Magnesium in PDB 4gxy: Rna Structure

The structure of Rna Structure, PDB code: 4gxy was solved by A.Serganov, A.Peselis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.35 / 3.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.633, 96.633, 132.684, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25

The structure of Rna Structure also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Iridium	(Ir)	7 atoms

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

Magnesium binding site 1 out of 2 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:81.0 occ:1.00 O6 A:G97 3.4 74.7 1.0 O6 A:G98 3.5 73.9 1.0 OP2 A:G130 3.7 76.2 1.0 C8 A:G130 4.1 94.4 1.0 N9 A:G130 4.3 0.3 1.0 O4' A:G130 4.5 97.9 1.0 N7 A:G130 4.5 95.8 1.0 C6 A:G97 4.5 69.4 1.0 C6 A:G98 4.6 68.9 1.0 C1' A:G130 4.6 98.2 1.0 C4 A:G130 4.8 0.6 1.0 P A:G130 4.8 75.4 1.0 OP1 A:G130 4.9 76.0 1.0 C5 A:G130 4.9 0.6 1.0

Magnesium binding site 2 out of 2 in the Rna Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg311 b:94.2 occ:1.00 O2' A:G65 4.3 64.3 1.0 N34 A:B1Z301 4.3 62.6 1.0 C20 A:B1Z301 4.3 59.8 1.0 C6B A:B1Z301 4.7 60.4 1.0 C7B A:B1Z301 4.8 62.6 1.0 C5B A:B1Z301 4.9 59.8 1.0 C32 A:B1Z301 4.9 56.7 1.0 C30 A:B1Z301 5.0 54.4 1.0

A.Peselis, A.Serganov. Structural Insights Into Ligand Binding and Gene Expression Control By An Adenosylcobalamin Riboswitch. Nat.Struct.Mol.Biol. V. 19 1182 2012.
ISSN: ISSN 1545-9993
PubMed: 23064646
DOI: 10.1038/NSMB.2405