Magnesium in PDB 1kxk: Crystal Structure of A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron

The structure of Crystal Structure of A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron, PDB code: 1kxk was solved by L.Zhang, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.987, 90.987, 235.891, 90.00, 90.00, 120.00
R / Rfree (%)	24.8 / 26.8

The binding sites of Magnesium atom in the Crystal Structure of A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron (pdb code 1kxk). 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 A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron, PDB code: 1kxk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron


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 A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg71 b:69.6 occ:1.00 OP1 A:U54 2.0 0.8 1.0 O3' A:C53 2.8 0.9 1.0 P A:U54 2.8 0.5 1.0 C5' A:C53 3.2 0.6 1.0 C3' A:C53 3.6 0.2 1.0 OP2 A:U54 3.6 0.5 1.0 C4' A:C53 3.7 0.2 1.0 O5' A:U54 4.2 0.8 1.0 O5' A:C53 4.3 0.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron


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 A Rna Molecule Containing Domain 5 and 6 of the Yeast AI5G Group II Self-Splicing Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg72 b:84.2 occ:1.00 OP1 A:G38 3.4 74.5 1.0 O5' A:G38 3.5 74.6 1.0 P A:G38 4.0 76.0 1.0 O2' A:A37 4.0 73.3 1.0 O3' A:A37 4.2 74.3 1.0 C5' A:G38 4.4 72.1 1.0 C2' A:A37 4.9 70.0 1.0

L.Zhang, J.A.Doudna. Structural Insights Into Group II Intron Catalysis and Branch-Site Selection. Science V. 295 2084 2002.
ISSN: ISSN 0036-8075
PubMed: 11859154
DOI: 10.1126/SCIENCE.1069268