:Y.161, H:E.242, H:E.270 Salt bridges: H:H.24, H:R.50, H:K.179, H:H.320

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.179, D.216, E.242, E.270 Ligands: TLA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.216, A:E.242, A:E.270, H2O.1 MG.4: 5 residues within 4Å: Chain B: K.179, D.216, E.242, E.270 Ligands: TLA.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.216, B:E.242, B:E.270, H2O.9 MG.6: 5 residues within 4Å: Chain C: K.179, D.216, E.242, E.270 Ligands: TLA.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.216, C:E.242, C:E.270, H2O.18 MG.8: 5 residues within 4Å: Chain D: K.179, D.216, E.242, E.270 Ligands: TLA.7 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.216, D:E.242, D:E.270, H2O.26 MG.10: 5 residues within 4Å: Chain E: K.179, D.216, E.242, E.270 Ligands: TLA.9 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.216, E:E.242, E:E.270, H2O.34 MG.12: 5 residues within 4Å: Chain F: K.179, D.216, E.242, E.270 Ligands: TLA.11 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.216, F:E.242, F:E.270, H2O.43 MG.14: 5 residues within 4Å: Chain G: K.179, D.216, E.242, E.270 Ligands: TLA.13 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.216, G:E.242, G:E.270, H2O.51 MG.16: 5 residues within 4Å: Chain H: K.179, D.216, E.242, E.270 Ligands: TLA.15 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.216, H:E.242, H:E.270, H2O.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE. To be Published

Release Date

2008-09-30

Peptides

Mandelate racemase/muconate lactonizing enzyme: 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

Mandelate racemase/muconate lactonizing enzyme

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