Magnesium in PDB 3dnb: Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer

The structure of Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer, PDB code: 3dnb was solved by G.G.Prive, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	32.520, 26.170, 34.300, 90.00, 118.90, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer (pdb code 3dnb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer, PDB code: 3dnb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg11 b:16.7 occ:1.00 O A:HOH17 2.0 31.6 1.0 O A:HOH14 2.0 25.5 1.0 OP2 A:DA6 2.0 13.0 1.0 O A:HOH16 2.0 16.8 1.0 O A:HOH18 2.0 19.5 1.0 O A:HOH15 2.0 18.6 1.0 P A:DA6 3.5 11.1 1.0 O A:HOH69 4.1 49.6 1.0 O3' A:DG5 4.2 11.3 1.0 OP1 A:DA6 4.3 19.1 1.0 O A:HOH47 4.3 42.7 0.9 C8 A:DA6 4.3 5.8 1.0 C2' A:DG5 4.3 10.3 1.0 C3' A:DG5 4.3 8.9 1.0 O A:HOH31 4.4 19.0 0.8 O5' A:DA6 4.4 12.6 1.0 N7 A:DA6 4.5 10.9 1.0 O A:HOH72 4.9 18.8 0.9

Magnesium binding site 2 out of 3 in the Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg12 b:30.8 occ:1.00 O A:HOH23 2.0 22.9 1.0 O A:HOH19 2.0 46.4 1.0 O A:HOH20 2.0 33.9 1.0 O A:HOH24 2.0 62.7 1.0 O A:HOH21 2.0 15.6 1.0 O A:HOH22 2.0 43.2 1.0 O A:HOH75 3.9 30.2 0.8 O A:HOH60 4.2 27.3 1.0 N2 A:DG5 4.2 7.7 1.0 O4' A:DA6 4.2 7.1 1.0 N3 A:DG5 4.3 9.2 1.0 O A:HOH38 4.6 23.1 1.0 O A:HOH79 4.7 29.4 0.6 C2 A:DG5 4.7 6.9 1.0 C4' A:DA6 4.8 3.1 1.0 O A:HOH59 4.8 32.5 0.7 O4' A:DG5 4.9 10.8 1.0

Magnesium binding site 3 out of 3 in the Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Helix Geometry, Hydration, and G.A Mismatch in A B-Dna Decamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg13 b:15.3 occ:1.00 O A:HOH30 2.0 15.6 1.0 O A:HOH25 2.0 21.8 1.0 O A:HOH28 2.0 12.2 1.0 O A:HOH26 2.0 21.4 1.0 O A:HOH29 2.0 26.9 1.0 O A:HOH27 2.0 29.1 1.0 N7 A:DG9 4.2 7.2 1.0 O A:HOH70 4.3 33.8 0.7 O6 A:DG10 4.3 8.1 1.0 O6 A:DG9 4.4 10.7 1.0 O A:HOH58 4.5 19.4 1.0 C2' A:DT8 5.0 5.9 1.0

G.G.Prive, K.Yanagi, R.E.Dickerson. Structure of the B-Dna Decamer C-C-A-A-C-G-T-T-G-G and Comparison with Isomorphous Decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J.Mol.Biol. V. 217 177 1991.
ISSN: ISSN 0022-2836
PubMed: 1988677
DOI: 10.1016/0022-2836(91)90619-H