Manganese in PDB 5cdp: 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

The structure of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna, PDB code: 5cdp 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)	39.78 / 2.45
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.364, 93.364, 411.244, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.1

The structure of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna (pdb code 5cdp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna, PDB code: 5cdp:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:36.8 occ:1.00 O B:HOH1142 2.0 35.1 1.0 OD2 B:ASP510 2.1 39.4 1.0 O B:HOH1102 2.3 31.2 1.0 OD2 B:ASP508 2.4 37.9 1.0 O E:HOH106 2.5 24.6 1.0 O B:HOH1145 2.7 44.7 1.0 CG B:ASP510 3.1 34.0 1.0 CG B:ASP508 3.3 37.6 1.0 OD1 B:ASP510 3.4 34.0 1.0 CB B:ASP508 3.5 32.9 1.0 OE1 B:GLU435 4.0 24.4 1.0 O E:HOH101 4.0 19.9 1.0 O B:HOH1104 4.1 27.6 1.0 O E:HOH103 4.2 24.0 1.0 O A:HOH754 4.3 35.0 1.0 CB B:ASP510 4.4 30.7 1.0 OD1 B:ASP508 4.5 38.6 1.0 CA B:GLY582 4.5 54.7 0.5 CA B:GLY582 4.7 52.0 0.5 OP1 E:DG8 4.7 29.9 1.0 N B:GLY582 4.8 57.3 0.5 CD B:GLU435 4.8 41.3 1.0 C5' E:DG8 5.0 30.2 1.0 OE2 B:GLU435 5.0 26.8 1.0

Manganese binding site 2 out of 4 in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn701 b:24.6 occ:0.60 MN D:MN701 0.0 24.6 0.6 O D:HOH821 1.9 8.4 0.4 O3' F:DG8 2.1 41.3 1.0 OD2 D:ASP508 2.1 35.4 0.6 O H:HOH2202 2.1 38.3 1.0 OE2 D:GLU435 2.1 41.5 0.4 OE2 D:GLU435 2.2 36.0 0.6 O D:HOH821 2.4 27.2 0.6 O D:HOH802 2.7 34.3 0.6 OD2 D:ASP508 2.8 49.6 0.4 O D:HOH802 3.2 20.2 0.4 CD D:GLU435 3.2 53.2 0.4 CG D:ASP508 3.2 32.3 0.6 CD D:GLU435 3.2 51.5 0.6 C3' F:DG8 3.4 38.3 1.0 CG D:ASP508 3.4 43.1 0.4 MN D:MN701 3.6 38.0 0.4 OD1 D:ASP508 3.6 42.7 0.4 CB D:ASP508 3.8 32.7 0.6 OE1 D:GLU435 3.9 41.3 0.6 OE1 D:GLU435 4.0 41.8 0.4 C4' F:DG8 4.0 36.7 1.0 O D:HOH809 4.0 38.2 1.0 CB D:GLU435 4.0 36.0 0.4 CG D:GLU435 4.1 41.6 0.4 CB D:GLU435 4.1 38.4 0.6 OD1 D:ASP508 4.2 30.9 0.6 CG D:GLU435 4.3 42.6 0.6 C2' F:DG8 4.4 36.6 1.0 C5' F:DG8 4.4 35.9 1.0 OD2 D:ASP510 4.5 45.9 0.6 CB D:ASP508 4.6 35.8 0.4 OP1 H:DG2009 4.7 52.9 0.6 OD1 D:ASP510 4.8 40.3 0.6 OP2 H:DG2009 4.8 65.0 0.4 CZ A:PHE123 5.0 35.8 1.0

Manganese binding site 3 out of 4 in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn701 b:38.0 occ:0.40 MN D:MN701 0.0 38.0 0.4 OD2 D:ASP510 1.0 45.9 0.6 CG D:ASP510 1.9 41.2 0.6 OD2 D:ASP510 2.0 52.4 0.4 O D:HOH821 2.1 27.2 0.6 O D:HOH802 2.1 20.2 0.4 OD2 D:ASP508 2.1 49.6 0.4 O C:HOH548 2.5 30.2 0.4 OD1 D:ASP510 2.5 40.3 0.6 O D:HOH821 2.7 8.4 0.4 CG D:ASP510 3.0 48.2 0.4 O D:HOH802 3.0 34.3 0.6 CG D:ASP508 3.0 43.1 0.4 CB D:ASP510 3.2 34.8 0.6 OD1 D:ASP510 3.2 48.4 0.4 CB D:ASP508 3.3 35.8 0.4 CB D:ASP508 3.5 32.7 0.6 MN D:MN701 3.6 24.6 0.6 O C:HOH548 3.9 21.8 0.6 OD2 D:ASP508 3.9 35.4 0.6 O D:HOH808 4.0 37.8 1.0 N D:GLY582 4.2 57.8 1.0 OD1 D:ASP508 4.2 42.7 0.4 C D:LYS581 4.2 64.0 1.0 CG D:ASP508 4.2 32.3 0.6 CB D:LYS581 4.3 67.6 1.0 CB D:ASP510 4.4 40.4 0.4 CA D:ASP510 4.4 32.9 0.6 O D:LYS581 4.5 62.9 1.0 N D:ASP510 4.5 33.1 0.6 CA D:GLY582 4.5 55.4 1.0 OE2 D:GLU435 4.6 41.5 0.4 CA D:LYS581 4.8 64.0 1.0 CA D:ASP508 4.8 31.7 0.6 CA D:ASP508 4.8 33.9 0.4 OE2 D:GLU435 4.8 36.0 0.6 C D:ASP508 4.8 36.7 0.6 C5' F:DG8 4.9 35.9 1.0 O3' F:DG8 4.9 41.3 1.0 CG D:LYS581 5.0 79.0 1.0 OP1 F:DG8 5.0 35.8 1.0

Manganese binding site 4 out of 4 in the 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.45A Structure of Etoposide with S.Aureus Dna Gyrase and Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn2101 b:54.8 occ:1.00 O G:HOH2220 2.7 53.4 1.0 O A:HOH935 2.8 47.8 1.0 O A:HOH735 2.9 40.4 1.0 O C:HOH754 3.1 40.7 1.0 OP2 G:DG2009 3.2 65.4 1.0 P G:DG2009 3.5 66.0 1.0 O A:HOH994 3.6 51.6 1.0 OD2 A:ASP83 3.9 49.8 1.0 OP1 G:DG2009 4.0 67.1 1.0 OD1 A:ASP83 4.3 48.3 1.0 C8 G:DG2009 4.4 61.6 1.0 N7 G:DG2009 4.5 61.3 1.0 CG A:ASP83 4.5 45.7 1.0 O G:HOH2202 4.7 48.7 1.0 OG A:SER84 4.9 47.2 1.0 O5' G:DG2009 4.9 66.3 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