Manganese in PDB 5bs3: Crystal Structure of S.A. Gyrase in Complex with Compound 7

All present enzymatic activity of Crystal Structure of S.A. Gyrase in Complex with Compound 7:
5.99.1.3;

The structure of Crystal Structure of S.A. Gyrase in Complex with Compound 7, PDB code: 5bs3 was solved by J.Lu, S.Patel, S.Soisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.71 / 2.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.337, 93.337, 411.068, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 21.3

The structure of Crystal Structure of S.A. Gyrase in Complex with Compound 7 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Manganese atom in the Crystal Structure of S.A. Gyrase in Complex with Compound 7 (pdb code 5bs3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of S.A. Gyrase in Complex with Compound 7, PDB code: 5bs3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of S.A. Gyrase in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of S.A. Gyrase in Complex with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1501 b:45.1 occ:1.00 OE2 B:GLU435 2.1 43.2 1.0 OD2 B:ASP508 2.1 37.0 1.0 OP1 E:G9 2.2 39.4 1.0 O B:HOH1606 2.4 49.3 1.0 O B:HOH1602 2.4 40.4 1.0 O3' E:G8 2.8 39.0 1.0 CG B:ASP508 3.0 39.8 1.0 CD B:GLU435 3.0 43.1 1.0 P E:G9 3.1 39.5 1.0 OE1 B:GLU435 3.4 44.5 1.0 CB B:ASP508 3.4 40.2 1.0 O B:HOH1605 3.7 28.9 1.0 OD1 B:ASP508 4.1 40.9 1.0 C3' E:G8 4.1 37.3 1.0 O5' E:G9 4.2 38.7 1.0 OP2 E:G9 4.2 39.3 1.0 C5' E:G9 4.3 38.5 1.0 CG B:GLU435 4.3 41.2 1.0 C4' E:G8 4.4 35.6 1.0 OD2 B:ASP510 4.4 49.6 1.0 OD1 B:ASP510 4.4 50.1 1.0 CB B:GLU435 4.5 40.3 1.0 O B:LYS581 4.5 65.2 1.0 CA B:ASP508 4.8 38.2 1.0 C5' E:G8 4.8 34.9 1.0 CG B:ASP510 4.8 46.6 1.0 C2' E:G8 4.9 37.0 1.0 N B:ASP508 4.9 37.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of S.A. Gyrase in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of S.A. Gyrase in Complex with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1501 b:44.4 occ:1.00 OD2 D:ASP508 2.0 44.5 1.0 O D:HOH1605 2.2 49.3 1.0 OE2 D:GLU435 2.3 44.3 1.0 OP1 F:G9 2.3 37.7 1.0 O D:HOH1618 2.6 42.3 1.0 O3' F:G8 2.8 37.0 1.0 CG D:ASP508 2.9 44.0 1.0 CD D:GLU435 2.9 43.7 1.0 P F:G9 3.1 37.4 1.0 OE1 D:GLU435 3.3 44.6 1.0 CB D:ASP508 3.4 44.0 1.0 O F:HOH201 3.4 26.1 1.0 OD2 D:ASP510 3.9 47.6 1.0 OD1 D:ASP508 4.0 44.2 1.0 C3' F:G8 4.0 35.7 1.0 CG D:GLU435 4.1 42.9 1.0 O D:LYS581 4.2 60.8 1.0 OP2 F:G9 4.2 36.4 1.0 O5' F:G9 4.3 37.4 1.0 C4' F:G8 4.3 35.9 1.0 CB D:GLU435 4.4 42.2 1.0 C5' F:G9 4.4 37.9 1.0 C5' F:G8 4.7 35.8 1.0 CA D:ASP508 4.8 40.4 1.0 C2' F:G8 4.8 34.9 1.0 CG D:ASP510 4.8 43.5 1.0 OD1 D:ASP510 4.9 46.4 1.0 N D:ASP508 4.9 40.8 1.0 CE2 B:PHE1123 5.0 40.5 1.0

S.B.Singh, D.E.Kaelin, J.Wu, L.Miesel, C.M.Tan, T.Black, R.Nargund, P.T.Meinke, D.B.Olsen, A.Lagrutta, J.Lu, S.Patel, K.W.Rickert, R.F.Smith, S.Soisson, E.Sherer, L.A.Joyce, C.Wei, X.Peng, X.Wang, H.Fukuda, R.Kishii, M.Takei, H.Takano, M.Shibasaki, M.Yajima, A.Nishimura, T.Shibata, Y.Fukuda. Tricyclic 1,5-Naphthyridinone Oxabicyclooctane-Linked Novel Bacterial Topoisomerase Inhibitors As Broad-Spectrum Antibacterial Agents-Sar of Left-Hand-Side Moiety (Part-2). Bioorg.Med.Chem.Lett. V. 25 1831 2015.
ISSN: ESSN 1464-3405
PubMed: 25851938
DOI: 10.1016/J.BMCL.2015.03.044