Magnesium 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:

Iodine

(I)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3', Benzimidazole Derivative Complex, PDB code: 442d:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg26 b:10.2 occ:1.00 O A:HOH73 2.1 11.9 1.0 OP1 A:DG12 2.1 11.8 1.0 O A:HOH74 2.1 9.2 1.0 O A:HOH75 2.1 12.8 1.0 O A:HOH72 2.2 10.1 1.0 P A:DG12 3.2 9.7 1.0 OP2 A:DG12 3.6 8.6 1.0 O5' A:DG12 4.0 8.3 1.0 O A:HOH33 4.2 16.1 1.0 C5' A:DG12 4.4 10.0 1.0 O3' A:DC11 4.4 10.5 1.0 C3' A:DG12 4.6 11.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg27 b:14.9 occ:1.00 O A:HOH76 1.7 17.7 1.0 OP2 A:DG10 2.1 14.3 1.0 O A:HOH77 2.2 27.2 1.0 O A:HOH78 2.3 21.0 1.0 P A:DG10 3.4 14.0 1.0 OP1 A:DG10 3.9 13.7 1.0 O3' A:DC9 4.4 12.2 1.0 O5' A:DG10 4.6 11.2 1.0 C3' A:DC9 4.7 12.3 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