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Chlorine in PDB 6m1s: The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O

Enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O

All present enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O:
5.6.2.2;

Protein crystallography data

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O, PDB code: 6m1s was solved by Z.H.Xu, Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.07 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.694, 46.928, 89.862, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.2

Other elements in 6m1s:

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O (pdb code 6m1s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O, PDB code: 6m1s:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6m1s

Go back to Chlorine Binding Sites List in 6m1s
Chlorine binding site 1 out of 3 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:53.3
occ:1.00
 OG B:SER174 3.0 41.8 1.0
NE2 B:HIS149 3.3 51.6 1.0
ND1 B:HIS130 3.4 41.9 1.0
CE1 B:HIS149 3.5 47.1 1.0
CD B:PRO175 3.7 42.5 1.0
CB B:SER174 4.1 35.7 1.0
CB B:HIS130 4.2 36.7 1.0
CG B:HIS130 4.2 37.5 1.0
CB B:GLU176 4.3 63.7 1.0
CE1 B:HIS130 4.3 45.1 1.0
N B:GLU176 4.4 52.7 1.0
N B:PRO175 4.4 32.2 1.0
CA B:SER174 4.4 39.2 1.0
CA B:HIS130 4.5 34.5 1.0
CD2 B:HIS149 4.6 57.3 1.0
CG B:PRO175 4.7 49.2 1.0
ND1 B:HIS149 4.8 44.9 1.0
C B:SER174 4.8 39.7 1.0
CA B:GLU176 5.0 57.8 1.0

Chlorine binding site 2 out of 3 in 6m1s

Go back to Chlorine Binding Sites List in 6m1s
Chlorine binding site 2 out of 3 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:50.5
occ:1.00
 N B:TRP185 3.7 26.8 1.0
OG B:SER184 3.7 30.9 1.0
OD1 B:ASP186 3.8 59.2 1.0
CA B:SER184 3.9 31.5 1.0
CE1 B:HIS182 4.1 59.4 1.0
CB B:SER184 4.1 27.6 1.0
C B:SER184 4.3 36.8 1.0
CB B:TRP185 4.3 27.5 1.0
N B:ASP186 4.3 27.4 1.0
CA B:TRP185 4.5 26.5 1.0
CG B:ASP186 4.7 63.2 1.0
O B:PHE183 4.8 34.9 1.0
NE2 B:HIS182 4.9 61.1 1.0
CB B:ASP186 5.0 50.7 1.0
C B:TRP185 5.0 33.9 1.0

Chlorine binding site 3 out of 3 in 6m1s

Go back to Chlorine Binding Sites List in 6m1s
Chlorine binding site 3 out of 3 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:57.2
occ:1.00
 N B:GLY26 3.3 47.4 1.0
CA B:GLY26 3.7 53.0 1.0
CD B:PRO25 3.8 41.4 1.0
N B:PRO25 4.1 37.5 1.0
C B:ARG24 4.2 40.7 1.0
CG B:PRO25 4.3 36.6 1.0
CA B:ARG24 4.3 49.2 1.0
C B:PRO25 4.5 35.9 1.0
N B:MET27 4.5 48.9 1.0
C B:GLY26 4.6 46.3 1.0
O B:ARG24 4.8 38.3 1.0
CA B:PRO25 4.8 33.0 1.0
CB B:ARG24 4.9 51.5 1.0

Reference:

Y.Hu, H.Shi, M.Zhou, Q.Ren, W.Zhu, W.Zhang, Z.Zhang, C.Zhou, Y.Liu, X.Ding, H.C.Shen, S.F.Yan, F.Dey, W.Wu, G.Zhai, Z.Zhou, Z.Xu, Y.Ji, H.Lv, T.Jiang, W.Wang, Y.Xu, M.Vercruysse, X.Yao, Y.Mao, X.Yu, K.Bradley, X.Tan. Discovery of Pyrido[2,3-B]Indole Derivatives with Gram-Negative Activity Targeting Both Dna Gyrase and Topoisomerase IV. J.Med.Chem. V. 63 9623 2020.
ISSN: ISSN 0022-2623
PubMed: 32787097
DOI: 10.1021/ACS.JMEDCHEM.0C00768
Page generated: Sun Jul 28 02:59:42 2024

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