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Zinc in PDB 6yks: Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D

Enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D

All present enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D:
6.1.1.4;

Protein crystallography data

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D, PDB code: 6yks was solved by L.Pang, 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) 65.60 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.023, 80.909, 224.177, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.7

Other elements in 6yks:

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D 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 Compound 11D (pdb code 6yks). 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 Compound 11D, PDB code: 6yks:

Zinc binding site 1 out of 1 in 6yks

Go back to Zinc Binding Sites List in 6yks
Zinc binding site 1 out of 1 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 11D


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 Compound 11D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:33.3
occ:1.00
 SG A:CYS452 2.2 38.8 1.0
SG A:CYS490 2.3 35.4 1.0
SG A:CYS493 2.3 35.9 1.0
SG A:CYS449 2.4 36.3 1.0
CB A:CYS490 3.0 34.1 1.0
CB A:CYS452 3.2 40.3 1.0
CB A:CYS493 3.3 39.2 1.0
CB A:CYS449 3.3 35.8 1.0
N A:CYS493 3.7 32.3 1.0
N A:CYS452 3.9 33.4 1.0
CA A:CYS493 4.1 33.3 1.0
CA A:CYS452 4.2 35.6 1.0
CB A:CYS492 4.4 49.0 1.0
CB A:LYS451 4.4 49.2 1.0
CA A:CYS490 4.4 34.3 1.0
C A:CYS492 4.6 35.4 1.0
O A:HOH1513 4.6 39.0 1.0
C A:CYS493 4.8 33.8 1.0
CA A:CYS449 4.8 32.5 1.0
CD A:LYS451 4.8 59.3 1.0
C A:LYS451 4.8 42.0 1.0
N A:CYS492 4.8 40.1 1.0
CA A:CYS492 4.8 40.3 1.0
CG A:LYS451 4.9 53.5 1.0
N A:GLY494 4.9 40.0 1.0
C A:CYS490 4.9 34.4 1.0
N A:GLY495 4.9 41.9 1.0

Reference:

D.De Ruysscher, L.Pang, S.M.G.Lenders, D.Cappoen, P.Cos, J.Rozenski, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Synthesis and Structure-Activity Studies of Novel Anhydrohexitol-Based Leucyl-Trna Synthetase Inhibitors. Eur.J.Med.Chem. 13021 2020.
ISSN: ISSN 0223-5234
PubMed: 33248851
DOI: 10.1016/J.EJMECH.2020.113021
Page generated: Tue Oct 29 15:10:08 2024

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