Manganese in PDB 7mvs: Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution

All present enzymatic activity of Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution:
5.6.2.2;

The structure of Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution, PDB code: 7mvs was solved by S.C.Ratigan, C.A.Mcelroy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.74 / 2.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	93.017, 93.017, 406.663, 90, 90, 120
R / Rfree (%)	19.6 / 25.2

The structure of Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Fluorine	(F)	2 atoms

The binding sites of Manganese atom in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution (pdb code 7mvs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution, PDB code: 7mvs:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:96.6 occ:1.00 OP1 C:DG9 1.8 76.1 1.0 OD2 A:ASP101 2.3 88.4 1.0 OE2 A:GLU28 2.4 77.3 1.0 O3' C:DG8 2.4 65.2 1.0 P C:DG9 2.7 49.8 1.0 O A:HOH810 2.8 63.3 1.0 CD A:GLU28 3.3 78.4 1.0 H5'' C:DG9 3.5 71.0 1.0 H5' C:DG9 3.5 71.0 1.0 CG A:ASP101 3.5 85.8 1.0 O5' C:DG9 3.7 65.6 1.0 HB2 A:GLU28 3.7 61.6 1.0 HB3 A:GLU28 3.7 61.6 1.0 C5' C:DG9 3.8 59.1 1.0 C3' C:DG8 3.8 63.2 1.0 OP2 C:DG9 3.8 81.1 1.0 HB2 A:ASP101 3.9 84.9 1.0 HE1 B:PHE324 3.9 85.1 1.0 H4' C:DG8 3.9 69.6 1.0 OE1 A:GLU28 4.0 57.3 1.0 HZ B:PHE324 4.0 73.1 1.0 CB A:GLU28 4.1 51.3 1.0 H2'' C:DG8 4.2 68.6 1.0 CB A:ASP101 4.3 70.7 1.0 CG A:GLU28 4.3 66.2 1.0 C4' C:DG8 4.4 58.0 1.0 H3' C:DG8 4.4 75.8 1.0 OD1 A:ASP101 4.4 75.6 1.0 CE1 B:PHE324 4.5 70.9 1.0 CZ B:PHE324 4.5 60.9 1.0 H5'' C:DG8 4.5 68.8 1.0 C2' C:DG8 4.5 57.1 1.0 HB3 A:ASP101 4.6 84.9 1.0 HG3 A:GLU28 4.8 79.4 1.0 OD2 A:ASP103 4.8 104.7 1.0 HA3 A:GLY141 4.8 134.4 1.0 H2' C:DG8 5.0 68.6 1.0 H A:ASP101 5.0 100.4 1.0

Manganese binding site 2 out of 2 in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn704 b:98.3 occ:1.00 OP1 D:DG9 2.1 94.9 1.0 OD2 B:ASP101 2.4 65.1 1.0 OE2 B:GLU28 2.4 72.7 1.0 O3' D:DG8 2.5 72.1 1.0 P D:DG9 2.8 53.8 1.0 CD B:GLU28 3.3 78.4 1.0 CG B:ASP101 3.5 76.5 1.0 HB2 B:ASP101 3.6 105.9 1.0 OE1 B:GLU28 3.7 80.3 1.0 H5' D:DG9 3.7 90.4 1.0 H4' D:DG8 3.8 76.9 1.0 C3' D:DG8 3.8 69.4 1.0 H5'' D:DG9 3.8 90.4 1.0 OP2 D:DG9 4.0 59.0 1.0 O5' D:DG9 4.0 49.6 1.0 HE1 A:PHE324 4.0 93.2 1.0 C5' D:DG9 4.1 75.3 1.0 HB2 B:GLU28 4.1 69.7 1.0 CB B:ASP101 4.1 88.2 1.0 HZ A:PHE324 4.1 110.9 1.0 HB3 B:GLU28 4.1 69.7 1.0 OD2 B:ASP103 4.2 92.1 1.0 C4' D:DG8 4.2 64.1 1.0 H2'' D:DG8 4.3 78.5 1.0 H5'' D:DG8 4.3 83.4 1.0 HB3 B:ASP101 4.4 105.9 1.0 H3' D:DG8 4.4 83.3 1.0 CB B:GLU28 4.4 58.0 1.0 CG B:GLU28 4.4 61.5 1.0 OD1 B:ASP101 4.5 83.3 1.0 CE1 A:PHE324 4.6 77.6 1.0 C2' D:DG8 4.6 65.4 1.0 CZ A:PHE324 4.6 92.4 1.0 O B:LYS140 4.7 105.8 1.0 HA3 B:GLY141 4.8 99.2 1.0 C5' D:DG8 4.8 69.5 1.0 HG3 B:GLU28 4.9 73.9 1.0 H B:ASP101 5.0 79.0 1.0 HB2 B:ASP105 5.0 120.2 1.0

Y.Lu, S.Vibhute, L.Li, A.Okumu, S.C.Ratigan, S.Nolan, J.L.Papa, C.A.Mann, A.English, A.Chen, J.T.Seffernick, B.Koci, L.R.Duncan, B.Roth, J.E.Cummings, R.A.Slayden, S.Lindert, C.A.Mcelroy, D.J.Wozniak, J.Yalowich, M.J.Mitton-Fry. Optimization of Topoiv Potency, Admet Properties, and Herg Inhibition of 5-Amino-1,3-Dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of A Lead with in Vivo Efficacy Against Mrsa. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34614347
DOI: 10.1021/ACS.JMEDCHEM.1C01250