Atomistry » Zinc » PDB 3ekz-3eyv » 3esj
Atomistry »
  Zinc »
    PDB 3ekz-3eyv »
      3esj »

Zinc in PDB 3esj: Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3esj was solved by W.N.Hunter, N.L.Ramsden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.69 / 2.70
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 144.498, 144.498, 144.498, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.8

Other elements in 3esj:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand (pdb code 3esj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3esj:

Zinc binding site 1 out of 1 in 3esj

Go back to Zinc Binding Sites List in 3esj
Zinc binding site 1 out of 1 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn900

b:31.9
occ:1.00
 NE2 A:HIS10 2.0 32.4 1.0
OD2 A:ASP8 2.0 28.3 1.0
ND1 A:HIS42 2.1 25.7 1.0
O A:HOH922 2.3 14.0 1.0
CG A:ASP8 2.9 28.1 1.0
CE1 A:HIS10 2.9 31.4 1.0
CD2 A:HIS10 3.0 31.7 1.0
CE1 A:HIS42 3.0 26.9 1.0
OD1 A:ASP8 3.0 28.5 1.0
CG A:HIS42 3.1 27.9 1.0
CB A:HIS42 3.5 27.4 1.0
ND1 A:HIS10 4.0 32.8 1.0
CG A:HIS10 4.1 31.6 1.0
NE2 A:HIS42 4.1 25.1 1.0
CD2 A:HIS42 4.2 27.4 1.0
CB A:ASP8 4.3 28.3 1.0
O A:HOH982 4.4 57.2 1.0
CD1 A:ILE57 4.6 39.6 1.0
O A:VAL9 4.7 30.0 1.0
O A:HOH977 4.8 40.5 1.0
CA A:VAL39 4.9 32.7 1.0
O A:ASP38 5.0 35.3 1.0
CA A:HIS42 5.0 27.9 1.0

Reference:

N.L.Ramsden, L.Buetow, A.Dawson, L.A.Kemp, V.Ulaganathan, R.Brenk, G.Klebe, W.N.Hunter. A Structure-Based Approach to Ligand Discovery For 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy J.Med.Chem. V. 52 2531 2009.
ISSN: ISSN 0022-2623
PubMed: 19320487
DOI: 10.1021/JM801475N
Page generated: Thu Oct 24 12:55:55 2024

Last articles

Mg in 1Y3S
Mg in 1Y37
Mg in 1Y2K
Mg in 1Y2J
Mg in 1Y2H
Mg in 1Y2E
Mg in 1Y2D
Mg in 1Y26
Mg in 1Y0V
Mg in 1Y2C
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy