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Zinc in PDB 6q8a: Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine

Enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine

All present enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine:
6.1.1.4;

Protein crystallography data

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine, PDB code: 6q8a was solved by L.Pang, S.De Graef, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.71 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.151, 81.695, 225.429, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.7

Other elements in 6q8a:

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine (pdb code 6q8a). 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 Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine, PDB code: 6q8a:

Zinc binding site 1 out of 1 in 6q8a

Go back to Zinc Binding Sites List in 6q8a
Zinc binding site 1 out of 1 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with 5'-O-(N- (L-Leucyl)-Sulfamoyl)Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:35.8
occ:1.00
SG A:CYS452 2.2 41.5 1.0
SG A:CYS490 2.3 35.0 1.0
SG A:CYS493 2.4 37.4 1.0
SG A:CYS449 2.4 40.3 1.0
CB A:CYS490 3.0 35.0 1.0
CB A:CYS452 3.1 39.9 1.0
CB A:CYS449 3.3 40.5 1.0
CB A:CYS493 3.4 41.5 1.0
N A:CYS493 3.6 35.6 1.0
N A:CYS452 3.9 43.7 1.0
CA A:CYS493 4.1 36.6 1.0
CA A:CYS452 4.1 44.1 1.0
CA A:CYS490 4.5 41.4 1.0
CB A:CYS492 4.5 49.2 1.0
C A:CYS492 4.6 42.6 1.0
C A:CYS493 4.8 36.9 1.0
CB A:LYS451 4.8 48.5 1.0
CA A:CYS449 4.8 37.9 1.0
N A:GLY494 4.8 37.5 1.0
N A:CYS492 4.9 45.2 1.0
CA A:CYS492 4.9 42.4 1.0
C A:LYS451 4.9 46.4 1.0
C A:CYS490 5.0 37.6 1.0
N A:GLY495 5.0 38.6 1.0

Reference:

M.Nautiyal, S.De Graef, L.Pang, B.Gadakh, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Comparative Analysis of Pyrimidine Substituted Aminoacyl-Sulfamoyl Nucleosides As Potential Inhibitors Targeting Class I Aminoacyl-Trna Synthetases. Eur.J.Med.Chem. V. 173 154 2019.
ISSN: ISSN 0223-5234
PubMed: 30995568
DOI: 10.1016/J.EJMECH.2019.04.003
Page generated: Wed Dec 16 12:33:44 2020

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