Manganese in PDB 4plb: Crystal Structure of S.A. Gyrase-AM8191 Complex

All present enzymatic activity of Crystal Structure of S.A. Gyrase-AM8191 Complex:
5.99.1.3;

The structure of Crystal Structure of S.A. Gyrase-AM8191 Complex, PDB code: 4plb 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)	27.12 / 2.69
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.310, 93.310, 410.197, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22

The structure of Crystal Structure of S.A. Gyrase-AM8191 Complex also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Manganese atom in the Crystal Structure of S.A. Gyrase-AM8191 Complex (pdb code 4plb). 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-AM8191 Complex, PDB code: 4plb:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of S.A. Gyrase-AM8191 Complex


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-AM8191 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1502 b:50.4 occ:1.00 OD2 B:ASP508 2.0 31.8 1.0 OE2 B:GLU435 2.1 39.6 1.0 OP1 E:DG9 2.2 38.8 1.0 O B:HOH1625 2.2 56.2 1.0 O B:HOH1626 2.3 36.6 1.0 O3' E:DG8 2.8 36.8 1.0 CD B:GLU435 3.1 44.4 1.0 CG B:ASP508 3.1 44.5 1.0 P E:DG9 3.1 37.1 1.0 OE1 B:GLU435 3.5 42.9 1.0 CB B:ASP508 3.6 46.0 1.0 O B:HOH1604 3.7 29.9 1.0 C3' E:DG8 4.1 35.4 1.0 OD2 B:ASP510 4.1 54.5 1.0 OD1 B:ASP508 4.2 40.5 1.0 O5' E:DG9 4.2 36.8 1.0 OP2 E:DG9 4.2 38.0 1.0 C5' E:DG9 4.3 37.1 1.0 CG B:GLU435 4.3 43.2 1.0 C4' E:DG8 4.3 34.3 1.0 OD1 B:ASP510 4.4 55.7 1.0 O B:LYS581 4.5 70.2 1.0 CB B:GLU435 4.5 43.3 1.0 CG B:ASP510 4.7 49.8 1.0 C5' E:DG8 4.8 34.0 1.0 C2' E:DG8 4.8 34.1 1.0 CA B:ASP508 5.0 42.9 1.0 CE1 D:PHE1123 5.0 45.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of S.A. Gyrase-AM8191 Complex


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-AM8191 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1503 b:47.5 occ:1.00 OE2 D:GLU435 2.1 41.6 1.0 OD2 D:ASP508 2.2 38.6 1.0 OP1 F:DG9 2.3 37.4 1.0 O D:HOH1620 2.3 41.3 1.0 O D:HOH1619 2.4 71.7 1.0 O3' F:DG8 2.7 36.6 1.0 CD D:GLU435 3.0 45.7 1.0 P F:DG9 3.1 36.7 1.0 CG D:ASP508 3.2 52.0 1.0 OE1 D:GLU435 3.3 45.8 1.0 CB D:ASP508 3.6 52.9 1.0 OD2 D:ASP510 3.8 52.7 1.0 O D:HOH1611 3.9 29.7 1.0 C3' F:DG8 4.0 36.5 1.0 C4' F:DG8 4.2 37.0 1.0 O5' F:DG9 4.2 36.5 1.0 CG D:GLU435 4.3 43.8 1.0 OP2 F:DG9 4.3 37.3 1.0 O D:LYS581 4.3 66.2 1.0 OD1 D:ASP508 4.3 46.7 1.0 C5' F:DG9 4.4 37.0 1.0 CB D:GLU435 4.5 44.4 1.0 OD1 D:ASP510 4.6 51.9 1.0 CG D:ASP510 4.6 49.3 1.0 C5' F:DG8 4.7 37.3 1.0 C2' F:DG8 4.7 36.3 1.0 CA D:ASP508 4.9 48.3 1.0 CZ B:PHE1123 4.9 49.3 1.0

S.B.Singh, D.E.Kaelin, J.Wu, L.Miesel, C.M.Tan, P.T.Meinke, D.Olsen, A.Lagrutta, P.Bradley, J.Lu, S.Patel, K.W.Rickert, R.F.Smith, S.Soisson, C.Wei, H.Fukuda, R.Kishii, M.Takei, Y.Fukuda. Oxabicyclooctane-Linked Novel Bacterial Topoisomerase Inhibitors As Broad Spectrum Antibacterial Agents. Acs Med.Chem.Lett. V. 5 609 2014.
ISSN: ISSN 1948-5875
PubMed: 24900889
DOI: 10.1021/ML500069W