Iodine in PDB 444d: 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: 444d 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.370, 40.480, 66.080, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

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 444d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex, PDB code: 444d:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 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 B:I25 b:33.3 occ:0.60 I B:IB25 0.0 33.3 0.6 C4 B:IB25 2.1 41.8 0.6 C10 B:IB25 2.4 31.7 0.4 N4 B:IB25 2.5 37.8 0.4 C5 B:IB25 2.9 38.1 0.6 C13 B:IB25 3.1 36.1 0.4 C11 B:IB25 3.1 32.3 0.4 CYT B:IB25 3.1 43.5 0.6 C9 B:IB25 3.5 30.4 0.4 O B:IB25 3.6 43.9 0.6 C15 B:IB25 3.7 39.4 0.4 C5' A:DC9 3.9 22.6 1.0 C1 B:IB25 4.2 32.5 0.6 N3 B:IB25 4.3 37.8 0.4 C2 B:IB25 4.4 41.9 0.6 C4' A:DC9 4.5 25.9 1.0 C16 B:IB25 4.5 41.0 0.4 C12 B:IB25 4.5 31.0 0.4 C4' B:DT19 4.6 28.0 1.0 O3' B:DT19 4.7 29.7 1.0 C14 B:IB25 4.7 38.1 0.4 C3 B:IB25 4.8 37.7 0.6 C8 B:IB25 4.8 29.6 0.4 C5' B:DT19 4.9 28.1 1.0 O3' A:DT8 4.9 27.2 1.0 O5' A:DC9 4.9 23.8 1.0 OP1 B:DT20 4.9 30.9 1.0

Iodine binding site 2 out of 2 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 2 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 B:I25 b:33.8 occ:0.40 I B:IB25 0.0 33.8 0.4 C4 B:IB25 2.1 34.6 0.4 C10 B:IB25 2.5 22.9 0.6 N4 B:IB25 2.9 31.7 0.6 C5 B:IB25 2.9 33.1 0.4 CYT B:IB25 3.2 36.1 0.4 C11 B:IB25 3.4 27.5 0.6 C13 B:IB25 3.5 30.8 0.6 C9 B:IB25 3.5 22.2 0.6 O B:IB25 3.6 37.6 0.4 O A:HOH35 3.8 52.9 1.0 C15 B:IB25 4.1 32.6 0.6 C5' B:DC21 4.2 24.4 1.0 C1 B:IB25 4.2 31.9 0.4 C2 B:IB25 4.4 35.5 0.4 N3 B:IB25 4.8 30.6 0.6 C16 B:IB25 4.8 34.8 0.6 C4' A:DT7 4.8 21.8 1.0 C12 B:IB25 4.8 23.3 0.6 C3 B:IB25 4.8 32.8 0.4 C8 B:IB25 4.9 23.3 0.6 C4' B:DC21 4.9 22.8 1.0 OP1 B:DC21 4.9 30.4 1.0 C5' A:DT7 4.9 24.0 1.0 O3' A:DT7 4.9 23.2 1.0 O B:HOH39 5.0 60.8 1.0 O3' B:DT20 5.0 29.5 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