Iodine in PDB 442d: 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex

The structure of 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex, PDB code: 442d was solved by G.R.Clark, C.J.Squire, R.F.Martin, J.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.560, 33.850, 61.150, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / n/a

The structure of 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iodine atom in the 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex (pdb code 442d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex, PDB code: 442d:

Iodine binding site 1 out of 1 in the 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I25 b:18.6 occ:1.00 I A:IB25 0.0 18.6 1.0 C4 A:IB25 2.1 6.3 1.0 CYT A:IB25 3.0 10.3 1.0 C5 A:IB25 3.0 10.6 1.0 O A:IB25 3.5 18.1 1.0 C5' B:DG22 3.9 14.1 1.0 O B:HOH61 4.1 18.5 1.0 C2 A:IB25 4.3 9.8 1.0 C1 A:IB25 4.3 7.7 1.0 O3' A:DA6 4.5 11.7 1.0 C4' A:DA6 4.6 8.8 1.0 C4' B:DG22 4.6 12.8 1.0 OP1 B:DG22 4.7 17.6 1.0 OP1 A:DT7 4.7 11.5 1.0 O A:HOH45 4.8 57.4 0.5 C3 A:IB25 4.8 10.6 1.0 CN2 A:IB25 4.9 24.4 1.0

C.J.Squire, L.J.Baker, G.R.Clark, R.F.Martin, J.White. Structures of M-Iodo Hoechst-Dna Complexes in Crystals with Reduced Solvent Content: Implications For Minor Groove Binder Drug Design. Nucleic Acids Res. V. 28 1252 2000.
ISSN: ISSN 0305-1048
PubMed: 10666470
DOI: 10.1093/NAR/28.5.1252