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Fluorine in PDB 5npp: 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna, PDB code: 5npp was solved by B.D.Bax, P.F.Chan, R.A.Stavenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.22
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 92.850, 92.850, 409.980, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.7

Other elements in 5npp:

The structure of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna (pdb code 5npp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna, PDB code: 5npp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5npp

Go back to Fluorine Binding Sites List in 5npp
Fluorine binding site 1 out of 2 in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:50.4
occ:0.50
F1 C:6EJ101 0.0 50.4 0.5
O9 C:6EJ101 0.9 59.1 0.5
C2 C:6EJ101 1.4 50.1 0.5
C8 C:6EJ101 2.0 54.2 0.5
C33 C:6EJ101 2.4 44.5 0.5
C3 C:6EJ101 2.4 46.5 0.5
N10 C:6EJ101 2.8 48.6 0.5
C12 C:6EJ101 3.0 43.9 0.5
C7 C:6EJ101 3.1 51.2 0.5
C14 C:6EJ101 3.1 43.8 0.5
C11 C:6EJ101 3.2 48.9 0.5
C6 C:DT2 3.5 49.5 1.0
C5 C:DT2 3.6 48.5 1.0
C34 C:6EJ101 3.6 42.1 0.5
C4 C:6EJ101 3.7 42.2 0.5
N1 C:DT2 3.9 49.0 1.0
N7 C:DA3 3.9 67.8 1.0
C20 C:6EJ101 3.9 42.6 0.5
C4 C:DT2 4.0 50.0 1.0
C2' C:DT2 4.0 49.0 1.0
C7 C:DT2 4.1 44.8 1.0
C34 C:6EJ101 4.1 48.8 0.5
N15 C:6EJ101 4.2 43.8 0.5
C5 C:6EJ101 4.2 40.9 0.5
N3 C:DT2 4.2 48.3 1.0
C2 C:DT2 4.2 52.0 1.0
C6 C:6EJ101 4.3 47.7 0.5
C5 C:DA3 4.4 61.1 1.0
C11 C:6EJ101 4.5 42.4 0.5
N6 C:DA3 4.5 51.7 1.0
C1' C:DT2 4.5 52.0 1.0
C8 C:DA3 4.6 62.2 1.0
O4 C:DT2 4.6 54.9 1.0
N10 C:6EJ101 4.6 41.5 0.5
C12 C:6EJ101 4.7 47.8 0.5
C6 C:DA3 4.7 52.2 1.0
C5 C:6EJ101 4.8 47.6 0.5
O2 C:DT2 5.0 50.1 1.0

Fluorine binding site 2 out of 2 in 5npp

Go back to Fluorine Binding Sites List in 5npp
Fluorine binding site 2 out of 2 in the 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2.22A Structure of THIOPHENE2 and GSK945237 with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F101

b:47.0
occ:0.50
F1 C:6EJ101 0.0 47.0 0.5
C2 C:6EJ101 1.4 47.5 0.5
O9 C:6EJ101 1.6 43.6 0.5
C33 C:6EJ101 2.4 46.7 0.5
C3 C:6EJ101 2.4 46.6 0.5
C8 C:6EJ101 2.6 39.8 0.5
C11 C:6EJ101 2.9 42.4 0.5
C12 C:6EJ101 3.0 47.8 0.5
N10 C:6EJ101 3.1 41.5 0.5
C14 C:6EJ101 3.1 44.8 0.5
C6 A:DT2 3.4 60.8 0.5
C5 A:DT2 3.5 58.6 0.5
C6 A:DT2 3.6 46.1 0.6
C34 C:6EJ101 3.6 48.8 0.5
C5 A:DT2 3.7 45.4 0.6
N7 A:DA3 3.7 72.6 1.0
C4 C:6EJ101 3.7 44.8 0.5
N1 A:DT2 3.8 62.9 0.5
C2' A:DT2 3.8 66.9 0.5
N1 A:DT2 3.8 47.7 0.6
C7 C:6EJ101 3.9 38.3 0.5
C4 A:DT2 3.9 44.7 0.6
C2' A:DT2 3.9 52.5 0.6
C4 A:DT2 4.0 59.3 0.5
C7 A:DT2 4.0 56.0 0.5
C2 A:DT2 4.1 49.8 0.6
N3 A:DT2 4.1 49.2 0.6
C5 C:6EJ101 4.1 47.6 0.5
C5 A:DA3 4.2 63.7 1.0
C2 A:DT2 4.2 63.8 0.5
N3 A:DT2 4.3 61.8 0.5
C8 A:DA3 4.3 70.4 1.0
C7 A:DT2 4.3 45.7 0.6
N15 C:6EJ101 4.3 42.1 0.5
C20 C:6EJ101 4.3 39.6 0.5
C1' A:DT2 4.4 66.3 0.5
C34 C:6EJ101 4.4 42.1 0.5
N6 A:DA3 4.4 67.4 1.0
C11 C:6EJ101 4.4 48.9 0.5
C1' A:DT2 4.4 50.4 0.6
C12 C:6EJ101 4.4 43.9 0.5
C6 A:DA3 4.5 59.2 1.0
O4 A:DT2 4.6 43.3 0.6
N10 C:6EJ101 4.6 48.6 0.5
O4 A:DT2 4.7 56.6 0.5
O2 A:DT2 4.8 52.4 0.6
O2 A:DT2 5.0 67.0 0.5
C4 A:DA3 5.0 64.5 1.0

Reference:

P.F.Chan, T.Germe, B.D.Bax, J.Huang, R.K.Thalji, E.Bacque, A.Checchia, D.Chen, H.Cui, X.Ding, K.Ingraham, L.Mccloskey, K.Raha, V.Srikannathasan, A.Maxwell, R.A.Stavenger. Thiophene Antibacterials That Allosterically Stabilize Dna-Cleavage Complexes with Dna Gyrase. Proc. Natl. Acad. Sci. V. 114 E4492 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28507124
DOI: 10.1073/PNAS.1700721114
Page generated: Sun Dec 13 12:28:56 2020

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