Manganese in PDB 5iwm: 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna.

All present enzymatic activity of 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna.:
5.99.1.3;

The structure of 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna., PDB code: 5iwm was solved by B.D.Bax, T.J.Miles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.785, 93.785, 413.350, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 22.4

The structure of 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna. also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna. (pdb code 5iwm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna., PDB code: 5iwm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:14.2 occ:1.00 OE2 B:GLU435 1.9 13.4 1.0 O B:HOH803 2.0 27.3 1.0 OD2 B:ASP508 2.1 12.6 1.0 OP1 E:DG9 2.3 12.5 0.5 OP1 F:DG9 2.3 16.2 0.5 O B:HOH814 2.5 11.5 1.0 O3' E:DG8 2.7 10.9 0.5 O3' F:DT8 2.9 14.5 0.5 CD B:GLU435 3.0 12.9 1.0 P E:DG9 3.0 11.6 0.5 CG B:ASP508 3.1 11.8 1.0 P F:DG9 3.2 15.2 0.5 OE1 B:GLU435 3.4 14.7 1.0 CB B:ASP508 3.4 11.5 1.0 O E:HOH105 3.5 7.5 1.0 C3' E:DG8 4.0 10.0 0.5 O B:LYS581 4.1 30.6 1.0 OP2 E:DG9 4.1 11.8 0.5 OD2 B:ASP510 4.1 13.5 1.0 OD1 B:ASP508 4.2 11.8 1.0 O5' E:DG9 4.2 12.3 0.5 C3' F:DT8 4.2 13.7 0.5 OP2 F:DG9 4.2 15.5 0.5 CG B:GLU435 4.3 12.5 1.0 O5' F:DG9 4.3 16.0 0.5 C4' E:DG8 4.4 9.7 0.5 CB B:GLU435 4.5 12.6 1.0 C5' F:DG9 4.6 16.0 0.5 C4' F:DT8 4.6 13.5 0.5 OD1 B:ASP510 4.6 14.6 1.0 CZ C:PHE123 4.7 14.0 1.0 C5' E:DG9 4.7 12.6 0.5 C2' E:DG8 4.7 9.5 0.5 CG B:ASP510 4.7 14.1 1.0 CA B:ASP508 4.8 11.9 1.0 C5' E:DG8 4.9 9.6 0.5 CA B:GLY582 4.9 22.0 1.0 C2' F:DT8 4.9 13.2 0.5 CE1 C:PHE123 4.9 13.6 1.0

Manganese binding site 2 out of 2 in the 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.5A Structure of GSK945237 with S.Aureus Dna Gyrase and Dna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1001 b:17.4 occ:1.00 OE2 D:GLU435 1.9 15.3 1.0 O D:HOH1121 1.9 6.6 1.0 OD2 D:ASP508 2.0 15.7 1.0 OP1 F:DG9 2.3 16.4 0.5 O D:HOH1106 2.4 9.6 1.0 O3' F:DT8 2.5 15.3 0.5 OP1 E:DG9 2.5 14.9 0.5 O3' E:DG8 2.5 14.1 0.5 P F:DG9 2.9 16.3 0.5 CD D:GLU435 3.0 15.5 1.0 P E:DG9 3.1 14.8 0.5 CG D:ASP508 3.1 16.3 1.0 OE1 D:GLU435 3.5 15.3 1.0 CB D:ASP508 3.6 15.1 1.0 O F:HOH203 3.6 20.6 1.0 C3' E:DG8 3.7 13.6 0.5 C3' F:DT8 3.8 14.3 0.5 OP2 F:DG9 3.9 17.2 0.5 C4' E:DG8 3.9 13.0 0.5 O5' F:DG9 4.1 17.1 0.5 OP2 E:DG9 4.1 15.4 0.5 OD1 D:ASP508 4.1 15.5 1.0 C4' F:DT8 4.2 13.8 0.5 CG D:GLU435 4.2 13.7 1.0 O5' E:DG9 4.2 15.2 0.5 CB D:GLU435 4.4 13.8 1.0 C5' E:DG9 4.4 16.3 0.5 C5' E:DG8 4.4 12.9 0.5 O D:LYS581 4.4 23.7 1.0 OD2 D:ASP510 4.4 16.0 1.0 OD1 D:ASP510 4.5 18.1 1.0 C5' F:DG9 4.5 18.6 0.5 C2' E:DG8 4.5 13.8 0.5 C2' F:DT8 4.5 14.2 0.5 C5' F:DT8 4.6 13.9 0.5 CG D:ASP510 4.9 16.1 1.0 CA D:ASP508 5.0 15.9 1.0 CZ A:PHE123 5.0 13.0 1.0

T.J.Miles, A.J.Hennessy, B.Bax, G.Brooks, B.S.Brown, P.Brown, N.Cailleau, D.Chen, S.Dabbs, D.T.Davies, J.M.Esken, I.Giordano, J.L.Hoover, G.E.Jones, S.K.Kusalakumari Sukmar, R.E.Markwell, E.A.Minthorn, S.Rittenhouse, M.N.Gwynn, N.D.Pearson. Novel Tricyclics (E.G., GSK945237) As Potent Inhibitors of Bacterial Type Iia Topoisomerases. Bioorg.Med.Chem.Lett. V. 26 2464 2016.
ISSN: ESSN 1464-3405
PubMed: 27055939
DOI: 10.1016/J.BMCL.2016.03.106