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Iodine in PDB 1ki6: Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside

Enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside

All present enzymatic activity of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside:
2.7.1.21;

Protein crystallography data

The structure of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside, PDB code: 1ki6 was solved by J.N.Champness, M.S.Bennett, F.Wien, P.Herdewijn, T.Ostrowski, W.C.Summers, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.37
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 113.600, 116.400, 108.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 31.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside (pdb code 1ki6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside, PDB code: 1ki6:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 1ki6

Go back to Iodine Binding Sites List in 1ki6
Iodine binding site 1 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1

b:24.2
occ:1.00
I A:AHU1 0.0 24.2 1.0
C5 A:AHU1 2.1 15.0 1.0
C6 A:AHU1 2.9 14.0 1.0
C4 A:AHU1 3.1 17.1 1.0
CE2 A:TYR132 3.5 19.2 1.0
O4 A:AHU1 3.5 18.6 1.0
OH A:TYR132 3.7 17.5 1.0
CZ A:TYR132 4.0 14.2 1.0
CZ2 A:TRP88 4.0 8.3 1.0
CB A:ALA167 4.2 2.4 1.0
O A:HOH771 4.2 27.5 1.0
NE A:ARG163 4.2 9.2 1.0
CD A:ARG163 4.2 7.0 1.0
N1 A:AHU1 4.3 13.4 1.0
CH2 A:TRP88 4.3 7.7 1.0
N3 A:AHU1 4.4 18.3 1.0
N A:ALA168 4.5 2.0 1.0
CB A:ALA168 4.5 3.0 1.0
CD2 A:TYR132 4.5 19.3 1.0
CE A:MET128 4.6 9.1 1.0
O A:MET128 4.6 11.3 1.0
CZ A:ARG163 4.6 9.8 1.0
C A:ALA167 4.6 2.0 1.0
CD1 A:TYR172 4.7 8.2 1.0
CA A:ALA168 4.7 3.4 1.0
CE1 A:TYR172 4.7 8.9 1.0
CB A:MET128 4.9 10.9 1.0
O A:ALA167 4.9 4.1 1.0
C2 A:AHU1 5.0 14.6 1.0

Iodine binding site 2 out of 2 in 1ki6

Go back to Iodine Binding Sites List in 1ki6
Iodine binding site 2 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with A 5-Iodouracil Anhydrohexitol Nucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I2

b:26.2
occ:1.00
I B:AHU2 0.0 26.2 1.0
C5 B:AHU2 2.1 16.5 1.0
C6 B:AHU2 3.0 16.4 1.0
C4 B:AHU2 3.1 17.2 1.0
O4 B:AHU2 3.5 18.4 1.0
CD B:ARG163 3.9 13.0 1.0
O B:HOH651 3.9 11.2 1.0
CE2 B:TYR132 3.9 16.8 1.0
CZ2 B:TRP88 3.9 6.8 1.0
OH B:TYR132 4.0 17.9 1.0
CH2 B:TRP88 4.2 7.7 1.0
CB B:ALA167 4.2 6.0 1.0
CZ B:TYR132 4.3 16.4 1.0
N1 B:AHU2 4.3 14.1 1.0
N3 B:AHU2 4.4 14.3 1.0
N B:ALA168 4.5 5.8 1.0
NE B:ARG163 4.5 11.9 1.0
CB B:ALA168 4.5 5.0 1.0
CE B:MET128 4.6 5.4 1.0
C B:ALA167 4.6 5.7 1.0
O B:MET128 4.7 9.1 1.0
O7' B:AHU2 4.7 23.9 1.0
CA B:ALA168 4.7 4.5 1.0
CD1 B:TYR172 4.7 10.1 1.0
CD2 B:TYR132 4.8 13.6 1.0
CE1 B:TYR172 4.8 11.7 1.0
C2 B:AHU2 4.8 12.8 1.0
NH1 B:ARG163 5.0 16.8 1.0
O B:ALA167 5.0 6.9 1.0

Reference:

J.N.Champness, M.S.Bennett, F.Wien, R.Visse, W.C.Summers, P.Herdewijn, E.De Clerq, T.Ostrowski, R.L.Jarvest, M.R.Sanderson. Exploring the Active Site of Herpes Simplex Virus Type-1 Thymidine Kinase By X-Ray Crystallography of Complexes with Aciclovir and Other Ligands. Proteins V. 32 350 1998.
ISSN: ISSN 0887-3585
PubMed: 9715911
DOI: 10.1002/(SICI)1097-0134(19980815)32:3<350::AID-PROT10>3.0.CO;2-8
Page generated: Sun Dec 13 19:20:11 2020

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