Chlorine 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:

Manganese	(Mn)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Gyrase Complexed with Uncleaved Dna and Compound 7 to 2.6A Resolution, PDB code: 7mvs:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl701 b:75.6 occ:1.00 HH11 A:ARG248 2.9 67.4 1.0 O A:HOH832 3.3 72.1 1.0 HH12 A:ARG248 3.4 67.4 1.0 NH1 A:ARG248 3.4 56.1 1.0 HB3 A:PRO245 3.7 56.8 1.0 HA A:SER359 3.7 53.9 1.0 HD11 A:ILE348 3.8 94.5 1.0 HG3 A:PRO245 3.9 54.3 1.0 HD2 A:ARG248 4.0 56.5 1.0 HA A:PRO245 4.0 66.3 1.0 HH21 A:ARG249 4.1 94.6 1.0 O A:SER359 4.3 64.1 1.0 HE A:ARG249 4.4 85.4 1.0 CB A:PRO245 4.4 47.3 1.0 O A:PRO358 4.5 54.4 1.0 NH2 A:ARG249 4.5 78.8 1.0 CA A:SER359 4.6 44.9 1.0 CG A:PRO245 4.6 45.2 1.0 CZ A:ARG248 4.6 45.2 1.0 CD1 A:ILE348 4.7 78.8 1.0 HD13 A:ILE348 4.7 94.5 1.0 CA A:PRO245 4.7 55.3 1.0 NE A:ARG249 4.8 71.1 1.0 OE2 A:GLU357 4.8 35.7 1.0 C A:SER359 4.8 38.2 1.0 CD A:ARG248 4.9 47.1 1.0 CZ A:ARG249 4.9 71.8 1.0 HH22 A:ARG249 4.9 94.6 1.0 CD A:GLU357 5.0 83.2 1.0

Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl701 b:82.7 occ:1.00 HE B:ARG630 3.1 100.0 1.0 HH12 A:ARG630 3.6 119.6 1.0 HH22 A:ARG630 3.8 137.8 1.0 NE B:ARG630 3.9 83.3 1.0 HH21 B:ARG630 4.0 107.8 1.0 HG3 B:ARG630 4.3 111.2 1.0 HD2 B:ARG630 4.3 102.5 1.0 NH1 A:ARG630 4.4 99.7 1.0 NH2 A:ARG630 4.6 114.8 1.0 CD B:ARG630 4.6 85.4 1.0 NH2 B:ARG630 4.7 89.8 1.0 CZ B:ARG630 4.7 84.9 1.0 CG B:ARG630 5.0 92.7 1.0

Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl702 b:97.9 occ:1.00 O B:HOH855 3.1 69.9 1.0 HH11 B:ARG189 3.3 111.2 1.0 HD2 B:ARG189 3.5 98.3 1.0 HE1 B:MET380 3.7 80.1 1.0 HE2 B:MET380 3.8 80.1 1.0 HB2 B:PRO544 4.0 70.7 1.0 NH1 B:ARG189 4.0 92.6 1.0 CE B:MET380 4.0 66.7 1.0 SD B:MET380 4.1 71.7 1.0 HG2 B:PRO544 4.3 85.2 1.0 HH12 B:ARG189 4.3 111.2 1.0 HG3 B:ARG189 4.3 81.7 1.0 HD13 B:ILE537 4.3 76.2 1.0 HG2 B:ARG189 4.4 81.7 1.0 CD B:ARG189 4.4 81.9 1.0 O B:PRO544 4.5 53.4 1.0 HB3 B:MET380 4.5 75.4 1.0 CG B:ARG189 4.6 68.1 1.0 HA B:LYS545 4.8 60.0 1.0 CB B:PRO544 4.8 58.9 1.0 HB2 B:MET380 4.9 75.4 1.0 CG B:PRO544 4.9 71.0 1.0 C B:PRO544 5.0 47.3 1.0 HE3 B:MET380 5.0 80.1 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