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Chlorine in PDB 5z9b: Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine

Enzymatic activity of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine

All present enzymatic activity of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine:
5.99.1.3;

Protein crystallography data

The structure of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine, PDB code: 5z9b was solved by X.Huang, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.80 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.782, 68.231, 102.529, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine (pdb code 5z9b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine, PDB code: 5z9b:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5z9b

Go back to Chlorine Binding Sites List in 5z9b
Chlorine binding site 1 out of 4 in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:48.3
occ:1.00
CL7 A:HX3303 0.0 48.3 1.0
C1 A:HX3303 1.7 37.8 1.0
C6 A:HX3303 2.7 34.7 1.0
C2 A:HX3303 2.7 35.1 1.0
CL8 A:HX3303 3.2 36.9 1.0
CG2 A:VAL167 3.5 18.8 1.0
CG1 A:VAL120 3.6 27.9 1.0
CG2 A:VAL120 3.7 27.7 1.0
CB A:VAL120 3.9 26.8 1.0
C5 A:HX3303 4.0 31.2 1.0
C3 A:HX3303 4.0 32.1 1.0
SD A:MET95 4.0 29.4 1.0
C4 A:HX3303 4.5 31.5 1.0
CB A:VAL167 4.6 19.4 1.0
CG1 A:VAL43 5.0 17.8 1.0
CB A:ASN46 5.0 22.7 1.0

Chlorine binding site 2 out of 4 in 5z9b

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Chlorine binding site 2 out of 4 in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:36.9
occ:1.00
CL8 A:HX3303 0.0 36.9 1.0
C2 A:HX3303 1.7 35.1 1.0
C3 A:HX3303 2.7 32.1 1.0
C1 A:HX3303 2.7 37.8 1.0
CL7 A:HX3303 3.2 48.3 1.0
CG2 A:ILE94 3.7 21.0 1.0
OD1 A:ASN46 3.8 27.3 1.0
C4 A:HX3303 4.0 31.5 1.0
C6 A:HX3303 4.0 34.7 1.0
CG2 A:ILE78 4.0 25.9 1.0
CB A:ASN46 4.2 22.7 1.0
CD1 A:ILE78 4.2 26.5 1.0
CG2 A:VAL120 4.2 27.7 1.0
CG A:ASN46 4.3 24.6 1.0
C5 A:HX3303 4.5 31.2 1.0
CG1 A:VAL120 4.7 27.9 1.0
CD1 A:ILE94 4.8 24.1 1.0
CB A:ILE78 4.9 25.6 1.0
CB A:ILE94 4.9 21.4 1.0

Chlorine binding site 3 out of 4 in 5z9b

Go back to Chlorine Binding Sites List in 5z9b
Chlorine binding site 3 out of 4 in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:60.1
occ:1.00
CL7 B:HX3303 0.0 60.1 1.0
C1 B:HX3303 1.7 44.8 1.0
C6 B:HX3303 2.7 43.6 1.0
C2 B:HX3303 2.7 41.9 1.0
CL8 B:HX3303 3.2 40.1 1.0
CG2 B:VAL120 3.2 28.2 1.0
CG2 B:VAL167 3.3 16.6 1.0
SD B:MET95 3.9 28.7 1.0
CB B:VAL120 3.9 26.8 1.0
CG1 B:VAL120 3.9 27.9 1.0
C5 B:HX3303 4.0 40.2 1.0
C3 B:HX3303 4.0 38.9 1.0
CB B:VAL167 4.5 16.5 1.0
C4 B:HX3303 4.5 39.4 1.0
CE B:MET95 4.8 24.6 1.0
CD1 B:ILE78 4.8 27.7 1.0
CG1 B:VAL167 4.8 16.6 1.0

Chlorine binding site 4 out of 4 in 5z9b

Go back to Chlorine Binding Sites List in 5z9b
Chlorine binding site 4 out of 4 in the Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacterial Gyrb Atpase Domain in Complex with (3,4-Dichlorophenyl) Hydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:40.1
occ:1.00
CL8 B:HX3303 0.0 40.1 1.0
C2 B:HX3303 1.7 41.9 1.0
C3 B:HX3303 2.7 38.9 1.0
C1 B:HX3303 2.7 44.8 1.0
CL7 B:HX3303 3.2 60.1 1.0
CG2 B:ILE94 3.7 21.9 1.0
C4 B:HX3303 4.0 39.4 1.0
C6 B:HX3303 4.0 43.6 1.0
CG1 B:VAL120 4.0 27.9 1.0
OD1 B:ASN46 4.0 26.1 1.0
CG2 B:ILE78 4.1 26.9 1.0
CD1 B:ILE78 4.3 27.7 1.0
CB B:ASN46 4.3 22.1 1.0
CG B:ASN46 4.3 23.6 1.0
C5 B:HX3303 4.5 40.2 1.0
CB B:VAL120 4.6 26.8 1.0
O B:HOH451 4.7 34.2 1.0
CD1 B:ILE94 5.0 23.5 1.0
CB B:ILE94 5.0 21.1 1.0

Reference:

X.Huang, J.Guo, Q.Liu, Q.Gu, J.Xu, H.Zhou. Identification of An Auxiliary Druggable Pocket in the Dna Gyrase Atpase Domain Using Fragment Probes Medchemcomm V. 9 1619 2018.
ISSN: ESSN 2040-2511
PubMed: 30429968
DOI: 10.1039/C8MD00148K
Page generated: Sat Jul 12 11:07:19 2025

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