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Fluorine in PDB 4jby: Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78

Enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78

All present enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78:
2.7.1.21;

Protein crystallography data

The structure of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78, PDB code: 4jby was solved by L.Pernot, I.Novakovic, Y.Westermaier, R.Perozzo, S.Raic-Malic, L.Scapozza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.08 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 113.166, 116.569, 108.309, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.8

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 F-SK78 (pdb code 4jby). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78, PDB code: 4jby:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4jby

Go back to Fluorine Binding Sites List in 4jby
Fluorine binding site 1 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78


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 F-SK78 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:38.5
occ:1.00
F A:FSK601 0.0 38.5 1.0
C14 A:FSK601 1.4 26.7 1.0
C12 A:FSK601 2.3 23.7 1.0
C13 A:FSK601 2.9 21.8 1.0
CD1 A:ILE97 3.2 19.9 0.5
CD1 A:ILE97 3.2 19.9 0.5
CD A:ARG222 3.2 25.4 1.0
C6 A:FSK601 3.2 20.4 1.0
C11 A:FSK601 3.3 22.0 1.0
N1 A:FSK601 3.8 24.9 1.0
NE A:ARG222 3.8 21.4 1.0
C5 A:FSK601 3.9 22.0 1.0
CG1 A:ILE97 4.0 20.4 0.5
CG1 A:ILE97 4.0 20.4 0.5
O3 A:FSK601 4.2 31.3 1.0
CZ3 A:TRP88 4.3 21.1 1.0
CG A:ARG222 4.5 30.1 1.0
CB A:ARG222 4.6 25.6 1.0
CE A:MET128 4.7 17.6 1.0
CZ A:ARG222 4.7 24.1 1.0
CE3 A:TRP88 4.8 17.3 1.0
CG2 A:ILE97 4.8 22.5 0.5
CG2 A:ILE97 4.8 22.5 0.5
CH2 A:TRP88 5.0 20.9 1.0
C1 A:FSK601 5.0 22.9 1.0

Fluorine binding site 2 out of 2 in 4jby

Go back to Fluorine Binding Sites List in 4jby
Fluorine binding site 2 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type 1 in Complex with F-SK78


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 F-SK78 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.3
occ:1.00
F B:FSK401 0.0 40.3 1.0
C14 B:FSK401 1.4 33.9 1.0
C12 B:FSK401 2.3 28.4 1.0
C13 B:FSK401 3.0 27.5 1.0
C6 B:FSK401 3.1 32.3 1.0
C11 B:FSK401 3.2 25.8 1.0
CD1 B:ILE97 3.2 31.4 1.0
CD B:ARG222 3.4 35.7 1.0
N1 B:FSK401 3.7 25.7 1.0
C5 B:FSK401 3.8 26.7 1.0
CG1 B:ILE97 3.9 28.4 1.0
NE B:ARG222 4.2 32.8 1.0
O3 B:FSK401 4.2 34.1 1.0
CZ3 B:TRP88 4.3 25.9 1.0
CE B:MET128 4.6 21.1 1.0
CG B:ARG222 4.6 36.3 1.0
CG2 B:ILE97 4.6 31.6 1.0
CB B:ARG222 4.7 31.0 1.0
C1 B:FSK401 4.8 20.0 1.0
CE3 B:TRP88 4.9 25.6 1.0
C3 B:FSK401 4.9 21.4 1.0
CH2 B:TRP88 4.9 21.7 1.0
CB B:ILE97 5.0 30.5 1.0
CZ B:ARG222 5.0 30.5 1.0

Reference:

L.Pernot, I.Novakovic, R.Perozzo, S.Raic-Malic, L.Scapozza. New Thymine Derivatives As HSV1-Tk Ligand For the Development of Pet Imaging Tracer To Be Published.
Page generated: Thu Aug 1 02:49:47 2024

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