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Chlorine in PDB 6qx2: 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna, PDB code: 6qx2 was solved by B.D.Bax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 162.15 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 187.640, 410.120, 93.940, 90.00, 120.22, 90.00
R / Rfree (%) 17.6 / 20.8

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna (pdb code 6qx2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna, PDB code: 6qx2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6qx2

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Chlorine binding site 1 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:52.8
occ:0.60
 CL A:JK8501 0.0 52.8 0.6
C19 A:JK8501 1.7 47.3 0.6
C14 A:JK8501 2.7 42.6 0.6
C18 A:JK8501 2.7 48.3 0.6
C11 A:JK8501 3.0 37.5 0.6
C10 A:JK8501 3.1 34.9 0.6
CG1 A:VAL31 3.2 93.7 1.0
CD A:PRO343 3.4 60.3 1.0
CE A:MET27 3.4 84.3 1.0
SD A:MET27 3.7 89.5 1.0
O A:GLY341 3.9 63.7 1.0
C15 A:JK8501 3.9 42.9 0.6
C17 A:JK8501 4.0 46.7 0.6
C12 A:JK8501 4.1 36.0 0.6
CA A:ARG342 4.1 67.2 1.0
C9 A:JK8501 4.2 33.7 0.6
CG2 A:ILE30 4.3 61.1 1.0
CG A:PRO343 4.4 66.4 1.0
C16 A:JK8501 4.5 44.7 0.6
N A:PRO343 4.5 59.1 1.0
CB A:ARG342 4.6 71.6 1.0
CG A:ARG342 4.6 70.0 1.0
CB A:VAL31 4.7 91.6 1.0
C A:GLY341 4.8 62.2 1.0
C A:ARG342 4.9 60.6 1.0
C13 A:JK8501 4.9 35.1 0.6
C8 A:JK8501 5.0 33.9 0.6
N A:ARG342 5.0 61.7 1.0

Chlorine binding site 2 out of 12 in 6qx2

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Chlorine binding site 2 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:64.1
occ:1.00
 CL C:JK8501 0.0 64.1 1.0
C19 C:JK8501 1.7 62.1 1.0
C18 C:JK8501 2.5 63.1 1.0
C14 C:JK8501 2.7 63.1 1.0
CE C:MET27 3.1 0.3 1.0
C10 C:JK8501 3.3 53.0 1.0
C11 C:JK8501 3.3 56.9 1.0
C17 C:JK8501 3.8 65.7 1.0
C15 C:JK8501 3.9 68.8 1.0
SD C:MET27 4.0 0.4 1.0
CG1 C:VAL31 4.0 82.0 1.0
O C:GLY341 4.2 60.2 1.0
CG C:ARG342 4.3 67.0 1.0
CB D:ALA637 4.3 89.3 1.0
C16 C:JK8501 4.3 67.1 1.0
C9 C:JK8501 4.4 47.8 1.0
C12 C:JK8501 4.5 50.5 1.0
CD C:PRO343 4.6 36.2 1.0
CA C:ARG342 4.6 51.4 1.0
CB C:ARG342 4.7 60.2 1.0
CG2 D:VAL638 4.9 71.0 1.0

Chlorine binding site 3 out of 12 in 6qx2

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Chlorine binding site 3 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl501

b:41.7
occ:1.00
 CL J:JK8501 0.0 41.7 1.0
C19 J:JK8501 1.7 49.8 1.0
C14 J:JK8501 2.7 54.1 1.0
C18 J:JK8501 2.7 48.3 1.0
C10 J:JK8501 2.8 46.1 1.0
C11 J:JK8501 3.0 49.3 1.0
CE J:MET27 3.1 60.5 1.0
CG1 J:VAL31 3.4 26.7 1.0
CD J:PRO343 3.7 37.9 1.0
C9 J:JK8501 3.9 44.7 1.0
C17 J:JK8501 4.0 50.6 1.0
C15 J:JK8501 4.0 53.5 1.0
C12 J:JK8501 4.1 46.7 1.0
CG2 J:ILE30 4.3 24.9 1.0
O J:GLY341 4.4 47.5 1.0
SD J:MET27 4.5 63.1 1.0
C16 J:JK8501 4.5 51.2 1.0
CA J:ARG342 4.6 43.2 1.0
CG J:PRO343 4.6 36.4 1.0
C8 J:JK8501 4.8 49.6 1.0
CG J:ARG342 4.8 48.1 1.0
CB J:ARG342 4.9 45.3 1.0
C13 J:JK8501 4.9 48.4 1.0
CB J:VAL31 4.9 26.0 1.0
N J:PRO343 4.9 36.4 1.0

Chlorine binding site 4 out of 12 in 6qx2

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Chlorine binding site 4 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl501

b:25.6
occ:0.60
 CL L:JK8501 0.0 25.6 0.6
C19 L:JK8501 1.7 23.1 0.6
C14 L:JK8501 2.7 22.0 0.6
C18 L:JK8501 2.7 22.5 0.6
C10 L:JK8501 2.8 20.2 0.6
C11 L:JK8501 3.0 21.2 0.6
CD L:PRO343 3.3 42.5 1.0
CE L:MET27 3.6 37.0 1.0
SD L:MET27 3.8 38.6 1.0
C9 L:JK8501 3.9 20.3 0.6
CG1 L:VAL31 3.9 51.9 1.0
C15 L:JK8501 3.9 21.3 0.6
C17 L:JK8501 3.9 21.7 0.6
CG L:PRO343 4.1 41.8 1.0
C12 L:JK8501 4.1 21.1 0.6
CG2 L:ILE30 4.2 44.3 1.0
CA L:ARG342 4.4 47.9 1.0
C16 L:JK8501 4.4 21.3 0.6
O L:GLY341 4.5 50.0 1.0
CB M:ALA637 4.5 55.2 1.0
N L:PRO343 4.5 39.4 1.0
CB L:ARG342 4.7 50.8 1.0
C8 L:JK8501 4.7 20.7 0.6
CG L:ARG342 4.7 54.2 1.0
C13 L:JK8501 4.9 21.1 0.6

Chlorine binding site 5 out of 12 in 6qx2

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Chlorine binding site 5 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl501

b:22.2
occ:0.60
 CL R:JK8501 0.0 22.2 0.6
C19 R:JK8501 1.7 18.9 0.6
C18 R:JK8501 2.6 18.4 0.6
C14 R:JK8501 2.7 18.3 0.6
C10 R:JK8501 2.8 17.3 0.6
C11 R:JK8501 3.1 17.7 0.6
CE R:MET27 3.6 82.3 1.0
SD R:MET27 3.8 83.4 1.0
CG R:MET27 3.9 67.3 1.0
C17 R:JK8501 3.9 17.9 0.6
C9 R:JK8501 3.9 17.2 0.6
C15 R:JK8501 3.9 17.9 0.6
CB S:ALA637 4.0 49.3 1.0
C16 R:JK8501 4.4 17.9 0.6
CG2 S:ILE633 4.4 54.1 1.0
C12 R:JK8501 4.4 17.3 0.6
CG1 R:VAL31 4.4 43.2 1.0
CB R:MET27 4.5 64.3 1.0
CG2 R:ILE30 4.5 44.1 1.0
CA R:MET27 4.6 59.0 1.0
CD1 R:ILE30 4.7 44.3 1.0
CD R:PRO343 4.8 48.7 1.0
CB R:ILE30 5.0 41.0 1.0
C8 R:JK8501 5.0 17.7 0.6

Chlorine binding site 6 out of 12 in 6qx2

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Chlorine binding site 6 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl701

b:11.7
occ:0.40
 CL U:JK8701 0.0 11.7 0.4
C19 U:JK8701 1.7 11.1 0.4
C18 U:JK8701 2.7 11.1 0.4
C14 U:JK8701 2.7 10.8 0.4
C11 U:JK8701 3.0 10.2 0.4
C10 U:JK8701 3.1 10.1 0.4
CD T:PRO343 3.6 50.7 1.0
C17 U:JK8701 3.9 11.2 0.4
C15 U:JK8701 4.0 10.9 0.4
CE T:MET27 4.0 44.4 1.0
C12 U:JK8701 4.1 10.0 0.4
CG T:ARG342 4.1 61.9 1.0
CA T:ARG342 4.2 49.0 1.0
CB U:ALA637 4.2 73.7 1.0
CB T:ARG342 4.2 56.4 1.0
C9 U:JK8701 4.2 10.1 0.4
CG1 T:VAL31 4.3 26.3 1.0
CD T:ARG342 4.4 68.9 1.0
O T:GLY341 4.5 34.0 1.0
C16 U:JK8701 4.5 11.0 0.4
SD T:MET27 4.5 45.6 1.0
CG T:PRO343 4.6 48.7 1.0
N T:PRO343 4.8 49.2 1.0
C13 U:JK8701 4.9 9.8 0.4
C8 U:JK8701 5.0 10.0 0.4
NE T:ARG342 5.0 70.7 1.0

Chlorine binding site 7 out of 12 in 6qx2

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Chlorine binding site 7 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl701

b:10.2
occ:0.30
 CL b:JK8701 0.0 10.2 0.3
C19 b:JK8701 1.7 9.6 0.3
C10 b:JK8701 2.3 9.3 0.3
C14 b:JK8701 2.6 9.4 0.3
C11 b:JK8701 2.6 9.3 0.3
C18 b:JK8701 2.7 9.6 0.3
C9 b:JK8701 3.3 9.2 0.3
CD a:PRO343 3.3 0.4 1.0
CE a:MET27 3.4 96.0 1.0
C12 b:JK8701 3.8 9.2 0.3
C15 b:JK8701 3.9 9.4 0.3
C17 b:JK8701 4.0 9.6 0.3
CG a:PRO343 4.0 1.0 1.0
C8 b:JK8701 4.2 9.2 0.3
C16 b:JK8701 4.4 9.5 0.3
C13 b:JK8701 4.4 9.0 0.3
SD a:MET27 4.5 93.4 1.0
CA a:ARG342 4.5 90.1 1.0
CB a:ARG342 4.6 87.6 1.0
N a:PRO343 4.6 95.7 1.0
CG a:ARG342 4.6 81.9 1.0
CB b:ALA637 4.7 68.9 1.0
CG2 a:ILE30 4.8 52.5 1.0
CG1 a:VAL31 4.8 60.4 1.0
CD a:ARG342 5.0 79.5 1.0

Chlorine binding site 8 out of 12 in 6qx2

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Chlorine binding site 8 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Cl701

b:41.4
occ:0.60
 CL d:JK8701 0.0 41.4 0.6
C19 d:JK8701 1.7 42.7 0.6
C18 d:JK8701 2.6 44.3 0.6
C14 d:JK8701 2.7 40.0 0.6
C10 d:JK8701 3.0 34.3 0.6
C11 d:JK8701 3.1 35.2 0.6
SD c:MET27 3.5 0.6 1.0
C17 d:JK8701 3.9 44.6 0.6
CB d:ALA637 4.0 88.5 1.0
C15 d:JK8701 4.0 42.0 0.6
C9 d:JK8701 4.1 34.4 0.6
CD c:PRO343 4.1 71.5 1.0
O c:GLY341 4.2 53.6 1.0
CG1 c:VAL31 4.2 86.4 1.0
C12 d:JK8701 4.4 34.6 0.6
CA c:ARG342 4.4 73.6 1.0
C16 d:JK8701 4.5 43.7 0.6
CB c:ARG342 4.6 74.5 1.0
CG c:MET27 4.8 0.1 1.0
CE c:MET27 4.8 0.6 1.0

Chlorine binding site 9 out of 12 in 6qx2

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Chlorine binding site 9 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Cl701

b:59.2
occ:1.00
 CL k:JK8701 0.0 59.2 1.0
C19 k:JK8701 1.8 51.9 1.0
C18 k:JK8701 2.7 47.5 1.0
C14 k:JK8701 2.8 45.0 1.0
C10 k:JK8701 2.9 38.0 1.0
C11 k:JK8701 3.1 38.6 1.0
SD j:MET27 3.2 63.9 1.0
CE j:MET27 3.2 57.5 1.0
CG1 j:VAL31 3.5 51.0 1.0
CD j:PRO343 3.9 37.0 1.0
C9 k:JK8701 4.0 39.2 1.0
C17 k:JK8701 4.0 46.0 1.0
C15 k:JK8701 4.1 43.6 1.0
CG2 j:ILE30 4.1 79.0 1.0
C12 k:JK8701 4.3 36.1 1.0
C16 k:JK8701 4.5 47.7 1.0
CG j:PRO343 4.6 36.1 1.0
CB j:ILE30 4.8 70.9 1.0
CB k:ALA637 4.9 55.5 1.0
O j:GLY341 4.9 42.1 1.0
CG j:MET27 4.9 52.5 1.0
C8 k:JK8701 4.9 40.5 1.0

Chlorine binding site 10 out of 12 in 6qx2

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Chlorine binding site 10 out of 12 in the 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of 3.4A Structure of Benzoisoxazole 3 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
l:Cl501

b:70.0
occ:1.00
 CL l:JK8501 0.0 70.0 1.0
C19 l:JK8501 1.7 65.9 1.0
C18 l:JK8501 2.6 70.1 1.0
C14 l:JK8501 2.7 60.4 1.0
C10 l:JK8501 3.2 45.1 1.0
C11 l:JK8501 3.2 51.5 1.0
CE l:MET27 3.7 26.4 1.0
O l:GLY341 3.7 49.1 1.0
CD l:PRO343 3.8 40.5 1.0
CG1 l:VAL31 3.8 40.0 1.0
C17 l:JK8501 3.9 72.2 1.0
CA l:ARG342 3.9 55.1 1.0
C15 l:JK8501 4.0 61.1 1.0
CG l:ARG342 4.0 68.1 1.0
CB l:ARG342 4.2 62.9 1.0
C9 l:JK8501 4.3 46.0 1.0
SD l:MET27 4.3 26.4 1.0
C12 l:JK8501 4.3 48.9 1.0
C16 l:JK8501 4.4 68.1 1.0
CB m:ALA637 4.6 48.2 1.0
C l:GLY341 4.6 48.0 1.0
N l:ARG342 4.7 52.5 1.0
CD l:ARG342 4.7 67.7 1.0
N l:PRO343 4.8 39.7 1.0
CG l:PRO343 4.8 40.4 1.0
C l:ARG342 4.9 47.5 1.0

Reference:

R.K.Thalji, K.Raha, D.Andreotti, A.Checchia, H.Cui, G.Meneghelli, R.Profeta, F.Tonelli, S.Tommasi, T.Bakshi, B.T.Donovan, A.Howells, S.Jain, C.Nixon, G.Quinque, L.Mccloskey, B.D.Bax, M.Neu, P.F.Chan, R.A.Stavenger. Structure-Guided Design of Antibacterials That Allosterically Inhibit Dna Gyrase. Bioorg.Med.Chem.Lett. V. 29 1407 2019.
ISSN: ESSN 1464-3405
PubMed: 30962087
DOI: 10.1016/J.BMCL.2019.03.029
Page generated: Mon Jul 29 14:13:06 2024

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