SMTL ID : 2ox4.1

Crystal structure of putative dehydratase from Zymomonas mobilis ZM4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.215, A:E.241, A:E.267, H2O.3, H2O.4, H2O.7 MG.5: 4 residues within 4Å: Chain B: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.215, B:E.241, B:E.267, H2O.19, H2O.23, H2O.29 MG.7: 4 residues within 4Å: Chain C: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.215, C:E.241, C:E.267, H2O.32, H2O.35, H2O.37 MG.10: 4 residues within 4Å: Chain D: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.215, D:E.241, D:E.267, H2O.50, H2O.51, H2O.51 MG.14: 4 residues within 4Å: Chain E: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.215, E:E.241, E:E.267, H2O.63, H2O.66, H2O.67 MG.16: 4 residues within 4Å: Chain F: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.215, F:E.241, F:E.267, H2O.80, H2O.81, H2O.81 MG.21: 4 residues within 4Å: Chain G: K.166, E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:E.215, G:E.241, G:E.267, H2O.96, H2O.97, H2O.99 MG.25: 3 residues within 4Å: Chain H: E.215, E.241, E.267 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:E.215, H:E.241, H:E.267, H2O.110, H2O.111, H2O.114

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.12, R.22, G.45, V.46, G.47, G.48 Chain B: D.57 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.12, A:G.45, A:G.47, A:G.48, A:S.49 Water bridges: A:R.22 GOL.3: 10 residues within 4Å: Chain A: W.103, L.117, L.118, G.119, K.301 Chain H: W.103, L.117, L.118, G.119, K.301 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain A Water bridges: H:T.70, H:L.118, H:K.301, A:L.118, A:K.301 Hydrogen bonds: A:L.118 GOL.6: 8 residues within 4Å: Chain A: D.57 Chain B: H.12, R.22, G.45, V.46, G.47, G.48, S.49 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.12, B:G.47, B:G.48, B:S.49 Water bridges: B:I.42, B:A.43, B:Y.44, B:G.45 GOL.8: 10 residues within 4Å: Chain B: W.103, L.117, L.118, G.119, K.301 Chain C: W.103, L.117, L.118, G.119, K.301 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Water bridges: C:L.118, C:G.119, C:K.301, B:L.118 Hydrogen bonds: B:L.118 GOL.9: 8 residues within 4Å: Chain C: H.12, R.22, G.45, V.46, G.47, G.48, S.49 Chain G: D.57 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.12, C:G.45, C:G.47, C:G.48, C:S.49 Water bridges: C:R.22, C:R.22 GOL.12: 8 residues within 4Å: Chain D: H.12, R.22, G.45, V.46, G.47, G.48, S.49 Chain E: D.57 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.12, D:G.47, D:G.48, D:S.49 Water bridges: D:H.12, D:R.22, D:Y.44, D:G.45, D:G.45 GOL.13: 8 residues within 4Å: Chain D: Q.21, Y.44, Q.132, F.135, R.141, A.319, H.344, K.346 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.21, D:R.141, D:R.141, D:K.346, D:K.346 GOL.15: 8 residues within 4Å: Chain D: D.57 Chain E: H.12, R.22, G.45, V.46, G.47, G.48, S.49 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:H.12, E:G.47, E:G.48, E:S.49 Water bridges: E:R.22, E:R.22 GOL.18: 8 residues within 4Å: Chain F: H.12, R.22, G.45, V.46, G.47, G.48, S.49 Chain H: D.57 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:H.12, F:G.47, F:G.48, F:S.49 Water bridges: F:R.22, F:R.22, F:I.42, F:G.45 GOL.19: 6 residues within 4Å: Chain F: K.27, Y.35, D.378, I.379, E.381, Y.384 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.378, F:Y.384, F:Y.384 Water bridges: F:K.27 GOL.22: 8 residues within 4Å: Chain C: D.57 Chain G: H.12, R.22, G.45, V.46, G.47, G.48, S.49 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:H.12, G:G.47, G:G.48, G:S.49 Water bridges: G:H.12, G:A.43, G:A.43, G:Y.44 GOL.23: 6 residues within 4Å: Chain D: L.112, K.116 Chain G: S.2, L.3, D.66, F.68 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:K.116, D:K.116, G:L.3, G:L.3 GOL.24: 6 residues within 4Å: Chain G: G.180, V.181, F.182, L.183, P.188, T.191 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:F.182, G:T.191 Water bridges: G:G.180, G:T.191 GOL.26: 7 residues within 4Å: Chain F: D.57 Chain H: H.12, R.22, G.45, V.46, G.47, G.48 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:H.12, H:G.45, H:G.47, H:G.48, H:S.49

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 8 residues within 4Å: Chain A: G.88, T.89, V.90, I.91 Chain B: G.88, T.89, V.90, I.91 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain D: G.88, T.89, V.90, I.91 Chain E: G.88, T.89, V.90, I.91 Ligand excluded by PLIP CL.17: 8 residues within 4Å: Chain F: G.88, T.89, V.90, I.91 Chain H: G.88, T.89, V.90, I.91 Ligand excluded by PLIP CL.20: 8 residues within 4Å: Chain C: G.88, T.89, V.90, I.91 Chain G: G.88, T.89, V.90, I.91 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Putative Dehydratase from Zymomonas Mobilis Zm4. To be Published

Release Date

2007-03-06

Peptides

Putative mandelate racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Putative mandelate racemase