Magnesium in PDB 431d: 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3'

The structure of 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3', PDB code: 431d was solved by D.Vlieghe, J.P.Turkenburg, L.Van Meervelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.106, 36.455, 52.559, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3' (pdb code 431d). 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(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3', PDB code: 431d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg21 b:11.2 occ:1.00 O B:HOH56 2.0 11.1 1.0 O B:HOH53 2.0 13.9 1.0 O B:HOH28 2.0 11.8 1.0 O B:HOH60 2.1 13.2 1.0 O B:HOH55 2.1 13.4 1.0 O B:HOH58 2.1 14.3 1.0 O B:HOH113 4.0 30.0 1.0 O B:HOH23 4.1 10.4 1.0 O B:HOH109 4.3 27.5 1.0 OP1 B:DC13 4.5 12.4 1.0 C4' B:DG12 4.7 10.9 1.0

Magnesium binding site 2 out of 2 in the 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 5'-D(*Gp*Gp*Cp*Cp*Ap*Ap*Tp*Tp*Gp*G)-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg22 b:14.7 occ:1.00 O B:HOH59 2.0 13.6 1.0 O B:HOH54 2.0 12.0 1.0 O B:HOH62 2.1 22.4 1.0 O B:HOH57 2.1 14.0 1.0 O B:HOH63 2.2 16.9 1.0 O B:HOH61 2.3 18.7 1.0 OP1 B:DA16 3.7 11.5 1.0 O A:HOH85 4.2 19.2 1.0 O A:HOH119 4.2 26.1 1.0 C5' B:DA16 4.3 11.4 1.0 O B:HOH107 4.4 11.5 0.6 O B:HOH33 4.7 10.8 1.0 O A:HOH67 4.8 20.8 1.0 P B:DA16 5.0 11.4 1.0 O5' B:DA16 5.0 12.2 1.0

D.Vlieghe, J.P.Turkenburg, L.Van Meervelt. B-Dna at Atomic Resolution Reveals Extended Hydration Patterns. Acta Crystallogr.,Sect.D V. 55 1495 1999.
ISSN: ISSN 0907-4449
PubMed: 10489444
DOI: 10.1107/S0907444999007933