Magnesium in PDB 443d: 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: 443d 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 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.913, 34.153, 61.296, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 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 443d). 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: 443d:
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:22.8 occ:1.00 O A:HOH69 2.0 15.5 1.0 O A:HOH68 2.0 20.2 1.0 O A:HOH71 2.1 15.2 1.0 OP1 A:DG12 2.1 12.8 1.0 O A:HOH70 2.2 20.1 1.0 P A:DG12 3.2 15.2 1.0 OP2 A:DG12 3.6 15.9 1.0 O5' A:DG12 4.1 12.9 1.0 O A:HOH36 4.1 27.7 1.0 O A:HOH37 4.4 20.1 1.0 O3' A:DC11 4.5 13.7 1.0 C5' A:DG12 4.5 14.6 1.0 C3' A:DG12 4.6 9.6 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 B:Mg27 b:58.6 occ:1.00 OP1 B:DC23 2.5 21.2 1.0 P B:DC23 3.7 18.2 1.0 O B:HOH34 3.8 30.9 1.0 O5' B:DC23 4.0 15.9 1.0 C5' B:DC23 4.2 17.7 1.0 OP2 B:DC23 4.4 15.1 1.0 O B:HOH52 4.6 41.2 1.0 O3' B:DG22 5.0 19.3 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