Iodine in PDB 1omk: The Crystal Structure of D(Cacg(5IU)G)

The structure of The Crystal Structure of D(Cacg(5IU)G), PDB code: 1omk was solved by G.Schuerman, K.Van Hecke, L.Van Meervelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	18.155, 30.034, 41.988, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of The Crystal Structure of D(Cacg(5IU)G) also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Iodine atom in the The Crystal Structure of D(Cacg(5IU)G) (pdb code 1omk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the The Crystal Structure of D(Cacg(5IU)G), PDB code: 1omk:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the The Crystal Structure of D(Cacg(5IU)G)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of D(Cacg(5IU)G) within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:12.2 occ:1.00 I5 A:5IU5 0.0 12.2 1.0 C5 A:5IU5 2.1 11.2 1.0 C6 A:5IU5 3.0 9.2 1.0 C4 A:5IU5 3.0 10.0 1.0 O4 A:5IU5 3.3 12.5 1.0 N4 B:DC7 3.7 12.5 1.0 C4 A:DG4 3.8 8.0 1.0 N9 A:DG4 3.8 8.5 1.0 C5 A:DG4 3.8 10.9 1.0 C8 A:DG4 3.8 11.5 1.0 N4 A:NCO31 3.9 12.3 1.0 O A:HOH123 3.9 21.4 1.0 N7 A:DG4 3.9 10.6 1.0 C2' A:DG4 4.1 11.1 1.0 O6 A:DG6 4.1 12.3 1.0 O B:HOH118 4.2 21.4 1.0 N2 A:NCO31 4.2 15.4 1.0 N1 A:5IU5 4.3 10.3 1.0 N3 A:5IU5 4.3 10.3 1.0 N3 A:DG4 4.3 8.2 1.0 C1' A:DG4 4.4 8.9 1.0 C6 A:DG4 4.5 8.5 1.0 C4 B:DC7 4.5 12.4 1.0 C2 A:DG4 4.8 9.8 1.0 C2 A:5IU5 4.8 10.1 1.0 N1 A:DG4 4.9 9.0 1.0

Iodine binding site 2 out of 2 in the The Crystal Structure of D(Cacg(5IU)G)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of D(Cacg(5IU)G) within 5.0Å range: probe atom residue distance (Å) B Occ B:I11 b:25.5 occ:1.00 I5 B:5IU11 0.0 25.5 1.0 C5 B:5IU11 2.1 12.8 1.0 C6 B:5IU11 3.0 13.1 1.0 C4 B:5IU11 3.0 13.0 1.0 O4 B:5IU11 3.2 20.2 1.0 O A:HOH103 3.6 19.1 1.0 C2' B:DG10 3.6 16.1 1.0 N4 A:DC1 3.7 14.6 1.0 N9 B:DG10 4.0 13.1 1.0 C8 B:DG10 4.0 13.3 1.0 C1' B:DG10 4.2 15.9 1.0 N1 B:5IU11 4.3 13.4 1.0 N3 B:5IU11 4.3 14.9 1.0 C4 B:DG10 4.4 10.6 1.0 N7 B:DG10 4.5 15.2 1.0 C4 A:DC1 4.5 13.1 1.0 C5 B:DG10 4.6 11.7 1.0 C2 B:5IU11 4.8 11.1 1.0 C5 A:DC1 4.9 13.3 1.0 N3 B:DG10 5.0 10.1 1.0 C3' B:DG10 5.0 16.3 1.0

G.Schuerman, K.Van Hecke, L.Van Meervelt. Exploration of the Influence of 5-Iodo-2'-Deoxyuridine Incorporation on the Structure of D[Cacg(Idu)G]. Acta Crystallogr.,Sect.D V. 59 1525 2003.
ISSN: ISSN 0907-4449
PubMed: 12876373
DOI: 10.1107/S0907444903012381