Sodium in PDB 5cdm: 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

The structure of 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna, PDB code: 5cdm was solved by B.D.Bax, V.Srikannathasan, P.F.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.79 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.884, 93.884, 412.482, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 19.2

The structure of 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna (pdb code 5cdm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna, PDB code: 5cdm:

Sodium binding site 1 out of 1 in the 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.5A Structure of Qpt-1 with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:41.6 occ:1.00 O A:THR325 2.3 51.3 1.0 O A:GLN328 2.3 45.2 1.0 O A:TYR322 2.4 53.8 1.0 O A:HOH689 2.4 41.5 1.0 O A:HOH684 2.5 43.0 1.0 HB3 A:GLN328 3.1 44.6 1.0 H A:GLN328 3.1 50.1 1.0 C A:GLN328 3.3 42.4 1.0 C A:THR325 3.4 52.1 1.0 H A:THR325 3.4 69.2 1.0 C A:TYR322 3.6 49.2 1.0 N A:GLN328 3.7 41.7 1.0 HA A:PRO326 3.8 47.8 1.0 CB A:GLN328 3.8 37.2 1.0 CA A:GLN328 3.8 41.7 1.0 N A:THR325 4.0 57.7 1.0 HG2 A:GLN328 4.0 46.9 1.0 O A:LYS323 4.1 53.8 1.0 HA A:TYR322 4.1 55.0 1.0 HA A:LYS323 4.2 58.0 1.0 C A:LYS323 4.2 51.7 1.0 N A:PRO326 4.2 49.5 1.0 HA A:THR329 4.2 56.2 1.0 CA A:THR325 4.3 55.8 1.0 CA A:PRO326 4.3 39.9 1.0 N A:THR329 4.4 44.5 1.0 N A:LYS323 4.5 50.9 1.0 CA A:TYR322 4.5 45.9 1.0 H A:LEU327 4.5 51.2 1.0 CG A:GLN328 4.5 39.1 1.0 CA A:LYS323 4.5 48.3 1.0 C A:PRO326 4.5 42.1 1.0 HB2 A:GLN328 4.6 44.6 1.0 N A:LEU327 4.6 42.6 1.0 O A:LEU321 4.6 45.8 1.0 N A:GLN324 4.7 53.6 1.0 O A:HOH711 4.8 38.6 1.0 HA A:THR325 4.8 67.0 1.0 HA A:GLN328 4.8 50.1 1.0 CA A:THR329 4.9 46.8 1.0 HG1 A:THR325 4.9 73.0 1.0 HG1 A:THR329 4.9 66.9 1.0 C A:GLN324 4.9 56.3 1.0 C A:LEU327 5.0 45.6 1.0 H A:GLN324 5.0 64.3 1.0

P.F.Chan, V.Srikannathasan, J.Huang, H.Cui, A.P.Fosberry, M.Gu, M.M.Hann, M.Hibbs, P.Homes, K.Ingraham, J.Pizzollo, C.Shen, A.J.Shillings, C.E.Spitzfaden, R.Tanner, A.J.Theobald, R.A.Stavenger, B.D.Bax, M.N.Gwynn. Structural Basis of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide and Moxifloxacin. Nat Commun V. 6 10048 2015.
ISSN: ESSN 2041-1723
PubMed: 26640131
DOI: 10.1038/NCOMMS10048