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Fluorine in PDB 5uvf: Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870

Enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870

All present enzymatic activity of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870, PDB code: 5uvf was solved by R.M.Counago, C.Bountra, P.Arruda, A.M.Edwards, O.Gileadi, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.141, 95.242, 192.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.4

Other elements in 5uvf:

The structure of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 (pdb code 5uvf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870, PDB code: 5uvf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 1 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.8
occ:1.00
 F1 A:7DZ401 0.0 69.8 1.0
C14 A:7DZ401 1.3 66.1 1.0
C13 A:7DZ401 2.3 61.9 1.0
C15 A:7DZ401 2.3 63.2 1.0
O1 A:7DZ401 2.7 62.4 1.0
C10 A:7DZ401 3.0 73.2 1.0
C16 A:7DZ401 3.6 62.0 1.0
C12 A:7DZ401 3.6 58.4 1.0
CD1 A:ILE51 3.7 69.6 1.0
O A:HOH658 3.8 82.7 1.0
C17 A:7DZ401 4.1 59.4 1.0
C9 A:7DZ401 4.2 72.6 1.0
C11 A:7DZ401 4.4 73.8 1.0
N2 A:7DZ401 4.6 61.1 1.0
C8 A:7DZ401 4.6 70.2 1.0
F A:7DZ401 4.7 66.2 1.0
O A:HOH501 4.7 44.9 1.0
C7 A:7DZ401 4.7 70.1 1.0
N4 A:7DZ401 4.8 56.0 1.0
CG1 A:ILE51 4.8 54.4 1.0

Fluorine binding site 2 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 2 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:66.2
occ:1.00
 F A:7DZ401 0.0 66.2 1.0
C16 A:7DZ401 1.3 62.0 1.0
C17 A:7DZ401 2.3 59.4 1.0
C15 A:7DZ401 2.4 63.2 1.0
O1 A:7DZ401 2.7 62.4 1.0
OH A:TYR87 3.2 47.3 1.0
O A:HOH501 3.2 44.9 1.0
CE A:MET131 3.2 52.2 1.0
CB A:PRO111 3.5 37.9 1.0
C14 A:7DZ401 3.6 66.1 1.0
C12 A:7DZ401 3.6 58.4 1.0
CG A:PRO111 3.7 40.2 1.0
CB A:MET131 3.9 42.0 1.0
CG A:MET131 4.0 47.6 1.0
CZ A:TYR87 4.0 49.2 1.0
C13 A:7DZ401 4.1 61.9 1.0
CG1 A:VAL196 4.2 38.4 1.0
CE2 A:PHE134 4.2 49.3 1.0
SD A:MET131 4.3 54.8 1.0
CB A:VAL196 4.5 39.0 1.0
CE2 A:TYR87 4.6 44.0 1.0
F1 A:7DZ401 4.7 69.8 1.0
N4 A:7DZ401 4.8 56.0 1.0
CE1 A:TYR87 4.8 47.8 1.0
O A:ASP132 4.8 44.4 1.0
CD2 A:PHE134 5.0 46.8 1.0
CA A:PRO111 5.0 36.8 1.0

Fluorine binding site 3 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 3 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:86.5
occ:1.00
 F1 B:7DZ402 0.0 86.5 1.0
C14 B:7DZ402 1.3 85.8 1.0
C13 B:7DZ402 2.3 84.3 1.0
C15 B:7DZ402 2.3 87.4 1.0
O1 B:7DZ402 2.7 89.1 1.0
C16 B:7DZ402 3.6 87.4 1.0
C12 B:7DZ402 3.6 82.2 1.0
C B:ILE43 3.9 97.9 1.0
C17 B:7DZ402 4.1 84.5 1.0
CB B:ILE43 4.4 73.7 1.0
O B:ILE43 4.5 66.1 1.0
CD1 B:ILE43 4.5 78.3 1.0
N2 B:7DZ402 4.6 70.4 1.0
CG1 B:ILE43 4.6 71.7 1.0
C7 B:7DZ402 4.7 79.6 1.0
F B:7DZ402 4.7 88.6 1.0
N4 B:7DZ402 4.8 77.7 1.0
CA B:ILE43 4.8 71.9 1.0
C8 B:7DZ402 5.0 82.0 1.0

Fluorine binding site 4 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 4 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:88.6
occ:1.00
 F B:7DZ402 0.0 88.6 1.0
C16 B:7DZ402 1.4 87.4 1.0
C15 B:7DZ402 2.4 87.4 1.0
C17 B:7DZ402 2.4 84.5 1.0
O1 B:7DZ402 2.7 89.1 1.0
C14 B:7DZ402 3.6 85.8 1.0
C12 B:7DZ402 3.6 82.2 1.0
C13 B:7DZ402 4.1 84.3 1.0
O B:GLY135 4.6 56.8 1.0
F1 B:7DZ402 4.7 86.5 1.0
N4 B:7DZ402 4.8 77.7 1.0
C B:GLY135 4.9 56.1 1.0

Fluorine binding site 5 out of 8 in 5uvf

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Fluorine binding site 5 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:64.8
occ:1.00
 F1 C:7DZ402 0.0 64.8 1.0
C14 C:7DZ402 1.3 61.0 1.0
C15 C:7DZ402 2.3 56.5 1.0
C13 C:7DZ402 2.4 57.5 1.0
O1 C:7DZ402 2.7 56.8 1.0
NZ C:LYS71 3.1 55.3 1.0
CE C:LYS71 3.2 69.0 1.0
C9 C:7DZ402 3.4 72.3 1.0
C16 C:7DZ402 3.6 51.0 1.0
C12 C:7DZ402 3.6 53.5 1.0
CD1 C:ILE51 3.8 73.6 1.0
C11 C:7DZ402 4.0 72.4 1.0
C17 C:7DZ402 4.1 50.8 1.0
C10 C:7DZ402 4.1 72.1 1.0
C8 C:7DZ402 4.2 72.0 1.0
CG2 C:VAL196 4.2 46.1 1.0
CD C:LYS71 4.3 61.4 1.0
CB C:VAL196 4.4 45.1 1.0
C7 C:7DZ402 4.5 70.7 1.0
N C:ASP197 4.6 41.2 1.0
N2 C:7DZ402 4.6 63.1 1.0
F C:7DZ402 4.7 46.9 1.0
O C:HOH501 4.8 49.9 1.0
N4 C:7DZ402 4.8 54.5 1.0
CG1 C:ILE51 4.9 66.7 1.0
CB C:ASP197 4.9 44.2 1.0
CA C:ASP197 5.0 42.0 1.0
CG C:LYS71 5.0 56.3 1.0

Fluorine binding site 6 out of 8 in 5uvf

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Fluorine binding site 6 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:46.9
occ:1.00
 F C:7DZ402 0.0 46.9 1.0
C16 C:7DZ402 1.3 51.0 1.0
C17 C:7DZ402 2.3 50.8 1.0
C15 C:7DZ402 2.3 56.5 1.0
O1 C:7DZ402 2.7 56.8 1.0
O C:HOH501 3.1 49.9 1.0
CE C:MET131 3.4 44.9 1.0
CB C:PRO111 3.4 41.7 1.0
CG C:PRO111 3.5 44.4 1.0
CB C:MET131 3.6 46.6 1.0
C14 C:7DZ402 3.6 61.0 1.0
C12 C:7DZ402 3.6 53.5 1.0
OH C:TYR87 3.7 45.5 1.0
CG C:MET131 3.8 48.5 1.0
C13 C:7DZ402 4.1 57.5 1.0
CG1 C:VAL196 4.1 44.2 1.0
CE2 C:PHE134 4.3 50.9 1.0
CB C:VAL196 4.4 45.1 1.0
SD C:MET131 4.4 49.8 1.0
CZ C:TYR87 4.7 47.7 1.0
F1 C:7DZ402 4.7 64.8 1.0
N4 C:7DZ402 4.7 54.5 1.0
CD C:PRO111 4.8 38.6 1.0
O C:ASP132 4.9 50.3 1.0
CA C:PRO111 4.9 40.0 1.0
N C:ASP132 5.0 47.5 1.0
CA C:MET131 5.0 46.2 1.0

Fluorine binding site 7 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 7 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:63.2
occ:1.00
 F1 D:7DZ403 0.0 63.2 1.0
C14 D:7DZ403 1.3 59.6 1.0
C15 D:7DZ403 2.3 55.4 1.0
C13 D:7DZ403 2.3 56.5 1.0
O1 D:7DZ403 2.7 54.9 1.0
C9 D:7DZ403 3.3 66.5 1.0
NZ D:LYS71 3.4 63.9 1.0
C16 D:7DZ403 3.6 52.7 1.0
C12 D:7DZ403 3.6 54.6 1.0
C8 D:7DZ403 3.6 68.7 1.0
C11 D:7DZ403 3.9 63.5 1.0
CE D:LYS71 3.9 71.1 1.0
C17 D:7DZ403 4.1 54.6 1.0
CD D:LYS71 4.2 69.2 1.0
CG2 D:VAL196 4.2 44.2 1.0
C10 D:7DZ403 4.4 67.3 1.0
CB D:VAL196 4.4 44.5 1.0
N2 D:7DZ403 4.6 60.4 1.0
C7 D:7DZ403 4.7 68.6 1.0
F D:7DZ403 4.7 50.6 1.0
N4 D:7DZ403 4.8 56.7 1.0
CG D:LYS71 4.8 67.2 1.0
N D:ASP197 4.8 39.5 1.0
CD1 D:ILE51 5.0 0.2 1.0

Fluorine binding site 8 out of 8 in 5uvf

Go back to Fluorine Binding Sites List in 5uvf
Fluorine binding site 8 out of 8 in the Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Human Vaccinia-Related Kinase Bound to Bi- D1870 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:50.6
occ:1.00
 F D:7DZ403 0.0 50.6 1.0
C16 D:7DZ403 1.3 52.7 1.0
C17 D:7DZ403 2.3 54.6 1.0
C15 D:7DZ403 2.3 55.4 1.0
O1 D:7DZ403 2.7 54.9 1.0
CE D:MET131 3.3 51.4 1.0
O D:HOH501 3.4 44.0 1.0
CB D:MET131 3.4 54.0 1.0
CG D:MET131 3.6 56.4 1.0
CB D:PRO111 3.6 42.0 1.0
C14 D:7DZ403 3.6 59.6 1.0
C12 D:7DZ403 3.6 54.6 1.0
CG D:PRO111 3.7 44.5 1.0
OH D:TYR87 3.8 41.6 1.0
CG1 D:VAL196 4.1 44.6 1.0
C13 D:7DZ403 4.1 56.5 1.0
SD D:MET131 4.2 57.6 1.0
CE2 D:PHE134 4.2 55.9 1.0
CB D:VAL196 4.3 44.5 1.0
F1 D:7DZ403 4.7 63.2 1.0
CZ D:TYR87 4.7 47.9 1.0
N4 D:7DZ403 4.8 56.7 1.0
CA D:MET131 4.9 53.8 1.0
NZ D:LYS71 4.9 63.9 1.0
O D:ASP132 4.9 59.8 1.0

Reference:

R.M.Counago, C.K.Allerston, P.Savitsky, H.Azevedo, P.H.Godoi, C.I.Wells, A.Mascarello, F.H.De Souza Gama, K.B.Massirer, W.J.Zuercher, C.R.W.Guimaraes, O.Gileadi. Structural Characterization of Human Vaccinia-Related Kinases (Vrk) Bound to Small-Molecule Inhibitors Identifies Different P-Loop Conformations. Sci Rep V. 7 7501 2017.
ISSN: ESSN 2045-2322
PubMed: 28790404
DOI: 10.1038/S41598-017-07755-Y
Page generated: Tue Jul 15 08:23:05 2025

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