Iodine in PDB 445d: 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: 445d was solved by C.J.Squire, L.J.Baker, G.R.Clark, 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 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.380, 40.710, 66.240, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 24.6

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 445d). 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: 445d:
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 A:I25 b:43.4 occ:0.20 I A:IA25 0.0 43.4 0.2 C4 A:IA25 2.1 38.6 0.2 N3 A:IA25 2.8 49.9 0.4 C5 A:IA25 3.0 37.2 0.2 C A:IA25 3.1 38.5 0.2 C10 A:IA25 3.5 48.5 0.4 C14 A:IA25 3.5 50.3 0.4 C19 A:IA25 3.7 51.1 0.4 C13 A:IA25 3.8 49.3 0.4 C11 A:IA25 4.1 48.5 0.4 C1 A:IA25 4.3 35.8 0.2 C2 A:IA25 4.4 37.1 0.2 C5' B:DC21 4.5 30.2 1.0 C9 A:IA25 4.6 49.2 0.4 C4' A:DT7 4.7 15.7 1.0 C15 A:IA25 4.8 49.6 0.4 C3 A:IA25 4.9 36.1 0.2 OP1 B:DC21 4.9 29.3 1.0 N4 A:IA25 4.9 49.1 0.4

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 A:I25 b:65.4 occ:0.40 I A:IA25 0.0 65.4 0.4 C14 A:IA25 0.7 42.5 0.2 C19 A:IA25 1.1 43.7 0.2 N3 A:IA25 1.8 41.1 0.2 C15 A:IA25 1.9 41.9 0.2 C4 A:IA25 1.9 58.4 0.4 C18 A:IA25 2.2 45.0 0.2 N4 A:IA25 2.7 41.0 0.2 C13 A:IA25 2.7 39.7 0.2 C16 A:IA25 2.8 42.9 0.2 C17 A:IA25 2.9 44.5 0.2 C A:IA25 3.0 58.1 0.4 C5 A:IA25 3.0 55.9 0.4 O4' B:DA18 3.4 31.6 1.0 O4' A:DC9 3.5 27.8 1.0 N6 A:IA25 3.5 46.0 0.2 N3 B:DA18 3.7 17.2 1.0 C1' B:DA18 3.9 24.1 1.0 O2 A:DT8 4.0 28.8 1.0 C5' B:DT19 4.0 32.0 1.0 C11 A:IA25 4.1 37.8 0.2 C4' B:DA18 4.2 33.6 1.0 C2 A:IA25 4.2 56.6 0.4 C4' A:DC9 4.3 29.4 1.0 C1 A:IA25 4.3 53.2 0.4 O2 A:DC9 4.4 22.5 1.0 C2 B:DA17 4.4 15.8 1.0 O4' B:DT19 4.4 25.4 1.0 O3' B:DA18 4.5 38.6 1.0 C4 B:DA18 4.5 15.0 1.0 C4' B:DT19 4.5 26.5 1.0 C1' A:DC9 4.5 27.1 1.0 C20 A:IA25 4.6 46.1 0.2 N9 B:DA18 4.6 19.5 1.0 C2 B:DA18 4.6 16.5 1.0 N3 B:DA17 4.7 15.1 1.0 C23 A:IA25 4.8 46.4 0.2 C3 A:IA25 4.8 55.4 0.4 C12 A:IA25 4.8 36.8 0.2 C3' B:DA18 4.8 33.8 1.0 C5' A:DC9 4.8 27.1 1.0 C2 A:DC9 4.9 22.6 1.0 N1 A:DC9 4.9 23.2 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