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Fluorine in PDB 4oql: Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu

Enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu

All present enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu:
2.7.1.21;

Protein crystallography data

The structure of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu, PDB code: 4oql was solved by L.Pernot, A.B.Neef, Y.Westermaier, R.Perozzo, N.Luedtke, L.Scapozza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.40 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 113.385, 116.419, 108.118, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu (pdb code 4oql). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu, PDB code: 4oql:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4oql

Go back to Fluorine Binding Sites List in 4oql
Fluorine binding site 1 out of 4 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:18.1
occ:1.00
 F14 A:F2U404 0.0 18.1 1.0
C13 A:F2U404 1.4 17.2 1.0
F15 A:F2U404 2.2 18.0 1.0
C09 A:F2U404 2.4 21.9 1.0
C16 A:F2U404 2.4 17.4 1.0
OH A:TYR172 2.9 15.7 1.0
N18 A:F2U404 2.9 11.7 1.0
C06 A:F2U404 3.0 20.7 1.0
C03 A:F2U404 3.0 16.5 1.0
O08 A:F2U404 3.2 16.7 1.0
CZ A:TYR172 3.2 12.8 1.0
C26 A:F2U404 3.2 14.1 1.0
CG A:HIS58 3.3 18.3 1.0
CB A:HIS58 3.3 17.8 1.0
ND1 A:HIS58 3.4 19.1 1.0
CE2 A:TYR172 3.4 11.2 1.0
O11 A:F2U404 3.6 19.8 1.0
O01 A:F2U404 3.8 28.2 1.0
NH2 A:ARG163 3.8 20.2 1.0
C19 A:F2U404 3.8 14.8 1.0
CD2 A:HIS58 4.0 24.9 1.0
CE1 A:TYR172 4.0 11.9 1.0
CE1 A:HIS58 4.1 20.7 1.0
O20 A:F2U404 4.3 12.8 1.0
C25 A:F2U404 4.3 13.7 1.0
O A:HOH617 4.3 30.1 1.0
CZ A:ARG163 4.4 20.9 1.0
CD2 A:TYR172 4.4 11.4 1.0
NE2 A:HIS58 4.4 24.1 1.0
CA A:HIS58 4.6 18.8 1.0
NE A:ARG163 4.6 16.9 1.0
O A:HOH510 4.7 15.6 1.0
N A:HIS58 4.7 17.1 1.0
N21 A:F2U404 4.8 13.2 1.0
CD1 A:TYR172 4.9 10.4 1.0

Fluorine binding site 2 out of 4 in 4oql

Go back to Fluorine Binding Sites List in 4oql
Fluorine binding site 2 out of 4 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:18.0
occ:1.00
 F15 A:F2U404 0.0 18.0 1.0
C13 A:F2U404 1.3 17.2 1.0
F14 A:F2U404 2.2 18.1 1.0
C16 A:F2U404 2.3 17.4 1.0
C09 A:F2U404 2.4 21.9 1.0
O11 A:F2U404 2.7 19.8 1.0
O A:HOH510 2.9 15.6 1.0
OH A:TYR101 3.0 15.5 1.0
N18 A:F2U404 3.2 11.7 1.0
O20 A:F2U404 3.3 12.8 1.0
CE1 A:HIS58 3.5 20.7 1.0
NE2 A:HIS58 3.5 24.1 1.0
ND1 A:HIS58 3.5 19.1 1.0
O08 A:F2U404 3.5 16.7 1.0
CD2 A:HIS58 3.5 24.9 1.0
CG A:HIS58 3.5 18.3 1.0
CE2 A:TYR172 3.5 11.2 1.0
C06 A:F2U404 3.6 20.7 1.0
C19 A:F2U404 3.6 14.8 1.0
CZ A:TYR101 4.0 16.8 1.0
OH A:TYR172 4.0 15.7 1.0
CZ A:TYR172 4.1 12.8 1.0
CE1 A:TYR101 4.1 19.7 1.0
C26 A:F2U404 4.3 14.1 1.0
CB A:HIS58 4.3 17.8 1.0
CD2 A:TYR172 4.3 11.4 1.0
C03 A:F2U404 4.4 16.5 1.0
OE2 A:GLU225 4.8 32.6 1.0
N21 A:F2U404 4.8 13.2 1.0
CD A:GLU225 4.9 25.4 1.0
OE1 A:GLU225 5.0 28.4 1.0

Fluorine binding site 3 out of 4 in 4oql

Go back to Fluorine Binding Sites List in 4oql
Fluorine binding site 3 out of 4 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:16.0
occ:1.00
 F14 B:F2U403 0.0 16.0 1.0
C13 B:F2U403 1.4 16.4 1.0
F15 B:F2U403 2.2 15.3 1.0
C16 B:F2U403 2.4 14.2 1.0
C09 B:F2U403 2.4 19.7 1.0
O01 B:F2U403 2.8 25.6 1.0
N18 B:F2U403 2.8 13.9 1.0
OH B:TYR172 2.9 13.0 1.0
O08 B:F2U403 2.9 19.8 1.0
C26 B:F2U403 3.0 15.6 1.0
C06 B:F2U403 3.0 22.4 1.0
CZ B:TYR172 3.3 10.2 1.0
NH2 B:ARG163 3.3 15.5 1.0
CB B:HIS58 3.5 16.1 1.0
C03 B:F2U403 3.5 22.3 1.0
CE1 B:TYR172 3.6 10.3 1.0
O11 B:F2U403 3.6 22.2 1.0
ND1 B:HIS58 3.7 16.0 1.0
CG B:HIS58 3.7 18.3 1.0
C19 B:F2U403 3.9 13.9 1.0
O B:HOH598 3.9 20.9 1.0
CE2 B:TYR172 4.0 9.8 1.0
CZ B:ARG163 4.0 12.7 1.0
C25 B:F2U403 4.1 13.0 1.0
NE B:ARG163 4.4 10.0 1.0
O20 B:F2U403 4.4 16.2 1.0
CA B:HIS58 4.5 18.1 1.0
CD1 B:TYR172 4.6 7.9 1.0
CE1 B:HIS58 4.6 17.2 1.0
N B:HIS58 4.6 16.1 1.0
CD2 B:HIS58 4.7 19.4 1.0
N21 B:F2U403 4.8 12.6 1.0
OE2 B:GLU83 4.9 18.0 1.0
NH1 B:ARG163 4.9 7.8 1.0
CD2 B:TYR172 4.9 9.1 1.0
C28 B:F2U403 4.9 11.1 1.0
C23 B:F2U403 5.0 10.7 1.0
O B:HOH599 5.0 17.4 1.0

Fluorine binding site 4 out of 4 in 4oql

Go back to Fluorine Binding Sites List in 4oql
Fluorine binding site 4 out of 4 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu


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 Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:15.3
occ:1.00
 F15 B:F2U403 0.0 15.3 1.0
C13 B:F2U403 1.3 16.4 1.0
F14 B:F2U403 2.2 16.0 1.0
C09 B:F2U403 2.3 19.7 1.0
C16 B:F2U403 2.4 14.2 1.0
O11 B:F2U403 2.7 22.2 1.0
ND1 B:HIS58 2.9 16.0 1.0
OH B:TYR101 3.1 29.5 1.0
O B:HOH599 3.1 17.4 1.0
CE1 B:TYR172 3.2 10.3 1.0
N18 B:F2U403 3.2 13.9 1.0
CG B:HIS58 3.2 18.3 1.0
CE1 B:HIS58 3.3 17.2 1.0
O08 B:F2U403 3.5 19.8 1.0
O20 B:F2U403 3.6 16.2 1.0
OH B:TYR172 3.6 13.0 1.0
C06 B:F2U403 3.6 22.4 1.0
CZ B:TYR172 3.7 10.2 1.0
C19 B:F2U403 3.7 13.9 1.0
CD2 B:HIS58 3.7 19.4 1.0
NE2 B:HIS58 3.7 22.4 1.0
CB B:HIS58 3.8 16.1 1.0
CD1 B:TYR172 4.1 7.9 1.0
CZ B:TYR101 4.2 24.1 1.0
C26 B:F2U403 4.2 15.6 1.0
CE2 B:TYR101 4.5 27.5 1.0
O01 B:F2U403 4.5 25.6 1.0
C03 B:F2U403 4.6 22.3 1.0
CE2 B:TYR172 4.8 9.8 1.0
N21 B:F2U403 4.9 12.6 1.0
OE1 B:GLU225 5.0 33.8 1.0

Reference:

L.Pernot, A.B.Neef, Y.Westermaier, R.Perozzo, N.Luedtke, L.Scapozza. Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with Df-Edu To Be Published.
Page generated: Sun Dec 13 12:09:57 2020

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