Manganese in PDB 2xcs: The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna

All present enzymatic activity of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna:
5.99.1.3;

The structure of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna, PDB code: 2xcs was solved by B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, O.Singh, C.Spitzfaden, C.Shen, A.Shillings, A.F.Theobald, A.Wohlkonig, N.D.Pearson, M.N.Gwynn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.318, 93.318, 412.812, 90.00, 90.00, 120.00
R / Rfree (%)	18.295 / 21.379

The binding sites of Manganese atom in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna (pdb code 2xcs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna, PDB code: 2xcs:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2492 b:53.3 occ:1.00 O B:HOH2385 2.1 44.6 1.0 O B:TYR1322 2.2 44.0 1.0 O B:HOH2384 2.3 39.3 1.0 O B:THR1325 2.4 34.8 1.0 O B:GLN1328 2.4 34.6 1.0 C B:GLN1328 3.5 34.5 1.0 C B:TYR1322 3.5 40.2 1.0 C B:THR1325 3.5 35.1 1.0 O B:LYS1323 3.6 38.3 0.5 O B:LYS1323 3.8 38.4 0.5 CB B:GLN1328 3.8 33.8 1.0 C B:LYS1323 3.9 38.2 0.5 C B:LYS1323 3.9 38.4 0.5 CA B:GLN1328 3.9 34.1 1.0 N B:GLN1328 4.0 34.3 1.0 N B:THR1325 4.0 36.4 1.0 CA B:LYS1323 4.2 39.0 0.5 CA B:LYS1323 4.2 39.3 0.5 N B:LYS1323 4.3 39.6 0.5 N B:LYS1323 4.3 39.7 0.5 O B:HOH2287 4.4 52.7 1.0 N B:PRO1326 4.4 34.4 1.0 CA B:THR1325 4.4 35.8 1.0 O B:HOH2227 4.4 44.8 1.0 CA B:PRO1326 4.5 34.9 1.0 CG B:GLN1328 4.5 34.6 1.0 N B:GLN1324 4.5 37.7 1.0 CA B:TYR1322 4.5 38.8 1.0 N B:THR1329 4.6 34.4 1.0 O B:LEU1321 4.7 36.5 1.0 C B:GLN1324 4.8 37.2 1.0 C B:PRO1326 4.8 35.1 1.0 N B:LEU1327 4.8 34.8 1.0

Manganese binding site 2 out of 4 in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2493 b:31.5 occ:1.00 OD2 B:ASP508 2.0 32.3 1.0 O B:HOH2386 2.1 33.0 1.0 OE2 B:GLU435 2.1 29.1 1.0 OP1 E:DG9 2.2 27.8 1.0 O B:HOH2387 2.3 31.7 1.0 O3' E:DG8 2.7 30.4 1.0 CD B:GLU435 2.9 29.2 1.0 CG B:ASP508 3.0 33.7 1.0 P E:DG9 3.0 30.6 1.0 OE1 B:GLU435 3.2 28.4 1.0 CB B:ASP508 3.4 32.9 1.0 O B:HOH2033 3.6 28.9 1.0 C3' E:DG8 4.0 28.9 1.0 OD2 B:ASP510 4.0 41.7 1.0 OD1 B:ASP508 4.1 32.6 1.0 OP2 E:DG9 4.1 29.2 1.0 O5' E:DG9 4.1 28.6 1.0 CG B:GLU435 4.2 28.6 1.0 C5' E:DG9 4.3 29.3 1.0 C4' E:DG8 4.3 28.1 1.0 O B:LYS581 4.4 41.2 1.0 OD1 B:ASP510 4.5 35.4 1.0 CB B:GLU435 4.5 30.1 1.0 CG B:ASP510 4.7 36.6 1.0 C2' E:DG8 4.7 27.4 1.0 CA B:ASP508 4.8 33.0 1.0 C5' E:DG8 4.8 29.0 1.0 N B:ASP508 5.0 32.4 1.0 CE2 D:PHE1123 5.0 41.0 1.0

Manganese binding site 3 out of 4 in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2491 b:32.9 occ:1.00 O D:HOH2367 2.0 31.4 1.0 OD2 D:ASP508 2.0 36.3 1.0 OE2 D:GLU435 2.1 29.6 1.0 OP1 F:DG9 2.3 32.5 1.0 O D:HOH2366 2.4 32.1 1.0 O3' F:DG8 2.7 29.9 1.0 CD D:GLU435 2.9 31.9 1.0 CG D:ASP508 3.0 35.1 1.0 P F:DG9 3.1 31.0 1.0 OE1 D:GLU435 3.2 31.7 1.0 CB D:ASP508 3.4 32.5 1.0 O D:HOH2022 3.6 31.6 1.0 C3' F:DG8 4.0 28.9 1.0 OD1 D:ASP508 4.1 32.1 1.0 OP2 F:DG9 4.2 30.4 1.0 OD2 D:ASP510 4.2 40.9 1.0 CG D:GLU435 4.2 32.9 1.0 O5' F:DG9 4.2 30.2 1.0 O D:LYS581 4.2 42.7 1.0 C5' F:DG9 4.3 33.1 1.0 C4' F:DG8 4.3 28.1 1.0 OD1 D:ASP510 4.4 37.6 1.0 CB D:GLU435 4.4 32.2 1.0 CG D:ASP510 4.7 37.7 1.0 C2' F:DG8 4.8 28.2 1.0 CA D:ASP508 4.8 33.3 1.0 C5' F:DG8 4.8 29.6 1.0 N D:ASP508 4.9 33.3 1.0 CZ B:PHE1123 5.0 33.6 1.0

Manganese binding site 4 out of 4 in the The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The 2.1A Crystal Structure of S. Aureus Gyrase Complex with GSK299423 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1022 b:49.4 occ:1.00 OP1 E:5UA1 1.9 56.5 1.0 C6' E:5UA1 2.0 52.4 1.0 OP3 E:5UA1 2.3 57.1 1.0 O E:HOH2040 2.5 50.6 1.0 O E:HOH2038 2.5 39.1 1.0 O E:HOH2039 2.7 55.2 1.0 O5' E:5UA1 3.0 50.5 1.0 C5' E:5UA1 4.4 41.4 1.0 N7 E:DG2 4.4 36.0 1.0 O6 E:DG2 4.7 33.9 1.0

B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, M.R.Saunders, O.Singh, C.Spitzfaden, C.Shen, A.Shillings, A.F.Theobald, A.Wohlkonig, N.D.Pearson, M.N.Gwynn. Type Iia Topoisomerase Inhibition By A New Class of Antibacterial Agents. Nature V. 466 935 2010.
ISSN: ISSN 0028-0836
PubMed: 20686482
DOI: 10.1038/NATURE09197