Fluorine 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
Manganese	(Mn)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution, PDB code: 7mvs:
Jump to Fluorine binding site number: 1; 2;

Fluorine 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 Fluorine with other atoms in the F 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 D:F101 b:57.9 occ:0.60 F01 D:Y1W101 0.0 57.9 0.6 O28 D:Y1W101 0.5 57.9 0.4 C29 D:Y1W101 1.0 73.2 0.4 C02 D:Y1W101 1.4 63.9 0.6 H292 D:Y1W101 1.4 87.8 0.4 H291 D:Y1W101 1.6 87.8 0.4 C27 D:Y1W101 1.6 66.0 0.4 H293 D:Y1W101 1.7 87.8 0.4 H051 D:Y1W101 2.1 87.9 0.6 O05 D:Y1W101 2.3 73.3 0.6 C34 D:Y1W101 2.4 68.1 0.6 C03 D:Y1W101 2.4 69.4 0.6 C26 D:Y1W101 2.5 69.4 0.4 H261 D:Y1W101 2.5 83.3 0.4 H341 D:Y1W101 2.5 81.8 0.6 C30 D:Y1W101 2.7 67.2 0.4 C04 D:Y1W101 2.8 78.8 0.6 H2' D:DG10 2.9 84.5 1.0 H301 D:Y1W101 2.9 80.7 0.4 C5 D:DG10 3.4 53.5 1.0 C8 D:DG10 3.4 67.4 1.0 N7 D:DG10 3.4 50.1 1.0 C4 D:DG10 3.5 58.3 1.0 N9 D:DG10 3.5 69.3 1.0 H061 D:Y1W101 3.5 101.6 0.6 H041 D:Y1W101 3.6 94.6 0.6 N33 D:Y1W101 3.6 60.4 0.6 C25 D:Y1W101 3.7 69.1 0.6 C2' D:DG10 3.7 70.3 1.0 C06 D:Y1W101 3.8 84.7 0.6 C25 D:Y1W101 3.8 68.9 0.4 H8 D:DG10 3.8 81.0 1.0 H5 D:DC11 3.8 89.5 1.0 C5 D:DC11 3.9 74.5 1.0 C31 D:Y1W101 4.0 61.5 0.4 H062 D:Y1W101 4.0 107.5 0.4 H2'' D:DG10 4.0 84.5 1.0 C6 D:DG10 4.1 71.2 1.0 C32 D:Y1W101 4.1 66.0 0.6 N3 D:DG10 4.1 54.6 1.0 C4 D:DC11 4.1 77.9 1.0 C1' D:DG10 4.2 77.2 1.0 H41 D:DC11 4.3 88.8 1.0 H062 D:Y1W101 4.3 101.6 0.6 N4 D:DC11 4.3 74.0 1.0 C6 D:DC11 4.4 86.7 1.0 C32 D:Y1W101 4.4 66.1 0.4 N1 D:DG10 4.6 66.5 1.0 C2 D:DG10 4.6 41.2 1.0 H6 D:DC11 4.6 104.1 1.0 O6 D:DG10 4.7 67.4 1.0 H311 D:Y1W101 4.7 73.8 0.4 N3 D:DC11 4.8 72.3 1.0 H3' D:DG10 4.8 98.7 1.0 O08 D:Y1W101 4.8 93.9 0.6 H42 D:DC11 4.8 88.8 1.0 H232 D:Y1W101 4.8 118.9 0.4 C06 D:Y1W101 4.8 89.5 0.4 C26 D:Y1W101 4.9 67.9 0.6 H1' D:DG10 4.9 92.7 1.0 C03 D:Y1W101 4.9 69.0 0.4 C07 D:Y1W101 4.9 92.5 0.6 C3' D:DG10 4.9 82.2 1.0 H041 D:Y1W101 4.9 96.6 0.4 H261 D:Y1W101 5.0 81.5 0.6 N1 D:DC11 5.0 78.3 1.0

Fluorine 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 Fluorine with other atoms in the F 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 D:F101 b:83.8 occ:0.40 F01 D:Y1W101 0.0 83.8 0.4 O28 D:Y1W101 0.4 85.5 0.6 C29 D:Y1W101 1.3 71.8 0.6 C02 D:Y1W101 1.4 71.8 0.4 C27 D:Y1W101 1.5 70.4 0.6 H292 D:Y1W101 1.6 86.1 0.6 H291 D:Y1W101 1.9 86.1 0.6 H293 D:Y1W101 2.0 86.1 0.6 O05 D:Y1W101 2.1 82.0 0.4 C03 D:Y1W101 2.4 69.0 0.4 C34 D:Y1W101 2.4 70.7 0.4 C26 D:Y1W101 2.4 67.9 0.6 C30 D:Y1W101 2.5 70.2 0.6 H341 D:Y1W101 2.6 84.8 0.4 H261 D:Y1W101 2.6 81.5 0.6 H301 D:Y1W101 2.6 84.2 0.6 C04 D:Y1W101 2.8 80.5 0.4 H051 D:Y1W101 2.8 98.4 0.4 H2' C:DG10 2.9 87.6 1.0 C4 C:DG10 3.2 57.6 1.0 C5 C:DG10 3.3 64.3 1.0 H041 D:Y1W101 3.4 96.6 0.4 N9 C:DG10 3.4 65.1 1.0 N3 C:DG10 3.6 71.4 1.0 N33 D:Y1W101 3.6 69.9 0.4 C2' C:DG10 3.6 73.0 1.0 C25 D:Y1W101 3.6 68.9 0.4 N7 C:DG10 3.7 80.2 1.0 C8 C:DG10 3.7 77.7 1.0 C31 D:Y1W101 3.7 69.5 0.6 H061 D:Y1W101 3.7 107.5 0.4 C25 D:Y1W101 3.7 69.1 0.6 C5 C:DC11 3.7 79.9 1.0 H2'' C:DG10 3.7 87.6 1.0 C06 D:Y1W101 3.8 89.5 0.4 C6 C:DG10 3.9 68.9 1.0 H5 C:DC11 3.9 96.0 1.0 C4 C:DC11 3.9 55.2 1.0 C2 C:DG10 4.0 68.1 1.0 C6 C:DC11 4.0 100.5 1.0 C32 D:Y1W101 4.1 66.1 0.4 C1' C:DG10 4.1 67.4 1.0 N1 C:DG10 4.1 76.1 1.0 H062 D:Y1W101 4.2 101.6 0.6 C32 D:Y1W101 4.2 66.0 0.6 H8 C:DG10 4.2 93.3 1.0 N4 C:DC11 4.3 57.2 1.0 H071 D:Y1W101 4.3 112.4 0.4 N3 C:DC11 4.3 60.5 1.0 H6 C:DC11 4.3 120.7 1.0 H41 C:DC11 4.4 68.7 1.0 N1 C:DC11 4.4 92.6 1.0 H311 D:Y1W101 4.5 83.4 0.6 H062 D:Y1W101 4.6 107.5 0.4 C07 D:Y1W101 4.6 93.6 0.4 C2 C:DC11 4.6 72.2 1.0 O6 C:DG10 4.6 79.5 1.0 H1' C:DG10 4.7 80.9 1.0 H42 C:DC11 4.7 68.7 1.0 H1 C:DG10 4.7 91.4 1.0 O4' C:DC11 4.8 70.2 1.0 H041 D:Y1W101 4.8 94.6 0.6 C26 D:Y1W101 4.8 69.4 0.4 O08 D:Y1W101 4.9 91.9 0.4 C03 D:Y1W101 4.9 69.4 0.6 O24 D:Y1W101 4.9 99.4 0.6 H3' C:DG10 4.9 78.4 1.0 N2 C:DG10 4.9 77.3 1.0 C3' C:DG10 4.9 65.3 1.0 H261 D:Y1W101 4.9 83.3 0.4

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