Magnesium in PDB 3opi: 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna

The structure of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna, PDB code: 3opi was solved by E.A.Kowal, M.Ganguly, P.S.Pallan, L.A.Marky, B.Gold, M.Egli, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.40 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.635, 40.310, 65.928, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

The structure of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna (pdb code 3opi). 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 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna, PDB code: 3opi:

Magnesium binding site 1 out of 1 in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:12.5 occ:1.00 O A:HOH410 2.1 14.2 1.0 O A:HOH408 2.1 14.3 1.0 O A:HOH407 2.1 13.1 1.0 OP1 A:7DA106 4.2 15.3 0.5 OP1 A:7DA106 4.3 23.3 0.5 O A:HOH443 4.3 18.4 1.0 O A:HOH456 4.3 22.7 1.0 NA A:NA401 4.4 19.1 1.0 OP2 A:7DA106 4.4 11.8 0.5 OP2 A:DT107 4.4 13.1 1.0 O5' A:7DA106 4.6 12.7 0.5 P A:7DA106 4.6 12.9 0.5 C3' A:7DA106 4.7 13.6 0.5 C3' A:7DA106 4.9 11.2 0.5 O5' A:7DA106 4.9 15.6 0.5

E.A.Kowal, M.Ganguly, P.S.Pallan, L.A.Marky, B.Gold, M.Egli, M.P.Stone. Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-Deoxyadenosine:Dt Base Pairing in Dna. J.Phys.Chem.B V. 115 13925 2011.
ISSN: ISSN 1089-5647
PubMed: 22059929
DOI: 10.1021/JP207104W