Sodium in PDB 6fqv: 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna

All present enzymatic activity of 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna:
5.99.1.3;

The structure of 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna, PDB code: 6fqv was solved by B.D.Bax, T.Germe, E.Basque, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.280, 124.640, 155.240, 90.00, 95.65, 90.00
R / Rfree (%)	20 / 23.6

The binding sites of Sodium atom in the 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna (pdb code 6fqv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna, PDB code: 6fqv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ R:Na504 b:66.9 occ:1.00 O R:TYR322 2.2 60.3 1.0 O R:THR325 2.2 55.3 1.0 O R:HOH667 2.3 58.2 1.0 O R:HOH629 2.5 55.8 1.0 O R:GLN328 2.6 50.9 1.0 C R:THR325 3.3 56.5 1.0 C R:TYR322 3.3 61.5 1.0 O R:LYS323 3.4 68.9 1.0 C R:LYS323 3.7 68.0 1.0 C R:GLN328 3.7 51.7 1.0 N R:THR325 3.7 57.6 1.0 N R:GLN328 4.0 50.3 1.0 CA R:LYS323 4.1 63.0 1.0 N R:LYS323 4.1 60.6 1.0 CB R:GLN328 4.1 49.9 1.0 CA R:GLN328 4.1 48.5 1.0 CA R:THR325 4.2 54.9 1.0 N R:GLN324 4.2 64.5 1.0 N R:PRO326 4.3 51.9 1.0 O R:LEU321 4.4 62.0 1.0 CA R:PRO326 4.4 50.0 1.0 CA R:TYR322 4.4 55.9 1.0 C R:GLN324 4.4 64.7 1.0 N R:LEU327 4.6 49.1 1.0 C R:PRO326 4.7 52.3 1.0 CA R:GLN324 4.8 64.7 1.0 N R:THR329 4.8 47.8 1.0

Sodium binding site 2 out of 2 in the 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.60A Binary Complex of S.Aureus Gyrase with Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ T:Na504 b:65.2 occ:1.00 O T:GLN328 2.4 57.3 1.0 O T:TYR322 2.4 57.2 1.0 O T:THR325 2.5 58.7 1.0 C T:GLN328 3.5 56.6 1.0 O T:LYS323 3.5 65.6 1.0 C T:THR325 3.6 58.9 1.0 C T:TYR322 3.6 58.5 1.0 C T:LYS323 3.8 64.3 1.0 N T:GLN328 4.1 51.9 1.0 N T:THR325 4.1 57.6 1.0 CA T:GLN328 4.1 50.3 1.0 CB T:GLN328 4.1 51.3 1.0 CA T:LYS323 4.2 59.8 1.0 N T:LYS323 4.3 57.6 1.0 CA T:THR325 4.4 56.0 1.0 N T:PRO326 4.5 53.7 1.0 CA T:PRO326 4.5 51.9 1.0 N T:GLN324 4.5 59.8 1.0 CA T:TYR322 4.7 53.4 1.0 N T:THR329 4.7 53.1 1.0 C T:GLN324 4.7 62.5 1.0 O T:LEU321 4.7 58.4 1.0 N T:LEU327 4.8 49.1 1.0 C T:PRO326 4.8 53.7 1.0 CG T:GLN328 4.9 46.9 1.0

T.Germe, J.Voros, F.Jeannot, T.Taillier, R.A.Stavenger, E.Bacque, A.Maxwell, B.D.Bax. A New Class of Antibacterials, the Imidazopyrazinones, Reveal Structural Transitions Involved in Dna Gyrase Poisoning and Mechanisms of Resistance. Nucleic Acids Res. V. 46 4114 2018.
ISSN: ESSN 1362-4962
PubMed: 29538767
DOI: 10.1093/NAR/GKY181