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Fluorine in PDB 4glx: Dna Ligase A in Complex with Inhibitor

Enzymatic activity of Dna Ligase A in Complex with Inhibitor

All present enzymatic activity of Dna Ligase A in Complex with Inhibitor:
6.5.1.2;

Protein crystallography data

The structure of Dna Ligase A in Complex with Inhibitor, PDB code: 4glx was solved by L.Prade, R.Lange, N.Tidten-Luksch, A.Chambovey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.990, 100.140, 86.570, 90.00, 105.50, 90.00
R / Rfree (%) 20.1 / 25

Other elements in 4glx:

The structure of Dna Ligase A in Complex with Inhibitor also contains other interesting chemical elements:

Bromine (Br) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dna Ligase A in Complex with Inhibitor (pdb code 4glx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dna Ligase A in Complex with Inhibitor, PDB code: 4glx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4glx

Go back to Fluorine Binding Sites List in 4glx
Fluorine binding site 1 out of 3 in the Dna Ligase A in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dna Ligase A in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:29.6
occ:1.00
F9 A:0XS603 0.0 29.6 1.0
C6 A:0XS603 1.3 28.8 1.0
F10 A:0XS603 2.2 36.0 1.0
F11 A:0XS603 2.2 30.2 1.0
C3 A:0XS603 2.4 25.8 1.0
BR1 A:0XS603 2.8 45.1 1.0
C2 A:0XS603 2.9 27.5 1.0
N5 A:0XS603 3.5 21.4 1.0
CG A:PRO307 3.6 16.3 1.0
CH2 A:TRP309 3.6 9.9 1.0
CD2 A:LEU82 3.8 13.2 1.0
CZ3 A:TRP309 4.0 10.5 1.0
C4 A:0XS603 4.2 22.1 1.0
CD A:PRO307 4.3 16.7 1.0
CZ2 A:TRP309 4.4 10.1 1.0
CB A:ALA310 4.5 9.2 1.0
CB A:PRO307 4.6 15.0 1.0
O A:HOH849 4.6 23.3 1.0
C8 A:0XS603 4.7 18.3 1.0
CG A:LEU82 4.7 13.7 1.0
C7 A:0XS603 5.0 17.4 1.0
CE3 A:TRP309 5.0 10.5 1.0

Fluorine binding site 2 out of 3 in 4glx

Go back to Fluorine Binding Sites List in 4glx
Fluorine binding site 2 out of 3 in the Dna Ligase A in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dna Ligase A in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:36.0
occ:1.00
F10 A:0XS603 0.0 36.0 1.0
C6 A:0XS603 1.3 28.8 1.0
F9 A:0XS603 2.2 29.6 1.0
F11 A:0XS603 2.2 30.2 1.0
C3 A:0XS603 2.3 25.8 1.0
C2 A:0XS603 3.0 27.5 1.0
O A:HOH849 3.1 23.3 1.0
N5 A:0XS603 3.1 21.4 1.0
BR1 A:0XS603 3.4 45.1 1.0
O A:HOH755 3.8 18.6 1.0
CH2 A:TRP309 3.9 9.9 1.0
O A:HOH847 4.0 30.0 1.0
C4 A:0XS603 4.2 22.1 1.0
CE1 A:TYR225 4.3 8.8 1.0
C8 A:0XS603 4.3 18.3 1.0
CD1 A:TYR225 4.3 9.2 1.0
CZ3 A:TRP309 4.5 10.5 1.0
C7 A:0XS603 4.8 17.4 1.0
NZ A:LYS290 4.9 12.4 1.0
CZ2 A:TRP309 4.9 10.1 1.0

Fluorine binding site 3 out of 3 in 4glx

Go back to Fluorine Binding Sites List in 4glx
Fluorine binding site 3 out of 3 in the Dna Ligase A in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dna Ligase A in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:30.2
occ:1.00
F11 A:0XS603 0.0 30.2 1.0
C6 A:0XS603 1.3 28.8 1.0
F10 A:0XS603 2.2 36.0 1.0
F9 A:0XS603 2.2 29.6 1.0
C3 A:0XS603 2.3 25.8 1.0
N5 A:0XS603 2.5 21.4 1.0
O A:HOH849 2.9 23.3 1.0
CZ3 A:TRP309 3.3 10.5 1.0
CH2 A:TRP309 3.5 9.9 1.0
NZ A:LYS290 3.5 12.4 1.0
C2 A:0XS603 3.6 27.5 1.0
CD A:LYS290 3.6 11.1 1.0
CE A:LYS290 3.6 11.3 1.0
C8 A:0XS603 3.9 18.3 1.0
CB A:ALA310 4.4 9.2 1.0
BR1 A:0XS603 4.4 45.1 1.0
CE3 A:TRP309 4.5 10.5 1.0
N13 A:0XS603 4.6 14.8 1.0
C4 A:0XS603 4.6 22.1 1.0
CD2 A:LEU82 4.7 13.2 1.0
CZ2 A:TRP309 4.7 10.1 1.0
C7 A:0XS603 4.7 17.4 1.0
O A:HOH847 4.9 30.0 1.0
CG A:LYS290 4.9 10.8 1.0
CB A:LYS290 4.9 10.0 1.0
O A:HOH774 4.9 33.5 1.0

Reference:

J.P.Surivet, R.Lange, C.Hubschwerlen, W.Keck, J.L.Specklin, D.Ritz, D.Bur, H.Locher, P.Seiler, D.S.Strasser, L.Prade, C.Kohl, C.Schmitt, G.Chapoux, E.Ilhan, N.Ekambaram, A.Athanasiou, A.Knezevic, D.Sabato, A.Chambovey, M.Gaertner, M.Enderlin, M.Boehme, V.Sippel, P.Wyss. Structure-Guided Design, Synthesis and Biological Evaluation of Novel Dna Ligase Inhibitors with in Vitro and in Vivo Anti-Staphylococcal Activity. Bioorg.Med.Chem.Lett. V. 22 6705 2012.
ISSN: ISSN 0960-894X
PubMed: 23006603
DOI: 10.1016/J.BMCL.2012.08.094
Page generated: Sun Dec 13 12:03:20 2020

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