Chlorine in PDB 5z9n: S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine

All present enzymatic activity of S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine:
5.99.1.3;

The structure of S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine, PDB code: 5z9n was solved by X.Huang, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.17 / 2.54
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.684, 97.684, 54.406, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.2

The binding sites of Chlorine atom in the S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine (pdb code 5z9n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine, PDB code: 5z9n:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:91.6 occ:1.00 CL9 A:HX5301 0.0 91.6 1.0 C6 A:HX5301 1.7 81.6 1.0 N5 A:HX5301 2.6 79.6 1.0 C1 A:HX5301 2.7 79.5 1.0 CG2 A:VAL120 3.0 42.0 1.0 CD1 A:ILE78 3.8 35.2 1.0 CB A:ASN46 3.8 38.7 1.0 C4 A:HX5301 3.8 78.2 1.0 C2 A:HX5301 3.9 78.7 1.0 CB A:VAL120 3.9 40.3 1.0 CG A:ASN46 4.0 39.7 1.0 ND2 A:ASN46 4.3 39.9 1.0 N3 A:HX5301 4.4 77.4 1.0 CG1 A:VAL120 4.5 40.1 1.0 OD1 A:ASN46 4.6 41.9 1.0 CG1 A:ILE78 4.6 36.1 1.0 CG2 A:ILE94 4.7 35.3 1.0

Chlorine binding site 2 out of 2 in the S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of S.Aureus Gyrb Atpase Domain in Complex with 4,6-Dichloro-2- (Methylthio)Pyrimidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:86.5 occ:1.00 CL1 A:HX5301 0.0 86.5 1.0 C2 A:HX5301 1.7 78.7 1.0 N3 A:HX5301 2.6 77.4 1.0 C1 A:HX5301 2.7 79.5 1.0 CD A:GLU50 2.9 53.7 1.0 O A:HOH405 3.0 35.5 1.0 CG A:GLU50 3.1 52.6 1.0 OE2 A:GLU50 3.2 55.5 1.0 OE1 A:GLU50 3.2 54.4 1.0 CB A:GLU50 3.4 50.9 1.0 OD2 A:ASP73 3.4 42.5 1.0 OG1 A:THR165 3.5 29.8 1.0 C4 A:HX5301 3.8 78.2 1.0 C6 A:HX5301 3.9 81.6 1.0 CB A:THR165 4.1 29.6 1.0 CG1 A:ILE78 4.1 36.1 1.0 CG A:ASP73 4.3 40.8 1.0 OD1 A:ASP73 4.4 41.0 1.0 N5 A:HX5301 4.4 79.6 1.0 O A:ASN46 4.5 37.9 1.0 CA A:GLU50 4.6 50.4 1.0 N A:ILE78 4.6 37.7 1.0 CG2 A:THR165 4.7 29.3 1.0 CD1 A:ILE78 4.8 35.2 1.0 C A:GLY77 4.9 39.0 1.0

X.Huang, J.Guo, Q.Liu, Q.Gu, J.Xu, H.Zhou. Identification of An Auxiliary Druggable Pocket in the Dna Gyrase Atpase Domain Using Fragment Probes Medchemcomm V. 9 1619 2018.
ISSN: ESSN 2040-2511
PubMed: 30429968
DOI: 10.1039/C8MD00148K