Manganese in PDB 5npp: 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

The structure of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna, PDB code: 5npp was solved by B.D.Bax, P.F.Chan, R.A.Stavenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.22
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	92.850, 92.850, 409.980, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.7

The structure of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna (pdb code 5npp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna, PDB code: 5npp:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2.22A Structure of THIOPHENE2 and 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 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1501 b:41.8 occ:1.00 OD2 B:ASP510 2.0 40.0 1.0 O B:HOH1740 2.3 37.1 1.0 O B:HOH1765 2.4 32.5 1.0 O D:HOH1714 2.4 46.1 1.0 OD2 B:ASP508 2.8 51.0 1.0 O B:HOH1796 2.8 41.7 1.0 CG B:ASP510 3.1 38.2 1.0 OD1 B:ASP510 3.5 41.8 1.0 CG B:ASP508 3.7 50.5 1.0 CB B:ASP508 3.8 42.5 1.0 O B:HOH1606 3.9 52.7 1.0 O B:HOH1612 4.3 33.8 1.0 OE2 B:GLU435 4.4 41.2 1.0 CB B:ASP510 4.4 33.3 1.0 OP1 E:DG-1 4.5 28.6 1.0 NH2 D:ARG1122 4.6 36.7 1.0 OE1 B:GLU435 4.6 46.3 1.0 OH D:TYR1123 4.7 35.5 1.0 C5' E:DG-1 4.8 30.5 1.0 CE1 D:TYR1123 4.9 37.0 1.0 OD1 B:ASP508 4.9 56.8 1.0 CD B:GLU435 4.9 48.3 1.0

Manganese binding site 2 out of 2 in the 2.22A Structure of THIOPHENE2 and 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 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1501 b:48.0 occ:1.00 O D:HOH1683 2.0 51.9 1.0 O D:HOH1738 2.2 53.1 1.0 OD2 D:ASP510 2.2 45.4 1.0 O F:HOH112 2.3 39.2 1.0 O D:HOH1673 2.3 44.4 1.0 OD2 D:ASP508 2.6 63.9 1.0 CG D:ASP510 3.1 40.6 1.0 OD1 D:ASP510 3.3 40.3 1.0 CG D:ASP508 3.4 57.6 1.0 CB D:ASP508 3.4 53.9 1.0 O D:HOH1659 4.1 35.8 1.0 O D:LYS581 4.2 0.2 1.0 O3' F:DG-1 4.3 56.8 1.0 OE2 D:GLU435 4.4 61.0 1.0 O D:HOH1708 4.5 75.7 1.0 CB D:ASP510 4.5 34.9 1.0 OH B:TYR1123 4.5 40.1 1.0 OD1 D:ASP508 4.6 62.0 1.0 OE1 D:GLU435 4.7 52.0 1.0 OP1 F:DG-1 4.7 29.0 1.0 CE1 B:TYR1123 4.8 34.6 1.0 C5' F:DG-1 4.9 34.7 1.0 CA D:ASP508 4.9 45.5 1.0 CD D:GLU435 4.9 57.4 1.0 CA D:GLY582 4.9 70.4 1.0 NH2 B:ARG1122 5.0 40.7 1.0

P.F.Chan, T.Germe, B.D.Bax, J.Huang, R.K.Thalji, E.Bacque, A.Checchia, D.Chen, H.Cui, X.Ding, K.Ingraham, L.Mccloskey, K.Raha, V.Srikannathasan, A.Maxwell, R.A.Stavenger. Thiophene Antibacterials That Allosterically Stabilize Dna-Cleavage Complexes with Dna Gyrase. Proc. Natl. Acad. Sci. V. 114 E4492 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28507124
DOI: 10.1073/PNAS.1700721114