Manganese in PDB 6fm4: The Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna

All present enzymatic activity of The Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna:
5.99.1.3;

The structure of The Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna, PDB code: 6fm4 was solved by R.Ombrato, B.Garofalo, G.Mangano, F.Mancini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.05 / 2.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	92.951, 92.951, 407.030, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 30

The binding sites of Manganese atom in the The Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna (pdb code 6fm4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna, PDB code: 6fm4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of S. Aureus Gyrase Complex with Id-130 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 Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1501 b:53.3 occ:0.00 O B:TYR1322 2.7 36.0 1.0 O B:GLN1328 3.2 38.8 1.0 O B:LYS1323 3.5 43.3 1.0 C B:LYS1323 3.8 45.0 1.0 C B:TYR1322 3.8 37.6 1.0 CA B:LYS1323 3.9 47.7 1.0 CB B:GLN1328 3.9 36.1 1.0 O B:THR1325 3.9 35.5 1.0 CG B:GLN1328 4.0 38.6 1.0 C B:GLN1328 4.1 35.7 1.0 N B:LYS1323 4.3 42.0 1.0 CD B:GLN1328 4.6 40.0 1.0 CA B:GLN1328 4.6 36.6 1.0 NE2 B:GLN1328 4.7 42.6 1.0 N B:GLN1324 4.8 40.7 1.0 N B:GLN1328 4.9 37.4 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of S. Aureus Gyrase Complex with Id-130 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 Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn101 b:31.5 occ:0.00 OD2 B:ASP508 0.8 24.0 1.0 OE2 B:GLU435 1.6 37.2 1.0 OP1 E:DG9 1.6 33.4 1.0 CG B:ASP508 2.0 31.8 1.0 O3' E:DG8 2.5 37.0 1.0 P E:DG9 2.6 34.9 1.0 CD B:GLU435 2.7 40.7 1.0 OD1 B:ASP508 2.9 31.2 1.0 OE1 B:GLU435 3.2 40.4 1.0 CB B:ASP508 3.2 30.5 1.0 OP2 E:DG9 3.6 31.7 1.0 O5' E:DG9 3.8 31.8 1.0 C3' E:DG8 3.9 32.6 1.0 OD2 B:ASP510 4.0 36.8 1.0 CG B:GLU435 4.0 41.0 1.0 C5' E:DG9 4.1 31.9 1.0 OD1 B:ASP510 4.3 41.7 1.0 CB B:GLU435 4.4 42.8 1.0 C4' E:DG8 4.4 31.5 1.0 CA B:ASP508 4.5 30.0 1.0 O B:LYS581 4.5 59.9 1.0 CG B:ASP510 4.6 35.3 1.0 C2' E:DG8 4.6 32.9 1.0 CZ D:PHE1123 4.8 49.3 1.0 N B:ASP508 4.8 28.5 1.0 CA B:GLY582 5.0 50.6 1.0 C5' E:DG8 5.0 28.4 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of S. Aureus Gyrase Complex with Id-130 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 Crystal Structure of S. Aureus Gyrase Complex with Id-130 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1501 b:32.9 occ:0.00 OD2 D:ASP508 0.9 26.1 1.0 OE2 D:GLU435 1.6 30.9 1.0 OP1 F:DG9 1.9 41.9 1.0 CG D:ASP508 2.2 33.2 1.0 CD D:GLU435 2.6 32.3 1.0 O3' F:DG8 2.6 36.9 1.0 P F:DG9 2.8 34.8 1.0 OD1 D:ASP508 3.1 27.8 1.0 OE1 D:GLU435 3.1 34.2 1.0 CB D:ASP508 3.3 33.7 1.0 OP2 F:DG9 3.8 38.0 1.0 CG D:GLU435 3.9 29.8 1.0 O5' F:DG9 4.0 31.6 1.0 C3' F:DG8 4.0 33.4 1.0 C5' F:DG9 4.1 31.3 1.0 O D:LYS581 4.1 54.7 1.0 OD2 D:ASP510 4.2 38.9 1.0 OD1 D:ASP510 4.3 34.5 1.0 CB D:GLU435 4.3 28.2 1.0 C4' F:DG8 4.4 32.9 1.0 CA D:ASP508 4.6 35.5 1.0 CG D:ASP510 4.7 33.3 1.0 C2' F:DG8 4.8 32.7 1.0 N D:ASP508 4.9 40.5 1.0 C5' F:DG8 4.9 35.4 1.0 CZ B:PHE1123 4.9 28.9 1.0 CE2 B:PHE1123 5.0 27.7 1.0

G.Magaro, F.Prati, B.Garofalo, G.Corso, G.Furlotti, C.Apicella, G.Mangano, N.D'atanasio, D.Robinson, F.P.Di Giorgio, R.Ombrato. Virtual Screening Approach and Investigation of Structure-Activity Relationships to Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens. J.Med.Chem. V. 62 7445 2019.
ISSN: ISSN 0022-2623
PubMed: 31276392
DOI: 10.1021/ACS.JMEDCHEM.9B00394