SMTL ID : 4mgg.1

Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: L.46, K.47, K.117 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: A.145, P.146, R.178 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain G: W.297, Y.327 Ligand excluded by PLIP

3 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: S.69, H.100 Chain G: S.69, H.100 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: A:H.100, G:H.100, H2O.1, H2O.1, H2O.58, H2O.58 NI.8: 2 residues within 4Å: Chain C: H.100 Chain E: H.100 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: C:H.100, E:H.100, H2O.25, H2O.25, H2O.41, H2O.41 NI.11: 3 residues within 4Å: Chain D: H.100 Chain H: S.69, H.100 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: D:H.100, H:H.100, H2O.34, H2O.67, H2O.67, H2O.67

17 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: G.199, W.200 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.199, H2O.1, H2O.1, H2O.1, H2O.12, H2O.41 MG.4: 7 residues within 4Å: Chain A: Q.165, K.167, D.195, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.195, A:E.220, A:D.243, H2O.1, H2O.1, H2O.1 MG.5: 6 residues within 4Å: Chain B: K.167, D.195, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.195, B:E.220, B:D.243, H2O.13, H2O.21, H2O.24 MG.6: 2 residues within 4Å: Chain B: G.199, W.200 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:G.199, H2O.13, H2O.13, H2O.13, H2O.13, H2O.34 MG.9: 3 residues within 4Å: Chain C: G.199, W.200 Chain G: E.316 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:G.199, H2O.25, H2O.25, H2O.31, H2O.33, H2O.59 MG.10: 6 residues within 4Å: Chain C: D.195, N.197, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.195, C:E.220, C:D.243, H2O.25, H2O.25, H2O.34 MG.12: 3 residues within 4Å: Chain D: G.199, W.200, E.204 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:G.199, H2O.25, H2O.25, H2O.34, H2O.34, H2O.40 MG.13: 6 residues within 4Å: Chain D: Q.165, D.195, N.197, E.220, D.243, K.267 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.195, D:E.220, D:D.243, H2O.34, H2O.35, H2O.36 MG.14: 4 residues within 4Å: Chain E: N.26, G.199, W.200 Chain H: E.316 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:G.199, H2O.41, H2O.41, H2O.50, H2O.67 MG.15: 6 residues within 4Å: Chain E: K.167, D.195, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.195, E:E.220, E:D.243, H2O.41, H2O.41, H2O.41 MG.16: 2 residues within 4Å: Chain F: G.199, W.200 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:G.199, H2O.1, H2O.50, H2O.50, H2O.50, H2O.58 MG.17: 7 residues within 4Å: Chain F: K.167, D.195, E.220, D.243, E.244, N.265, K.267 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.195, F:E.220, F:D.243, H2O.50, H2O.50, H2O.58 MG.18: 6 residues within 4Å: Chain G: D.195, N.197, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.195, G:E.220, G:D.243, H2O.59, H2O.59, H2O.59 MG.19: 2 residues within 4Å: Chain G: G.155, E.159 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain G: G.199, W.200 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:G.199, H2O.13, H2O.59, H2O.59, H2O.59 MG.22: 7 residues within 4Å: Chain H: Q.165, K.167, D.195, E.220, D.243, N.265, K.267 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.195, H:E.220, H:D.243, H2O.67, H2O.67, H2O.67 MG.23: 4 residues within 4Å: Chain F: E.316 Chain H: G.199, W.200, E.204 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:G.199, H2O.50, H2O.67, H2O.67, H2O.67, H2O.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Crystal structure of an enolase (mandelate racemase subgroup) from labrenzia aggregata iam 12614 (target nysgrc-012903) with bound mg, space group p212121. To be Published

Release Date

2013-10-16

Peptides

Muconate lactonizing enzyme: 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

Muconate lactonizing enzyme