Magnesium in PDB 5dnb: 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

The structure of 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, PDB code: 5dnb was solved by G.G.Prive, K.Yanagi, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	32.250, 25.530, 34.380, 90.00, 113.40, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the 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 (pdb code 5dnb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 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, PDB code: 5dnb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg11 b:24.1 occ:1.00 O A:HOH78 2.0 24.8 1.0 O A:HOH79 2.0 24.2 1.0 O A:HOH77 2.1 26.6 1.0 O A:HOH74 2.1 24.1 1.0 O A:HOH76 2.1 28.2 1.0 O A:HOH75 2.1 30.0 1.0 O A:HOH62 4.0 18.5 0.4 O A:HOH60 4.2 44.2 0.9 O A:HOH23 4.2 16.7 1.0 O A:HOH32 4.3 20.4 0.7 O A:HOH28 4.3 34.0 0.9 O A:HOH22 4.4 19.9 1.0 O4' A:DG6 4.5 16.6 1.0 O2 A:DC5 4.5 15.6 1.0 C5' A:DG6 4.6 19.0 1.0 C4' A:DG6 4.6 18.5 1.0 O A:HOH39 4.8 28.0 1.0

Magnesium binding site 2 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg12 b:29.6 occ:0.50 O A:HOH80 2.1 24.9 1.0 O A:HOH81 2.2 21.9 1.0 O A:HOH82 2.2 23.7 1.0 O A:HOH26 4.0 20.4 0.8

Magnesium binding site 3 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg13 b:35.2 occ:1.00 O A:HOH84 2.1 33.6 1.0 O A:HOH86 2.1 37.4 1.0 O A:HOH87 2.2 25.8 1.0 O A:HOH15 2.2 49.3 1.0 O A:HOH83 2.2 18.9 1.0 O A:HOH85 2.2 38.8 1.0 O A:HOH18 4.0 14.9 0.9 O A:HOH33 4.0 21.3 1.0 O A:HOH36 4.4 18.9 0.8 OP1 A:DC5 4.4 33.2 1.0 O A:HOH56 4.7 21.7 0.6

Magnesium binding site 4 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg14 b:34.8 occ:1.00 O A:HOH90 2.1 30.8 1.0 O A:HOH89 2.1 32.3 1.0 O A:HOH17 2.1 35.0 1.0 O A:HOH92 2.1 49.3 1.0 O A:HOH16 2.2 27.1 1.0 O A:HOH91 2.2 26.9 1.0 O A:HOH67 3.9 34.4 0.6 OP2 A:DT7 4.1 22.4 1.0 O A:HOH72 4.2 48.6 0.8 O A:HOH44 4.4 25.8 0.7 O A:HOH45 4.5 27.8 0.8 O A:HOH48 4.7 28.5 0.9 P A:DT7 4.9 20.4 1.0 OP1 A:DT7 4.9 21.8 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