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Fluorine in PDB 5cdq: 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna

Enzymatic activity of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna

All present enzymatic activity of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna:
5.99.1.3;

Protein crystallography data

The structure of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna, PDB code: 5cdq was solved by B.D.Bax, V.Srikannathasan, P.F.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.930, 170.550, 125.670, 90.00, 103.30, 90.00
R / Rfree (%) 17.5 / 21.8

Other elements in 5cdq:

The structure of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna also contains other interesting chemical elements:

Magnesium (Mg) 14 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna (pdb code 5cdq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna, PDB code: 5cdq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5cdq

Go back to Fluorine Binding Sites List in 5cdq
Fluorine binding site 1 out of 6 in the 2.95A Structure of Moxifloxacin 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 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F2101

b:70.7
occ:1.00
 F E:MFX2101 0.0 70.7 1.0
C15 E:MFX2101 1.3 67.7 1.0
C17 E:MFX2101 2.3 67.9 1.0
C11 E:MFX2101 2.5 64.8 1.0
C04 E:MFX2101 2.8 65.0 1.0
C2 E:DC2012 2.9 79.0 1.0
N01 E:MFX2101 3.0 65.2 1.0
N7 E:DA2013 3.1 76.4 1.0
N1 E:DC2012 3.1 80.9 1.0
N3 E:DC2012 3.2 78.8 1.0
C5 E:DA2013 3.2 74.9 1.0
O2 E:DC2012 3.4 77.8 1.0
C8 E:DA2013 3.4 76.2 1.0
C6 E:DC2012 3.5 82.0 1.0
C4 E:DC2012 3.5 80.1 1.0
C4 E:DA2013 3.6 73.5 1.0
C14 E:MFX2101 3.6 67.8 1.0
N9 E:DA2013 3.7 74.7 1.0
C5 E:DC2012 3.7 82.0 1.0
C03 E:MFX2101 3.7 68.4 1.0
C6 E:DA2013 3.8 74.2 1.0
C1' E:DC2012 3.8 82.7 1.0
C13 E:MFX2101 3.8 62.9 1.0
C2' E:DC2012 3.8 85.1 1.0
C02 E:MFX2101 4.1 67.0 1.0
N6 E:DA2013 4.2 75.4 1.0
C12 E:MFX2101 4.3 65.3 1.0
N2 F:DG2009 4.3 81.1 1.0
N1 F:DG2009 4.4 81.7 1.0
N3 E:DA2013 4.4 71.6 1.0
N4 E:DC2012 4.4 80.3 1.0
N1 E:DA2013 4.5 72.5 1.0
O4' E:DA2013 4.5 76.4 1.0
C01 E:MFX2101 4.5 67.8 1.0
C2 E:DA2013 4.6 71.4 1.0
C2 F:DG2009 4.7 81.1 1.0
C1' E:DA2013 4.7 74.6 1.0
O E:HOH2206 4.7 58.0 1.0
C19 E:MFX2101 4.8 69.7 1.0
O01 E:MFX2101 4.9 62.0 1.0
O02 E:MFX2101 5.0 72.0 1.0

Fluorine binding site 2 out of 6 in 5cdq

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Fluorine binding site 2 out of 6 in the 2.95A Structure of Moxifloxacin 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 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F2101

b:90.2
occ:1.00
 F F:MFX2101 0.0 90.2 1.0
C15 F:MFX2101 1.3 89.1 1.0
C17 F:MFX2101 2.3 89.2 1.0
C11 F:MFX2101 2.5 89.6 1.0
C04 F:MFX2101 2.9 96.4 1.0
N7 F:DA2013 3.0 80.3 1.0
N01 F:MFX2101 3.0 94.0 1.0
C2 F:DC2012 3.0 89.0 1.0
C5 F:DA2013 3.1 79.9 1.0
N1 F:DC2012 3.2 90.9 1.0
N3 F:DC2012 3.2 89.1 1.0
C8 F:DA2013 3.3 82.0 1.0
O2 F:DC2012 3.5 88.1 1.0
C4 F:DA2013 3.5 81.7 1.0
C6 F:DC2012 3.5 92.4 1.0
C4 F:DC2012 3.6 90.5 1.0
N9 F:DA2013 3.6 83.3 1.0
C14 F:MFX2101 3.6 88.8 1.0
C5 F:DC2012 3.7 92.3 1.0
C6 F:DA2013 3.7 78.0 1.0
C03 F:MFX2101 3.7 98.6 1.0
C13 F:MFX2101 3.8 87.5 1.0
C1' F:DC2012 3.9 92.7 1.0
C2' F:DC2012 3.9 95.9 1.0
C02 F:MFX2101 4.1 99.1 1.0
N6 F:DA2013 4.1 76.2 1.0
C12 F:MFX2101 4.3 87.0 1.0
N2 E:DG2009 4.3 78.4 1.0
N1 E:DG2009 4.3 79.2 1.0
N3 F:DA2013 4.4 82.0 1.0
N4 F:DC2012 4.4 90.7 1.0
N1 F:DA2013 4.5 78.7 1.0
O4' F:DA2013 4.5 88.8 1.0
C01 F:MFX2101 4.5 0.8 1.0
C2 E:DG2009 4.6 78.9 1.0
C1' F:DA2013 4.6 86.5 1.0
C2 F:DA2013 4.7 80.5 1.0
C19 F:MFX2101 4.8 90.9 1.0
O01 F:MFX2101 4.9 88.4 1.0
O02 F:MFX2101 5.0 92.7 1.0

Fluorine binding site 3 out of 6 in 5cdq

Go back to Fluorine Binding Sites List in 5cdq
Fluorine binding site 3 out of 6 in the 2.95A Structure of Moxifloxacin 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 3 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F2103

b:76.9
occ:1.00
 F F:MFX2103 0.0 76.9 1.0
C15 F:MFX2103 1.4 75.0 1.0
C17 F:MFX2103 2.4 72.6 1.0
C11 F:MFX2103 2.5 75.4 1.0
N01 F:MFX2103 2.6 79.2 1.0
N3 F:DA2 3.3 90.9 1.0
O4' F:DA2 3.4 94.1 1.0
C8 F:DG1 3.4 90.0 1.0
C04 F:MFX2103 3.4 80.9 1.0
N9 F:DG1 3.5 89.2 1.0
N7 F:DG1 3.5 90.5 1.0
C4 F:DA2 3.5 91.1 1.0
C5 F:DG1 3.6 90.2 1.0
C4 F:DG1 3.6 89.3 1.0
C14 F:MFX2103 3.6 70.0 1.0
C2 F:DA2 3.8 90.5 1.0
N02 F:MFX2103 3.8 82.0 1.0
C13 F:MFX2103 3.8 72.0 1.0
N9 F:DA2 3.8 91.9 1.0
C03 F:MFX2103 3.8 81.0 1.0
C2' F:DG1 3.9 86.4 1.0
C1' F:DA2 4.0 92.7 1.0
C1' F:DG1 4.2 88.5 1.0
C02 F:MFX2103 4.2 81.3 1.0
C5 F:DA2 4.2 90.8 1.0
N3 F:DG1 4.3 88.6 1.0
C12 F:MFX2103 4.3 68.7 1.0
C6 F:DG1 4.3 90.4 1.0
N1 F:DA2 4.5 90.2 1.0
C01 F:MFX2103 4.5 81.3 1.0
C4' F:DA2 4.6 94.8 1.0
C8 F:DA2 4.6 91.8 1.0
C6 F:DA2 4.7 90.4 1.0
C10 F:MFX2103 4.7 83.0 1.0
C2 F:DG1 4.8 88.8 1.0
N1 F:DG1 4.8 89.8 1.0
C19 F:MFX2103 4.8 70.0 1.0
N7 F:DA2 4.9 91.1 1.0
C05 F:MFX2103 4.9 81.8 1.0
O6 F:DG1 4.9 90.8 1.0
O01 F:MFX2103 5.0 72.2 1.0
O02 F:MFX2103 5.0 70.2 1.0

Fluorine binding site 4 out of 6 in 5cdq

Go back to Fluorine Binding Sites List in 5cdq
Fluorine binding site 4 out of 6 in the 2.95A Structure of Moxifloxacin 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 4 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
V:F2101

b:69.4
occ:1.00
 F V:MFX2101 0.0 69.4 1.0
C15 V:MFX2101 1.3 66.8 1.0
C17 V:MFX2101 2.3 68.4 1.0
C11 V:MFX2101 2.5 66.0 1.0
C04 V:MFX2101 2.8 70.7 1.0
N01 V:MFX2101 3.0 68.9 1.0
C2 V:DC2012 3.0 77.0 1.0
N7 V:DA2013 3.1 77.3 1.0
N1 V:DC2012 3.2 78.9 1.0
C5 V:DA2013 3.2 75.9 1.0
C8 V:DA2013 3.2 78.0 1.0
N3 V:DC2012 3.3 77.1 1.0
O2 V:DC2012 3.4 76.0 1.0
C4 V:DA2013 3.5 75.8 1.0
N9 V:DA2013 3.5 77.3 1.0
C14 V:MFX2101 3.6 67.4 1.0
C6 V:DC2012 3.6 80.8 1.0
C4 V:DC2012 3.7 78.9 1.0
C13 V:MFX2101 3.8 64.0 1.0
C03 V:MFX2101 3.8 71.0 1.0
C1' V:DC2012 3.8 80.2 1.0
C2' V:DC2012 3.8 82.6 1.0
C5 V:DC2012 3.8 81.1 1.0
C6 V:DA2013 3.9 74.2 1.0
C02 V:MFX2101 4.1 72.0 1.0
C12 V:MFX2101 4.2 64.5 1.0
N3 V:DA2013 4.3 74.2 1.0
C1' V:DA2013 4.3 78.7 1.0
N2 W:DG2009 4.3 77.6 1.0
N1 W:DG2009 4.3 78.0 1.0
O4' V:DA2013 4.4 81.2 1.0
N6 V:DA2013 4.4 74.5 1.0
N4 V:DC2012 4.5 79.8 1.0
N1 V:DA2013 4.6 72.4 1.0
C01 V:MFX2101 4.6 71.5 1.0
C2 V:DA2013 4.6 72.7 1.0
C2 W:DG2009 4.6 77.5 1.0
C19 V:MFX2101 4.8 68.1 1.0
O01 V:MFX2101 4.9 65.1 1.0
O02 V:MFX2101 5.0 69.0 1.0

Fluorine binding site 5 out of 6 in 5cdq

Go back to Fluorine Binding Sites List in 5cdq
Fluorine binding site 5 out of 6 in the 2.95A Structure of Moxifloxacin 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 5 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:F2101

b:89.6
occ:1.00
 F W:MFX2101 0.0 89.6 1.0
C15 W:MFX2101 1.3 85.3 1.0
C17 W:MFX2101 2.3 81.7 1.0
C11 W:MFX2101 2.5 84.9 1.0
C04 W:MFX2101 2.9 90.1 1.0
N7 W:DA2013 3.0 87.9 1.0
C2 W:DC2012 3.0 84.1 1.0
N01 W:MFX2101 3.0 88.7 1.0
C5 W:DA2013 3.1 87.5 1.0
N3 W:DC2012 3.2 83.9 1.0
N1 W:DC2012 3.2 87.9 1.0
C8 W:DA2013 3.4 89.5 1.0
C4 W:DC2012 3.4 85.9 1.0
C6 W:DC2012 3.5 89.3 1.0
O2 W:DC2012 3.5 82.3 1.0
C4 W:DA2013 3.5 88.7 1.0
C6 W:DA2013 3.6 86.4 1.0
C14 W:MFX2101 3.6 79.0 1.0
C5 W:DC2012 3.6 88.7 1.0
N9 W:DA2013 3.7 90.3 1.0
C03 W:MFX2101 3.7 91.9 1.0
C13 W:MFX2101 3.8 79.7 1.0
C1' W:DC2012 3.9 91.7 1.0
C2' W:DC2012 4.0 96.6 1.0
N6 W:DA2013 4.0 85.7 1.0
C02 W:MFX2101 4.1 91.8 1.0
N4 W:DC2012 4.3 85.8 1.0
C12 W:MFX2101 4.3 77.4 1.0
N1 V:DG2009 4.3 85.3 1.0
N1 W:DA2013 4.3 86.3 1.0
N3 W:DA2013 4.4 88.3 1.0
N2 V:DG2009 4.4 85.4 1.0
C01 W:MFX2101 4.5 92.8 1.0
C2 W:DA2013 4.6 86.8 1.0
O4' W:DA2013 4.6 95.4 1.0
C2 V:DG2009 4.7 85.0 1.0
C19 W:MFX2101 4.8 79.7 1.0
C1' W:DA2013 4.8 92.4 1.0
O02 W:MFX2101 4.9 82.7 1.0
O W:HOH2212 4.9 62.8 1.0
O01 W:MFX2101 4.9 79.5 1.0

Fluorine binding site 6 out of 6 in 5cdq

Go back to Fluorine Binding Sites List in 5cdq
Fluorine binding site 6 out of 6 in the 2.95A Structure of Moxifloxacin 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 6 of 2.95A Structure of Moxifloxacin with S.Aureus Dna Gyrase and Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:F2103

b:81.1
occ:1.00
 F W:MFX2103 0.0 81.1 1.0
C15 W:MFX2103 1.4 77.3 1.0
C17 W:MFX2103 2.4 72.3 1.0
C11 W:MFX2103 2.5 77.3 1.0
C04 W:MFX2103 2.9 86.8 1.0
N01 W:MFX2103 3.1 83.3 1.0
N3 W:DA2 3.3 90.1 1.0
C02 W:MFX2103 3.4 88.8 1.0
C5 W:DG1 3.4 95.2 1.0
N7 W:DG1 3.5 96.3 1.0
C8 W:DG1 3.5 96.0 1.0
C4 W:DA2 3.5 90.0 1.0
C4 W:DG1 3.5 94.2 1.0
N9 W:DG1 3.6 94.5 1.0
O4' W:DA2 3.6 93.8 1.0
C14 W:MFX2103 3.7 68.2 1.0
C2 W:DA2 3.7 89.1 1.0
C01 W:MFX2103 3.8 89.3 1.0
C13 W:MFX2103 3.8 71.8 1.0
C03 W:MFX2103 3.8 86.6 1.0
N9 W:DA2 4.0 91.2 1.0
C2' W:DG1 4.0 91.7 1.0
C6 W:DG1 4.0 95.5 1.0
N3 W:DG1 4.2 93.5 1.0
C1' W:DA2 4.2 92.5 1.0
C5 W:DA2 4.2 88.8 1.0
C12 W:MFX2103 4.3 67.8 1.0
N1 W:DA2 4.4 88.4 1.0
C1' W:DG1 4.4 93.3 1.0
N1 W:DG1 4.6 94.3 1.0
O6 W:DG1 4.6 96.5 1.0
C2 W:DG1 4.6 93.3 1.0
C6 W:DA2 4.6 88.0 1.0
C8 W:DA2 4.7 90.9 1.0
N02 W:MFX2103 4.8 89.2 1.0
C19 W:MFX2103 4.9 66.3 1.0
C4' W:DA2 4.9 94.9 1.0
N7 W:DA2 4.9 89.6 1.0
O01 W:MFX2103 5.0 71.3 1.0

Reference:

P.F.Chan, V.Srikannathasan, J.Huang, H.Cui, A.P.Fosberry, M.Gu, M.M.Hann, M.Hibbs, P.Homes, K.Ingraham, J.Pizzollo, C.Shen, A.J.Shillings, C.E.Spitzfaden, R.Tanner, A.J.Theobald, R.A.Stavenger, B.D.Bax, M.N.Gwynn. Structural Basis of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide and Moxifloxacin. Nat Commun V. 6 10048 2015.
ISSN: ESSN 2041-1723
PubMed: 26640131
DOI: 10.1038/NCOMMS10048
Page generated: Sun Dec 13 12:20:10 2020

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