Zinc in PDB 6wqi: Xanthomonas Citri Methionyl-Trna Synthetase (Apo)

All present enzymatic activity of Xanthomonas Citri Methionyl-Trna Synthetase (Apo):
6.1.1.10;

The structure of Xanthomonas Citri Methionyl-Trna Synthetase (Apo), PDB code: 6wqi was solved by G.F.Mercaldi, C.E.Benedetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.83 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.017, 95.253, 84.08, 90, 90.52, 90
R / Rfree (%)	18.5 / 23

The binding sites of Zinc atom in the Xanthomonas Citri Methionyl-Trna Synthetase (Apo) (pdb code 6wqi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Xanthomonas Citri Methionyl-Trna Synthetase (Apo), PDB code: 6wqi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Xanthomonas Citri Methionyl-Trna Synthetase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xanthomonas Citri Methionyl-Trna Synthetase (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:32.5 occ:1.00 SG A:CYS159 1.9 35.9 1.0 SG A:CYS156 2.0 35.1 1.0 SG A:CYS146 2.4 32.2 1.0 SG A:CYS143 2.4 35.0 1.0 CB A:CYS143 3.1 31.8 1.0 CB A:CYS156 3.1 33.4 1.0 CB A:CYS159 3.2 31.8 1.0 CB A:CYS146 3.3 34.5 1.0 N A:CYS146 3.7 39.3 1.0 N A:CYS159 3.9 28.6 1.0 CA A:CYS146 4.0 36.2 1.0 CA A:CYS159 4.1 31.7 1.0 CB A:ALA161 4.4 31.4 1.0 CB A:ASN145 4.5 37.4 1.0 CA A:CYS143 4.5 36.8 1.0 CA A:CYS156 4.6 30.9 1.0 C A:ASN145 4.7 35.8 1.0 C A:CYS146 4.7 37.7 1.0 C A:CYS159 4.7 32.5 1.0 N A:GLY147 4.8 34.1 1.0 CB A:SER148 4.8 34.1 1.0 OG A:SER148 4.8 40.4 1.0 N A:ALA161 4.8 30.1 1.0 ND2 A:ASN145 4.8 37.1 1.0 N A:GLY160 4.9 30.6 1.0 N A:SER148 4.9 29.6 1.0 C A:VAL158 4.9 29.4 1.0 CA A:ASN145 4.9 35.9 1.0 N A:ASN145 5.0 38.0 1.0

Zinc binding site 2 out of 2 in the Xanthomonas Citri Methionyl-Trna Synthetase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xanthomonas Citri Methionyl-Trna Synthetase (Apo) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:34.5 occ:1.00 SG B:CYS156 2.1 36.2 1.0 SG B:CYS159 2.2 33.6 1.0 SG B:CYS143 2.3 32.4 1.0 SG B:CYS146 2.3 35.2 1.0 CB B:CYS143 3.0 34.4 1.0 CB B:CYS156 3.1 34.5 1.0 CB B:CYS159 3.3 32.5 1.0 CB B:CYS146 3.3 37.3 1.0 N B:CYS146 3.8 35.5 1.0 N B:CYS159 3.9 29.1 1.0 CA B:CYS146 4.1 36.5 1.0 CA B:CYS159 4.1 29.4 1.0 CA B:CYS143 4.5 32.9 1.0 OG B:SER148 4.5 39.0 1.0 CB B:ALA161 4.5 29.0 1.0 CA B:CYS156 4.5 34.0 1.0 CB B:SER148 4.6 35.5 1.0 CB B:ASN145 4.6 34.5 1.0 C B:CYS146 4.7 40.1 1.0 N B:GLY147 4.7 39.7 1.0 C B:CYS159 4.8 29.0 1.0 C B:ASN145 4.8 32.8 1.0 N B:GLY160 4.9 24.7 1.0 C B:VAL158 4.9 31.1 1.0 ND2 B:ASN145 4.9 34.3 1.0 N B:SER148 4.9 32.1 1.0 CB B:VAL158 4.9 33.1 1.0 N B:ALA161 5.0 27.6 1.0

G.F.Mercaldi, M.De Oliveira Andrade, J.De Lima Zanella, A.T.Cordeiro, C.E.Benedetti. Molecular Basis For Diaryldiamine Selectivity and Competition with Trna in A Type-2METHIONYL-Trna Synthetase From A Gram-Negative Bacterium J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X