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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

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