Sodium 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:

Magnesium

(Mg)

1 atom

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna, PDB code: 3opi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na400 b:16.0 occ:1.00 O2 A:DT107 2.7 12.3 1.0 O2 B:DT219 2.8 13.5 1.0 O B:HOH441 2.8 17.8 1.0 O B:HOH450 2.9 19.8 1.0 O4' A:DT108 3.3 13.5 1.0 O4' B:DT220 3.4 17.4 1.0 C4' B:DT220 3.7 17.8 1.0 C4' A:DT108 3.8 14.0 1.0 C2 A:DT107 3.9 11.4 1.0 C2 B:DT219 3.9 11.9 1.0 C5' B:DT220 3.9 20.9 1.0 C1' A:DT108 4.2 12.6 1.0 C1' A:DT107 4.2 12.4 1.0 C5' A:DT108 4.3 14.6 1.0 C1' B:DT219 4.3 14.2 1.0 C1' B:DT220 4.3 17.1 1.0 C2 A:7DA106 4.5 10.6 0.5 C2 B:7DA218 4.5 12.2 1.0 C2 A:7DA106 4.6 12.8 0.5 N1 A:DT107 4.6 11.2 1.0 N1 B:DT219 4.6 12.9 1.0 N1 A:DT108 4.6 11.9 1.0 O B:HOH412 4.7 13.5 1.0 O B:HOH492 4.8 26.4 1.0 O A:HOH413 4.8 16.9 1.0 O2 A:DT108 4.9 12.0 1.0 N1 B:DT220 4.9 15.8 1.0 N3 A:DT107 4.9 11.6 1.0 N3 B:DT219 4.9 11.9 1.0 C2 A:DT108 4.9 11.1 1.0 O4' B:DT219 5.0 14.8 1.0

Sodium binding site 2 out of 4 in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.1 occ:1.00 O A:HOH443 2.7 18.4 1.0 OP1 A:DT107 2.7 14.0 1.0 P A:DT107 3.6 12.5 1.0 OP2 A:DT107 3.7 13.1 1.0 O A:HOH474 3.9 24.9 1.0 O A:HOH410 3.9 14.2 1.0 O3' A:7DA106 4.0 12.7 0.5 O3' A:7DA106 4.1 12.1 0.5 O A:HOH518 4.3 42.8 1.0 MG A:MG301 4.4 12.5 1.0 O A:HOH407 4.4 13.1 1.0 O A:HOH483 4.6 26.9 1.0 C3' A:7DA106 4.8 13.6 0.5 C3' A:7DA106 4.9 11.2 0.5

Sodium binding site 3 out of 4 in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.5 occ:1.00 N3 A:DG104 2.7 14.8 0.5 O A:HOH484 2.9 18.8 0.5 N3 A:DG104 2.9 16.0 0.5 N2 A:DG104 3.0 13.9 0.5 O A:HOH519 3.0 35.9 1.0 O4' A:DA105 3.2 15.1 0.5 C2 A:DG104 3.3 15.8 0.5 O4' A:DA105 3.4 18.8 0.5 C1' A:DG104 3.5 14.8 0.5 N2 A:DG104 3.6 11.4 0.5 C2 A:DG104 3.6 12.8 0.5 C4 A:DG104 3.6 15.5 0.5 O4' A:DG104 3.7 14.7 0.5 N9 A:DG104 3.9 12.2 0.5 C4' A:DA105 4.1 17.8 0.5 C4' A:DA105 4.1 18.9 0.5 O4' A:DG104 4.1 12.7 0.5 C4 A:DG104 4.1 13.3 0.5 C1' A:DG104 4.1 13.6 0.5 N2 B:DG222 4.2 13.4 1.0 O B:HOH428 4.2 19.4 1.0 C5' A:DA105 4.3 18.6 0.5 C1' A:DA105 4.3 19.9 0.5 C1' A:DA105 4.4 11.7 0.5 N9 A:DA105 4.5 13.2 0.5 C5' A:DA105 4.5 16.5 0.5 N9 A:DG104 4.6 12.9 0.5 N1 A:DG104 4.6 13.2 0.5 O3' A:DG104 4.7 19.1 0.5 C4' A:DG104 4.7 15.6 0.5 N9 A:DA105 4.7 16.9 0.5 C4' A:DG104 4.8 15.6 0.5 C4 A:DA105 4.9 11.8 0.5 C2' A:DG104 4.9 16.2 0.5 N1 A:DG104 4.9 14.1 0.5 C5 A:DG104 4.9 13.1 0.5 C8 A:DA105 5.0 12.8 0.5

Sodium binding site 4 out of 4 in the 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 7-Deaza-2'-Deoxyadenosine Modification in B-Form Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:23.2 occ:1.00 OP1 B:DC215 2.7 16.5 1.0 O B:HOH533 2.8 16.9 0.5 O3' B:DG214 3.3 14.3 1.0 P B:DC215 3.6 14.4 1.0 C5' B:DC215 4.2 13.8 1.0 O5' B:DC215 4.5 13.9 1.0 C3' B:DG214 4.6 15.2 1.0 C4' B:DG214 4.7 13.7 1.0 O B:HOH504 4.7 20.0 0.5 OP2 B:DC215 4.9 17.0 1.0

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