Magnesium in PDB 5u0q: Rna-Dna Heptamer Duplex with One 2'-5'-Linkage

The structure of Rna-Dna Heptamer Duplex with One 2'-5'-Linkage, PDB code: 5u0q was solved by Z.Luo, J.Sheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.11 / 1.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.554, 52.923, 27.622, 90.00, 96.05, 90.00
R / Rfree (%)	15.3 / 17.7

The structure of Rna-Dna Heptamer Duplex with One 2'-5'-Linkage also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Magnesium atom in the Rna-Dna Heptamer Duplex with One 2'-5'-Linkage (pdb code 5u0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rna-Dna Heptamer Duplex with One 2'-5'-Linkage, PDB code: 5u0q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rna-Dna Heptamer Duplex with One 2'-5'-Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna-Dna Heptamer Duplex with One 2'-5'-Linkage within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:24.4 occ:1.00 O B:HOH228 1.7 20.2 1.0 O B:HOH214 3.2 50.1 1.0 OP2 B:G11 3.8 23.7 1.0 OP1 B:A10 4.0 27.0 1.0 O B:HOH233 4.3 46.0 1.0 O B:HOH223 4.6 57.2 1.0 P B:G11 4.8 20.1 1.0 OP1 B:G11 4.9 21.7 1.0

Magnesium binding site 2 out of 3 in the Rna-Dna Heptamer Duplex with One 2'-5'-Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna-Dna Heptamer Duplex with One 2'-5'-Linkage within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:29.6 occ:1.00 O C:HOH220 2.5 53.5 1.0 O C:HOH215 3.0 43.8 1.0 OP1 C:U5 3.9 28.2 1.0 OP2 C:C6 4.3 22.6 1.0 OP1 C:C6 4.7 25.2 1.0 O C:HOH213 4.7 49.0 1.0 P C:C6 4.9 20.5 1.0

Magnesium binding site 3 out of 3 in the Rna-Dna Heptamer Duplex with One 2'-5'-Linkage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna-Dna Heptamer Duplex with One 2'-5'-Linkage within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:21.7 occ:1.00 O D:HOH216 2.1 41.3 1.0 O D:HOH203 3.9 49.6 1.0 O D:HOH225 4.0 62.7 1.0 N7 D:G11 4.0 20.4 1.0 O D:HOH208 4.1 43.9 1.0 O D:HOH214 4.2 34.0 1.0 O6 D:G11 4.4 20.9 1.0 O D:HOH218 4.8 49.4 1.0 C5 D:G11 4.9 16.8 1.0 N7 D:A10 5.0 18.4 1.0

Z.Luo, J.Sheng, R.Wang. Rna-Dna Heptamer Duplex with One 2'-5'-Linkage To Be Published.