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

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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: Fri Aug 2 19:26:29 2024

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