Magnesium in PDB 3qxr: Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr was solved by D.Wei, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.90 / 1.62
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	37.570, 51.350, 58.340, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.3

The structure of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Potassium	(K)	9 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna (pdb code 3qxr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna, PDB code: 3qxr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg28 b:26.6 occ:1.00 OP2 A:DG21 2.0 12.2 1.0 O A:HOH61 2.0 16.5 1.0 O A:HOH65 2.0 23.3 1.0 O A:HOH63 2.1 22.5 1.0 O A:HOH64 2.2 16.7 1.0 O A:HOH62 2.4 16.4 1.0 O A:HOH192 2.9 14.5 0.5 P A:DG21 3.4 13.9 1.0 O A:HOH189 3.7 30.1 1.0 O A:HOH48 4.0 25.5 1.0 O5' A:DG21 4.1 13.6 1.0 C5' A:DG21 4.1 13.4 1.0 OP1 A:DG21 4.2 14.3 1.0 O A:HOH188 4.3 9.6 0.5 O A:HOH33 4.3 17.9 1.0 C3' A:DG20 4.4 12.7 1.0 O3' A:DG20 4.4 13.4 1.0 OP2 A:DG22 4.4 16.3 1.0 O A:HOH72 4.7 14.2 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Brominated Ckit-1 Proto-Oncogene Promoter Quadruplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg29 b:22.6 occ:1.00 O A:HOH69 2.0 24.6 1.0 O A:HOH68 2.1 23.9 1.0 O A:HOH66 2.2 16.8 1.0 N7 A:DG17 2.3 13.2 1.0 O A:HOH67 2.3 28.2 1.0 C8 A:DG17 3.1 13.9 1.0 C5 A:DG17 3.5 14.2 1.0 O6 A:DG17 4.0 15.1 1.0 O A:HOH38 4.1 15.8 1.0 C6 A:DG17 4.1 16.0 1.0 O A:HOH143 4.1 36.3 1.0 N9 A:DG17 4.4 12.8 1.0 O A:HOH115 4.5 34.7 1.0 C4 A:DG17 4.6 14.8 1.0 O A:HOH119 4.7 34.5 1.0 OP2 A:DG17 4.7 17.7 1.0 C2' A:DA16 4.7 14.6 1.0 O A:HOH186 4.7 43.9 1.0 O A:HOH151 4.8 32.5 1.0

D.Wei, G.N.Parkinson, A.P.Reszka, S.Neidle. Crystal Structure of A C-Kit Promoter Quadruplex Reveals the Structural Role of Metal Ions and Water Molecules in Maintaining Loop Conformation. Nucleic Acids Res. V. 40 4691 2012.
ISSN: ISSN 0305-1048
PubMed: 22287624
DOI: 10.1093/NAR/GKS023