Manganese in PDB 5cdr: 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna

All present enzymatic activity of 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna:
5.99.1.3;

The structure of 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna, PDB code: 5cdr was solved by B.D.Bax, V.Srikannathasan, P.F.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.74 / 2.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.395, 93.395, 410.583, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 21

The binding sites of Manganese atom in the 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna (pdb code 5cdr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna, PDB code: 5cdr:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:76.0 occ:1.00 O A:HOH705 2.1 38.8 1.0 O A:GLN328 2.4 40.4 1.0 O A:THR325 2.4 38.1 1.0 O A:TYR322 2.5 40.3 1.0 O A:HOH809 2.6 56.1 1.0 C A:GLN328 3.4 40.0 1.0 C A:THR325 3.5 39.0 1.0 C A:TYR322 3.7 40.4 1.0 CB A:GLN328 3.8 37.2 1.0 N A:GLN328 3.8 36.5 1.0 CA A:GLN328 3.9 35.5 1.0 O A:LYS323 3.9 40.1 0.5 O A:LYS323 4.0 40.1 0.5 N A:THR325 4.1 36.9 1.0 C A:LYS323 4.1 40.3 0.5 C A:LYS323 4.1 40.4 0.5 CA A:PRO326 4.2 35.2 1.0 O A:HOH660 4.3 33.1 1.0 N A:PRO326 4.3 35.5 1.0 CA A:THR325 4.4 36.4 1.0 CA A:LYS323 4.5 36.6 0.5 N A:LYS323 4.5 37.0 0.5 N A:LYS323 4.5 37.0 0.5 CA A:LYS323 4.5 36.8 0.5 N A:LEU327 4.6 35.1 1.0 C A:PRO326 4.6 39.1 1.0 N A:THR329 4.6 36.1 1.0 CA A:TYR322 4.6 36.0 1.0 N A:GLN324 4.6 36.6 1.0 C A:GLN324 4.7 41.0 1.0 O A:LEU321 4.7 40.0 1.0 CG A:GLN328 4.8 43.7 1.0 O A:HOH811 4.8 39.1 1.0

Manganese binding site 2 out of 3 in the 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:37.9 occ:1.00 O B:HOH818 2.1 40.5 1.0 O B:HOH842 2.2 35.4 1.0 OD2 B:ASP510 2.2 46.4 1.0 OD2 B:ASP508 2.4 49.4 1.0 O E:HOH211 2.4 32.0 1.0 O B:HOH848 2.6 54.1 1.0 CG B:ASP510 3.1 42.1 1.0 OD1 B:ASP510 3.3 42.1 1.0 CG B:ASP508 3.4 44.9 1.0 CB B:ASP508 3.6 35.5 1.0 OE2 B:GLU435 3.9 43.9 1.0 O B:HOH816 4.2 45.2 1.0 O E:HOH203 4.2 37.1 1.0 O A:HOH622 4.2 41.9 1.0 O B:HOH802 4.3 36.3 1.0 O B:HOH844 4.5 39.4 1.0 CB B:ASP510 4.5 36.3 1.0 OD1 B:ASP508 4.5 46.3 1.0 OP1 E:DG8 4.7 38.9 1.0 CD B:GLU435 4.8 51.0 1.0 C5' E:DG8 4.8 38.0 1.0

Manganese binding site 3 out of 3 in the 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.65 Structure of S.Aureus Dna Gyrase and Artificially Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1001 b:41.8 occ:1.00 O D:HOH1108 2.0 57.0 1.0 OD2 D:ASP510 2.3 51.8 1.0 O D:HOH1116 2.3 30.3 1.0 OD2 D:ASP508 2.3 57.0 1.0 O D:HOH1110 2.3 34.3 1.0 O D:HOH1130 2.5 37.8 1.0 CG D:ASP510 3.2 48.8 1.0 CG D:ASP508 3.3 51.0 1.0 OD1 D:ASP510 3.4 50.2 1.0 CB D:ASP508 3.5 42.2 1.0 OE2 D:GLU435 3.7 43.7 1.0 O D:HOH1120 3.8 33.1 1.0 O D:HOH1105 4.1 43.1 1.0 O D:HOH1102 4.3 29.9 1.0 O D:HOH1115 4.3 41.6 1.0 O F:HOH2106 4.3 50.9 1.0 O C:HOH601 4.4 36.5 1.0 OD1 D:ASP508 4.4 51.5 1.0 CB D:ASP510 4.6 40.1 1.0 CD D:GLU435 4.6 57.4 1.0 C5' F:DG8 4.7 45.4 1.0 OP1 F:DG8 4.7 44.4 1.0 OE1 D:GLU435 5.0 47.9 1.0

P.F.Chan, V.Srikannathasan, J.Huang, H.Cui, A.P.Fosberry, M.Gu, M.M.Hann, M.Hibbs, P.Homes, K.Ingraham, J.Pizzollo, C.Shen, A.J.Shillings, C.E.Spitzfaden, R.Tanner, A.J.Theobald, R.A.Stavenger, B.D.Bax, M.N.Gwynn. Structural Basis of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide and Moxifloxacin. Nat Commun V. 6 10048 2015.
ISSN: ESSN 2041-1723
PubMed: 26640131
DOI: 10.1038/NCOMMS10048