Manganese in PDB 6qtk: 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna

All present enzymatic activity of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna:
5.99.1.3;

The structure of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna, PDB code: 6qtk was solved by B.D.Bax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.99 / 2.31
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	92.730, 92.730, 408.775, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.3

The structure of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna (pdb code 6qtk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna, PDB code: 6qtk:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:28.8 occ:0.70 MN B:MN701 0.0 28.8 0.7 OD2 B:ASP508 1.9 32.4 0.7 O E:HOH2205 2.0 42.1 0.3 OE2 B:GLU435 2.2 38.0 0.7 O B:HOH849 2.3 31.0 0.7 O3' E:DG8 2.4 39.1 1.0 O B:HOH804 2.4 26.6 0.7 OE2 B:GLU435 2.4 32.2 0.3 O B:HOH817 2.8 29.4 0.3 CD B:GLU435 3.0 34.1 0.7 CG B:ASP508 3.1 30.1 0.7 OD2 B:ASP508 3.2 21.9 0.3 CD B:GLU435 3.4 33.6 0.3 P E:DG2009 3.4 31.7 0.7 OE1 B:GLU435 3.5 32.3 0.7 O B:HOH804 3.5 13.6 0.3 C3' E:DG8 3.6 33.4 1.0 CB B:ASP508 3.8 33.7 0.7 OP2 E:DG2009 3.8 31.6 0.7 O B:HOH831 3.8 35.0 1.0 MN B:MN701 4.0 32.7 0.3 O5' E:DG2009 4.0 32.4 0.7 OD1 B:ASP508 4.1 30.9 0.7 OE1 B:GLU435 4.1 31.3 0.3 C4' E:DG8 4.1 31.2 1.0 CG B:GLU435 4.1 34.6 0.7 CB B:GLU435 4.2 36.5 0.7 C2' E:DG8 4.2 31.0 1.0 CG B:GLU435 4.2 35.4 0.3 CG B:ASP508 4.3 22.4 0.3 OD2 B:ASP510 4.4 40.5 0.7 OP1 E:DG2009 4.5 28.6 0.7 C5' E:DG2009 4.6 31.6 0.7 CB B:GLU435 4.6 38.2 0.3 O B:LYS581 4.6 55.8 1.0 CZ C:PHE123 4.6 36.9 1.0 O B:GLU435 4.6 41.8 0.3 O E:HOH2207 4.7 41.2 1.0 C5' E:DG8 4.8 29.2 1.0 NH2 C:ARG122 4.8 42.1 1.0 OD1 B:ASP508 4.8 22.2 0.3 OD1 B:ASP510 4.8 41.7 0.7 CE1 C:PHE123 4.9 37.6 1.0 O E:HOH2231 5.0 0.8 0.3

Manganese binding site 2 out of 3 in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:32.7 occ:0.30 MN B:MN701 0.0 32.7 0.3 OD2 B:ASP510 0.7 40.5 0.7 CG B:ASP510 1.7 40.1 0.7 O B:HOH817 1.9 29.4 0.3 O B:HOH864 2.1 16.7 0.3 O B:LYS581 2.2 55.8 1.0 O B:HOH804 2.2 13.6 0.3 OD2 B:ASP510 2.3 19.1 0.3 O B:HOH849 2.5 31.0 0.7 OD1 B:ASP510 2.5 41.7 0.7 OD2 B:ASP508 2.6 21.9 0.3 CB B:ASP510 2.9 37.9 0.7 CG B:ASP510 3.3 19.8 0.3 O B:HOH804 3.4 26.6 0.7 C B:LYS581 3.4 56.4 1.0 O E:HOH2207 3.5 41.2 1.0 CG B:ASP508 3.6 22.4 0.3 OD1 B:ASP510 3.7 18.6 0.3 O B:HOH811 3.8 43.1 1.0 O A:HOH671 3.8 38.0 1.0 CB B:ASP508 3.8 33.7 0.7 CB B:ASP508 3.8 22.4 0.3 MN B:MN701 4.0 28.8 0.7 CA B:ASP510 4.1 38.9 0.7 N B:ASP510 4.2 40.3 0.7 CA B:LYS581 4.2 56.3 1.0 OD2 B:ASP508 4.2 32.4 0.7 N B:GLY582 4.5 52.1 1.0 CG B:ASP508 4.5 30.1 0.7 CB B:ASP510 4.7 20.3 0.3 OD1 B:ASP508 4.7 22.2 0.3 CB B:LYS581 4.8 53.4 1.0 CA B:GLY582 4.8 50.7 1.0 OE2 B:GLU435 5.0 32.2 0.3 C B:ASP510 5.0 36.7 0.7 O3' E:DG8 5.0 39.1 1.0

Manganese binding site 3 out of 3 in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn701 b:35.9 occ:1.00 OD2 D:ASP508 2.0 41.5 1.0 OE2 D:GLU435 2.2 32.7 1.0 O D:HOH828 2.2 30.1 1.0 O3' F:DG8 2.4 43.2 1.0 O D:HOH814 2.4 29.6 1.0 CD D:GLU435 3.0 28.2 1.0 CG D:ASP508 3.1 43.9 1.0 OE1 D:GLU435 3.4 27.2 1.0 P F:DG2009 3.4 40.2 1.0 O D:HOH825 3.7 34.9 1.0 C3' F:DG8 3.7 36.6 1.0 OP2 F:DG2009 3.8 35.5 1.0 CB D:ASP508 3.8 36.1 1.0 O5' F:DG2009 4.1 40.7 1.0 OD1 D:ASP508 4.1 41.7 1.0 CG D:GLU435 4.2 30.3 1.0 CB D:GLU435 4.2 33.9 1.0 C4' F:DG8 4.2 32.0 1.0 C2' F:DG8 4.3 35.7 1.0 OD2 D:ASP510 4.4 36.0 1.0 O D:HOH827 4.4 37.1 1.0 O D:LYS581 4.4 42.8 1.0 OP1 F:DG2009 4.5 38.6 1.0 C5' F:DG2009 4.6 37.3 1.0 CZ A:PHE123 4.7 29.9 1.0 OD1 D:ASP510 4.7 42.6 1.0 NH2 A:ARG122 4.7 34.0 1.0 C5' F:DG8 4.9 29.5 1.0 CG D:ASP510 5.0 39.4 1.0

E.G.Gibson, B.Bax, P.F.Chan, N.Osheroff. Mechanistic and Structural Basis For the Actions of the Antibacterial Gepotidacin Against Staphylococcus Aureus Gyrase. Acs Infect Dis. V. 5 570 2019.
ISSN: ESSN 2373-8227
PubMed: 30757898
DOI: 10.1021/ACSINFECDIS.8B00315