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Magnesium in PDB 3ltr: 5-Ome-Du Containing Dna 8MER

Protein crystallography data

The structure of 5-Ome-Du Containing Dna 8MER, PDB code: 3ltr was solved by J.Sheng, A.E.A.Hassan, W.Zhang, J.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.40 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.992, 42.992, 23.822, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-Ome-Du Containing Dna 8MER (pdb code 3ltr). 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 5-Ome-Du Containing Dna 8MER, PDB code: 3ltr:

Magnesium binding site 1 out of 1 in 3ltr

Go back to Magnesium Binding Sites List in 3ltr
Magnesium binding site 1 out of 1 in the 5-Ome-Du Containing Dna 8MER


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Ome-Du Containing Dna 8MER within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg11

b:17.4
occ:1.00
O A:HOH120 2.6 23.1 1.0
O4 A:UMS2 2.9 9.0 1.0
O6 A:DG3 2.9 9.4 1.0
C4 A:UMS2 3.8 8.4 1.0
C6 A:DG3 3.9 9.4 1.0
N7 A:DG3 4.0 9.7 1.0
C5 A:UMS2 4.2 8.3 1.0
C5 A:DG3 4.3 9.2 1.0
O A:HOH125 4.5 26.6 1.0
O A:HOH117 4.6 32.0 1.0
N3 A:UMS2 4.9 8.0 1.0

Reference:

J.Sheng, W.Zhang, A.E.Hassan, J.Gan, A.S.Soares, S.Geng, Y.Ren, Z.Huang. Hydrogen Bond Formation Between the Naturally Modified Nucleobase and Phosphate Backbone. Nucleic Acids Res. V. 40 8111 2012.
ISSN: ISSN 0305-1048
PubMed: 22641848
DOI: 10.1093/NAR/GKS426
Page generated: Wed Aug 14 18:39:01 2024

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