Atomistry » Fluorine » PDB 8fm3-8fy1 » 8fvd
Atomistry »
  Fluorine »
    PDB 8fm3-8fy1 »
      8fvd »

Fluorine in PDB 8fvd: E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)

Enzymatic activity of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)

All present enzymatic activity of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2):
6.3.4.2;

Protein crystallography data

The structure of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2), PDB code: 8fvd was solved by T.Holyoak, M.J.Mcleod, N.Tran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.93 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 161.069, 110.013, 129.511, 90, 90, 90
R / Rfree (%) 20.9 / 23.2

Other elements in 8fvd:

The structure of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) (pdb code 8fvd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2), PDB code: 8fvd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8fvd

Go back to Fluorine Binding Sites List in 8fvd
Fluorine binding site 1 out of 4 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:67.2
occ:1.00
 F1 A:GTF602 0.0 67.2 1.0
C2' A:GTF602 1.4 60.9 1.0
C3' A:GTF602 2.2 59.4 1.0
F2 A:GTF602 2.2 60.9 1.0
C1' A:GTF602 2.4 59.5 1.0
N1 A:GTF602 2.7 56.5 1.0
C6 A:GTF602 2.9 56.3 1.0
O4' A:GTF602 3.1 59.3 1.0
C4' A:GTF602 3.2 56.6 1.0
O3' A:GTF602 3.3 67.6 1.0
C2 A:GTF602 3.7 56.3 1.0
C5 A:GTF602 4.1 51.6 1.0
C5' A:GTF602 4.1 57.4 1.0
O2 A:GTF602 4.2 57.8 1.0
CZ A:PHE227 4.6 63.8 1.0
N3 A:GTF602 4.7 56.0 1.0
C4 A:GTF602 4.8 47.6 1.0
OE1 B:GLU149 5.0 67.6 1.0

Fluorine binding site 2 out of 4 in 8fvd

Go back to Fluorine Binding Sites List in 8fvd
Fluorine binding site 2 out of 4 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:60.9
occ:1.00
 F2 A:GTF602 0.0 60.9 1.0
C2' A:GTF602 1.4 60.9 1.0
C3' A:GTF602 2.2 59.4 1.0
F1 A:GTF602 2.2 67.2 1.0
O3' A:GTF602 2.3 67.6 1.0
C1' A:GTF602 2.4 59.5 1.0
OE1 B:GLU149 3.1 67.6 1.0
N1 A:GTF602 3.2 56.5 1.0
C4' A:GTF602 3.4 56.6 1.0
O2 A:GTF602 3.5 57.8 1.0
O4' A:GTF602 3.6 59.3 1.0
C2 A:GTF602 3.7 56.3 1.0
CD B:GLU149 3.7 66.5 1.0
C6 A:GTF602 4.2 56.3 1.0
CG B:GLU149 4.2 53.5 1.0
CB B:GLU149 4.3 51.0 1.0
OE2 B:GLU149 4.4 66.0 1.0
C5' A:GTF602 4.7 57.4 1.0
N3 A:GTF602 5.0 56.0 1.0

Fluorine binding site 3 out of 4 in 8fvd

Go back to Fluorine Binding Sites List in 8fvd
Fluorine binding site 3 out of 4 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:61.0
occ:1.00
 F1 B:GTF701 0.0 61.0 1.0
C2' B:GTF701 1.4 56.9 1.0
C3' B:GTF701 2.2 57.6 1.0
F2 B:GTF701 2.2 59.4 1.0
O3' B:GTF701 2.3 65.2 1.0
C1' B:GTF701 2.4 58.0 1.0
OE1 A:GLU149 3.0 70.1 1.0
N1 B:GTF701 3.2 56.2 1.0
C4' B:GTF701 3.4 57.3 1.0
O2 B:GTF701 3.4 54.8 1.0
O4' B:GTF701 3.6 63.9 1.0
C2 B:GTF701 3.6 53.7 1.0
CD A:GLU149 3.7 59.2 1.0
CB A:GLU149 4.2 52.5 1.0
C6 B:GTF701 4.2 53.9 1.0
CG A:GLU149 4.2 54.5 1.0
OE2 A:GLU149 4.4 62.7 1.0
C5' B:GTF701 4.7 57.1 1.0
N3 B:GTF701 4.9 50.9 1.0

Fluorine binding site 4 out of 4 in 8fvd

Go back to Fluorine Binding Sites List in 8fvd
Fluorine binding site 4 out of 4 in the E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of E Coli. Ctp Synthase in Complex with Df-Dctp (Potassium Malonate + 100 Mm MGCL2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:59.4
occ:1.00
 F2 B:GTF701 0.0 59.4 1.0
C2' B:GTF701 1.4 56.9 1.0
C3' B:GTF701 2.1 57.6 1.0
F1 B:GTF701 2.2 61.0 1.0
C1' B:GTF701 2.4 58.0 1.0
N1 B:GTF701 2.7 56.2 1.0
C6 B:GTF701 2.9 53.9 1.0
O4' B:GTF701 3.1 63.9 1.0
C4' B:GTF701 3.2 57.3 1.0
O3' B:GTF701 3.3 65.2 1.0
C2 B:GTF701 3.7 53.7 1.0
C5' B:GTF701 4.0 57.1 1.0
C5 B:GTF701 4.0 49.9 1.0
O2 B:GTF701 4.2 54.8 1.0
CZ B:PHE227 4.6 57.2 1.0
N3 B:GTF701 4.7 50.9 1.0
C4 B:GTF701 4.8 47.5 1.0
OE1 A:GLU149 4.9 70.1 1.0

Reference:

M.J.Mcleod, N.Tran, G.D.Mccluskey, T.D.Gillis, S.L.Bearne, T.Holyoak. A Metal Dependent Conformational Change Provides A Structural Basis For the Inhibition of Ctp Synthase By Gemcitabine-5'-Triphosphate. Protein Sci. E4648 2023.
ISSN: ESSN 1469-896X
PubMed: 37106216
DOI: 10.1002/PRO.4648
Page generated: Wed Jul 16 04:46:30 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy