Magnesium in PDB 2xzo: UPF1 Helicase - Rna Complex

All present enzymatic activity of UPF1 Helicase - Rna Complex:
3.6.4.13;

The structure of UPF1 Helicase - Rna Complex, PDB code: 2xzo was solved by S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.066, 101.896, 112.320, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.3

The structure of UPF1 Helicase - Rna Complex also contains other interesting chemical elements:

Aluminium	(Al)	1 atom
Fluorine	(F)	4 atoms

The binding sites of Magnesium atom in the UPF1 Helicase - Rna Complex (pdb code 2xzo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the UPF1 Helicase - Rna Complex, PDB code: 2xzo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the UPF1 Helicase - Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of UPF1 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:23.3 occ:1.00 F4 A:ALF1005 2.1 27.9 1.0 O2B A:ADP1004 2.1 21.6 1.0 O A:HOH1106 2.2 30.2 1.0 O A:HOH1195 2.3 26.3 1.0 OG1 A:THR499 2.3 24.1 1.0 O A:HOH1119 2.4 20.1 1.0 O1B A:ADP1004 3.0 26.9 1.0 PB A:ADP1004 3.1 21.3 1.0 CB A:THR499 3.4 26.9 1.0 AL A:ALF1005 3.4 20.2 1.0 F2 A:ALF1005 3.8 24.9 1.0 N A:THR499 3.8 20.6 1.0 F3 A:ALF1005 3.9 22.6 1.0 O3B A:ADP1004 4.1 23.1 1.0 CA A:THR499 4.2 23.2 1.0 OD2 A:ASP636 4.2 29.0 1.0 CD A:GLU637 4.2 47.5 1.0 O3A A:ADP1004 4.2 27.0 1.0 OE2 A:GLU637 4.3 36.2 1.0 OE1 A:GLU637 4.3 47.0 1.0 OD1 A:ASP636 4.3 30.0 1.0 O1A A:ADP1004 4.3 24.4 1.0 CA A:GLY831 4.4 23.9 1.0 O A:HOH1166 4.4 30.9 1.0 O A:HOH1104 4.4 25.4 1.0 O2A A:ADP1004 4.5 20.0 1.0 CG2 A:THR499 4.5 21.9 1.0 CB A:LYS498 4.5 22.8 1.0 O A:GLY831 4.6 26.2 1.0 PA A:ADP1004 4.6 18.6 1.0 CG A:ASP636 4.6 33.1 1.0 CG A:GLU637 4.7 36.0 1.0 C A:LYS498 4.7 20.0 1.0 CE A:LYS498 4.8 24.7 1.0 C A:GLY831 5.0 29.2 1.0 NZ A:LYS498 5.0 19.1 1.0

Magnesium binding site 2 out of 2 in the UPF1 Helicase - Rna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of UPF1 Helicase - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:69.3 occ:1.00 N A:SER810 2.9 70.2 1.0 O A:MET807 2.9 59.2 1.0 OG A:SER812 3.0 76.3 1.0 OG1 A:THR815 3.2 64.6 1.0 CB A:SER810 3.2 69.3 1.0 C A:MET807 3.2 53.4 1.0 CA A:SER810 3.3 65.2 1.0 C A:SER810 3.3 67.2 1.0 CB A:SER812 3.3 75.6 1.0 O A:TYR806 3.3 67.2 1.0 N A:SER812 3.5 78.3 1.0 O A:SER810 3.5 69.8 1.0 N A:PHE809 3.7 59.5 1.0 N A:GLN808 3.7 54.4 1.0 C A:GLN808 3.8 63.2 1.0 N A:GLY811 3.8 67.6 1.0 CA A:MET807 3.9 50.5 1.0 OG A:SER810 4.0 52.9 1.0 CA A:SER812 4.0 75.4 1.0 C A:PHE809 4.0 71.1 1.0 CA A:GLN808 4.1 61.1 1.0 C A:TYR806 4.1 59.5 1.0 O A:GLN808 4.3 63.3 1.0 CA A:PHE809 4.3 68.8 1.0 CB A:THR815 4.4 70.2 1.0 N A:MET807 4.4 55.5 1.0 O A:GLN805 4.4 48.4 1.0 C A:GLY811 4.5 75.7 1.0 CG2 A:THR815 4.6 63.0 1.0 CA A:GLY811 4.6 66.1 1.0 CA A:THR815 4.9 71.2 1.0

S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti. Molecular Mechanisms For the Rna-Dependent Atpase Activity of UPF1 and Its Regulation By UPF2. Mol.Cell V. 41 693 2011.
ISSN: ISSN 1097-2765
PubMed: 21419344
DOI: 10.1016/J.MOLCEL.2011.02.010