Iodine in PDB 1ki7: Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with 5-Iododeoxyuridine

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

The structure of Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with 5-Iododeoxyuridine, PDB code: 1ki7 was solved by J.N.Champness, M.S.Bennett, F.Wien, R.Visse, 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 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.600, 116.600, 108.400, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 28.6

The binding sites of Iodine atom in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with 5-Iododeoxyuridine (pdb code 1ki7). 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 5-Iododeoxyuridine, PDB code: 1ki7:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with 5-Iododeoxyuridine


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 5-Iododeoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ A:I1 b:15.0 occ:1.00 I A:ID21 0.0 15.0 1.0 C5 A:ID21 2.1 11.3 1.0 C4 A:ID21 3.0 11.2 1.0 C6 A:ID21 3.1 12.0 1.0 O4 A:ID21 3.2 13.3 1.0 CE2 A:TYR132 3.7 15.3 1.0 CZ2 A:TRP88 4.0 8.9 1.0 CD A:ARG163 4.0 7.3 1.0 CH2 A:TRP88 4.1 6.3 1.0 CB A:ALA167 4.2 6.6 1.0 OH A:TYR132 4.3 16.9 1.0 N3 A:ID21 4.3 8.8 1.0 CB A:ALA168 4.4 2.6 1.0 N1 A:ID21 4.4 8.6 1.0 CZ A:TYR132 4.4 12.4 1.0 N A:ALA168 4.5 4.4 1.0 NE A:ARG163 4.5 11.6 1.0 CD1 A:TYR172 4.6 6.6 1.0 CD2 A:TYR132 4.6 19.5 1.0 NH1 A:ARG163 4.6 13.8 1.0 CE1 A:TYR172 4.6 6.5 1.0 CA A:ALA168 4.7 2.0 1.0 C A:ALA167 4.8 6.8 1.0 O5' A:ID21 4.8 5.2 1.0 O A:MET128 4.8 13.1 1.0 CE A:MET128 4.8 2.0 1.0 CZ A:ARG163 4.8 11.0 1.0 C2 A:ID21 4.9 10.0 1.0 CB A:MET128 4.9 9.0 1.0 O A:HOH628 5.0 33.7 1.0 CE2 A:TRP88 5.0 6.6 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Thymidine Kinase From Herpes Simplex Virus Type I Complexed with 5-Iododeoxyuridine


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 5-Iododeoxyuridine within 5.0Å range: probe atom residue distance (Å) B Occ B:I2 b:21.3 occ:1.00 I B:ID22 0.0 21.3 1.0 C5 B:ID22 2.1 12.6 1.0 C6 B:ID22 3.1 12.2 1.0 C4 B:ID22 3.1 12.3 1.0 O4 B:ID22 3.4 15.0 1.0 CD B:ARG163 3.9 9.6 1.0 O B:HOH623 4.0 8.0 1.0 CZ2 B:TRP88 4.0 7.6 1.0 NE B:ARG163 4.1 13.6 1.0 CB B:ALA167 4.2 6.1 1.0 CH2 B:TRP88 4.2 3.0 1.0 N3 B:ID22 4.3 8.9 1.0 CE1 B:TYR132 4.4 11.9 1.0 CE B:MET128 4.4 13.3 1.0 OH B:TYR132 4.4 13.3 1.0 N1 B:ID22 4.4 5.0 1.0 N B:ALA168 4.5 9.7 1.0 CD2 B:TYR172 4.5 6.9 1.0 CB B:ALA168 4.5 2.0 1.0 CZ B:TYR132 4.5 11.6 1.0 CA B:ALA168 4.6 6.5 1.0 CE2 B:TYR172 4.7 2.0 1.0 C B:ALA167 4.7 9.1 1.0 O5' B:ID22 4.8 6.9 1.0 CZ B:ARG163 4.9 9.8 1.0 C2 B:ID22 4.9 6.4 1.0 CE2 B:TRP88 5.0 8.2 1.0 CB B:ARG163 5.0 11.2 1.0 CG B:ARG163 5.0 10.8 1.0 O B:MET128 5.0 9.1 1.0

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