Magnesium in PDB 403d: 5'-D(*Cp*Gp*Cp*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole

The structure of 5'-D(*Cp*Gp*Cp*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole, PDB code: 403d was solved by H.Robinson, Y.-G.Gao, C.Bauer, C.Roberts, C.Switzer, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.759, 41.084, 64.307, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 31.6

The binding sites of Magnesium atom in the 5'-D(*Cp*Gp*Cp*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole (pdb code 403d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 5'-D(*Cp*Gp*Cp*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole, PDB code: 403d:

Magnesium binding site 1 out of 1 in the 5'-D(*Cp*Gp*Cp*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole


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*(Hyd)Ap*Ap*Ap*Tp*Tp*Tp*Gp*Cp*G)-3', 2'-(4- Ethoxyphenyl)-5-(4-Methyl-1-Piperazinyl)-2,5'-Bi- Benzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg26 b:16.4 occ:1.00 O A:HOH1140 2.0 17.3 1.0 O B:HOH1143 2.0 15.5 1.0 O A:HOH1139 2.1 15.9 1.0 O B:HOH1138 2.1 15.5 1.0 O A:HOH1141 2.1 18.4 1.0 O B:HOH1142 2.1 16.4 1.0 O B:HOH1002 4.1 19.0 1.0 O A:HOH1005 4.1 27.2 1.0 O6 B:DG22 4.1 17.9 1.0 O A:HOH1040 4.2 38.6 1.0 O6 A:DG2 4.4 15.8 1.0 O A:HOH1006 4.4 19.8 1.0 C5 A:DC1 4.4 17.8 1.0 N7 A:DG2 4.5 17.0 1.0 O A:HOH1015 4.7 26.6 1.0 N4 A:DC3 4.8 25.0 1.0 C6 A:DC1 4.8 13.6 1.0 O B:HOH1067 5.0 53.4 1.0

H.Robinson, Y.G.Gao, C.Bauer, C.Roberts, C.Switzer, A.H.Wang. 2'-Deoxyisoguanosine Adopts More Than One Tautomer to Form Base Pairs with Thymidine Observed By High-Resolution Crystal Structure Analysis. Biochemistry V. 37 10897 1998.
ISSN: ISSN 0006-2960
PubMed: 9692982
DOI: 10.1021/BI980818L