Magnesium in PDB 3p59: First Crystal Structure of A Rna Nanosquare

The structure of First Crystal Structure of A Rna Nanosquare, PDB code: 3p59 was solved by S.Dibrov, T.Hermann, J.Mclean, J.Parsons, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.06 / 2.18
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.378, 62.378, 126.268, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 19.2

The structure of First Crystal Structure of A Rna Nanosquare also contains other interesting chemical elements:

Cobalt	(Co)	10 atoms
Bromine	(Br)	4 atoms

The binding sites of Magnesium atom in the First Crystal Structure of A Rna Nanosquare (pdb code 3p59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the First Crystal Structure of A Rna Nanosquare, PDB code: 3p59:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of First Crystal Structure of A Rna Nanosquare within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg61 b:29.1 occ:1.00 O B:HOH46 2.1 28.0 1.0 O A:HOH63 2.2 30.3 1.0 O2 A:C55 2.4 33.1 1.0 O A:HOH96 3.0 43.3 1.0 O A:HOH62 3.1 33.7 1.0 C2 A:C55 3.5 29.0 1.0 O A:HOH6 3.9 19.9 1.0 N7 B:A109 4.0 14.8 1.0 O6 B:G110 4.0 20.2 1.0 N6 B:A109 4.1 18.7 1.0 N7 B:G110 4.2 18.8 1.0 N3 A:C55 4.2 24.0 1.0 O B:HOH25 4.2 24.9 1.0 O B:HOH22 4.4 20.6 1.0 N1 A:A54 4.4 16.0 1.0 N4 B:C108 4.5 10.3 1.0 N1 A:C55 4.5 26.1 1.0 C1' A:C55 4.6 25.3 1.0 C5 B:A109 4.7 8.7 1.0 C6 B:G110 4.8 25.4 1.0 C2' A:C55 4.8 26.2 1.0 C5 B:G110 4.8 28.1 1.0 C6 B:A109 4.8 12.8 1.0 C8 B:A109 4.9 17.3 1.0 O2' A:C55 4.9 29.6 1.0 C2 A:A54 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of First Crystal Structure of A Rna Nanosquare within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg61 b:33.3 occ:1.00 O E:HOH109 2.4 46.5 1.0 N7 E:G51 3.0 34.6 1.0 O E:HOH64 3.0 34.8 1.0 O6 E:G51 3.1 36.7 1.0 OP2 E:G51 3.6 0.6 1.0 C5 E:G51 3.7 35.0 1.0 C6 E:G51 3.8 29.6 1.0 N7 E:A50 3.8 38.0 1.0 C8 E:G51 4.1 38.1 1.0 C5 E:A50 4.2 36.9 1.0 N6 E:A50 4.4 41.1 1.0 C8 E:A50 4.5 35.3 1.0 C6 E:A50 4.5 36.6 1.0 O6 E:G52 4.6 31.9 1.0 OP2 E:A50 4.6 86.2 1.0 C4 E:A50 5.0 40.7 1.0

S.M.Dibrov, J.Mclean, J.Parsons, T.Hermann. Self-Assembling Rna Square. Proc.Natl.Acad.Sci.Usa V. 108 6405 2011.
ISSN: ISSN 0027-8424
PubMed: 21464284
DOI: 10.1073/PNAS.1017999108