Zinc in PDB 6ykk: Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15

Enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15

All present enzymatic activity of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15:
6.1.1.4;

Protein crystallography data

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15, PDB code: 6ykk 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) 112.01 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.165, 80.973, 224.022, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.1

Other elements in 6ykk:

The structure of Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15 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 15 (pdb code 6ykk). 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 15, PDB code: 6ykk:

Zinc binding site 1 out of 1 in 6ykk

Go back to Zinc Binding Sites List in 6ykk
Zinc binding site 1 out of 1 in the Neisseria Gonorrhoeae Leucyl-Trna Synthetase in Complex with Compound 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1106

b:32.6
occ:1.00
SG A:CYS452 2.3 35.4 1.0
SG A:CYS490 2.4 36.3 1.0
SG A:CYS493 2.4 34.9 1.0
SG A:CYS449 2.4 37.0 1.0
CB A:CYS490 3.0 32.4 1.0
CB A:CYS452 3.3 33.9 1.0
CB A:CYS449 3.3 33.4 1.0
CB A:CYS493 3.4 37.1 1.0
N A:CYS493 3.7 34.7 1.0
N A:CYS452 3.9 34.6 1.0
CA A:CYS493 4.1 35.9 1.0
CA A:CYS452 4.2 32.4 1.0
CB A:CYS492 4.3 47.6 1.0
CB A:LYS451 4.5 37.0 1.0
CA A:CYS490 4.5 40.3 1.0
C A:CYS492 4.6 34.7 1.0
O A:HOH1411 4.6 36.1 1.0
C A:CYS493 4.8 36.3 1.0
CA A:CYS449 4.8 41.2 1.0
C A:LYS451 4.8 43.6 1.0
N A:CYS492 4.8 32.8 1.0
CA A:CYS492 4.8 33.5 1.0
N A:GLY494 4.9 35.6 1.0
N A:GLY495 5.0 39.0 1.0
C A:CYS490 5.0 32.5 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: Wed Dec 16 13:17:09 2020

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