Magnesium in PDB 4j7l: Crystal Structure of Mouse Dxo in Complex with Product Rna and Two Magnesium Ions

The structure of Crystal Structure of Mouse Dxo in Complex with Product Rna and Two Magnesium Ions, PDB code: 4j7l was solved by J.H.Chang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.010, 87.660, 53.940, 90.00, 112.18, 90.00
R / Rfree (%)	18.3 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Mouse Dxo in Complex with Product Rna and Two Magnesium Ions (pdb code 4j7l). 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 Mouse Dxo in Complex with Product Rna and Two Magnesium Ions, PDB code: 4j7l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mouse Dxo in Complex with Product Rna and Two Magnesium Ions


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 Mouse Dxo in Complex with Product Rna and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.9 occ:1.00 O A:LEU254 2.1 13.1 1.0 OE2 A:GLU253 2.2 19.6 1.0 O A:HOH501 2.2 16.8 1.0 OD2 A:ASP236 2.2 15.4 1.0 OP2 B:U2 2.2 16.8 1.0 OP1 B:U2 2.5 29.1 1.0 P B:U2 2.9 31.9 1.0 CG A:ASP236 3.2 16.0 1.0 C A:LEU254 3.3 15.1 1.0 CD A:GLU253 3.3 20.2 1.0 OD1 A:ASP236 3.4 15.6 1.0 N A:LEU254 3.6 12.4 1.0 MG A:MG403 3.7 19.9 1.0 CA A:LEU254 3.9 14.0 1.0 O5' B:U2 3.9 25.5 1.0 C5' B:U2 3.9 26.0 1.0 OE2 A:GLU192 3.9 18.4 1.0 OE1 A:GLU253 4.0 19.1 1.0 OP3 B:U2 4.0 26.1 1.0 CD A:LYS255 4.2 18.4 1.0 O A:HOH502 4.2 14.7 1.0 O A:HOH504 4.2 18.9 1.0 CG A:GLU253 4.2 17.3 1.0 CB A:LEU254 4.2 11.9 1.0 CE A:LYS255 4.3 21.5 1.0 N A:LYS255 4.4 13.8 1.0 NZ A:LYS255 4.5 22.2 1.0 CB A:ASP236 4.5 14.8 1.0 C A:GLU253 4.6 11.7 1.0 O A:HOH503 4.6 24.3 1.0 CG A:LYS255 4.6 18.3 1.0 CA A:LYS255 4.7 15.2 1.0 CA A:GLU253 4.9 14.2 1.0 CD A:GLU192 4.9 22.1 1.0 O B:HOH101 4.9 27.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mouse Dxo in Complex with Product Rna and Two Magnesium Ions


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 Mouse Dxo in Complex with Product Rna and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:19.9 occ:1.00 OP2 B:U2 2.1 16.8 1.0 OE2 A:GLU234 2.2 23.3 1.0 OD1 A:ASP236 2.2 15.6 1.0 O A:HOH504 2.3 18.9 1.0 O A:HOH503 2.4 24.3 1.0 O B:HOH101 2.4 27.1 1.0 CD A:GLU234 3.2 31.2 1.0 CG A:ASP236 3.3 16.0 1.0 P B:U2 3.4 31.9 1.0 OE1 A:GLU234 3.6 35.0 1.0 OD2 A:ASP236 3.7 15.4 1.0 MG A:MG402 3.7 23.9 1.0 OE2 A:GLU192 3.9 18.4 1.0 OP3 B:U2 3.9 26.1 1.0 O5' B:U2 4.0 25.5 1.0 O A:HOH838 4.0 51.0 1.0 O A:HOH744 4.1 35.1 1.0 C5' B:U2 4.2 26.0 1.0 OE2 A:GLU253 4.2 19.6 1.0 O A:GLU234 4.3 14.6 1.0 CG A:GLU234 4.4 23.5 1.0 N A:ASP236 4.4 13.6 1.0 O A:HOH501 4.5 16.8 1.0 OE1 A:GLU253 4.5 19.1 1.0 CB A:GLU234 4.5 17.6 1.0 CB A:ASP236 4.5 14.8 1.0 C A:GLU234 4.6 14.1 1.0 OP1 B:U2 4.6 29.1 1.0 CA A:ASP236 4.6 15.7 1.0 C A:VAL235 4.7 15.3 1.0 CD A:GLU253 4.8 20.2 1.0 CD A:GLU192 5.0 22.1 1.0 N A:VAL235 5.0 15.0 1.0

X.Jiao, J.H.Chang, T.Kilic, L.Tong, M.Kiledjian. A Mammalian Pre-Mrna 5' End Capping Quality Control Mechanism and An Unexpected Link of Capping to Pre-Mrna Processing. Mol.Cell V. 50 104 2013.
ISSN: ISSN 1097-2765
PubMed: 23523372
DOI: 10.1016/J.MOLCEL.2013.02.017