Magnesium in PDB 7opk: Crystal Structure of C. Thermophilum XRN2

The structure of Crystal Structure of C. Thermophilum XRN2, PDB code: 7opk was solved by J.H.Overbeck, R.Sprangers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.69 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	198.78, 198.78, 69.14, 90, 90, 120
R / Rfree (%)	18 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of C. Thermophilum XRN2 (pdb code 7opk). 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 C. Thermophilum XRN2, PDB code: 7opk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of C. Thermophilum XRN2


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 C. Thermophilum XRN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:51.0 occ:1.00 OE2 A:GLU211 1.8 58.1 1.0 CD A:GLU211 3.0 74.8 1.0 OD2 A:ASP104 3.2 88.7 1.0 NZ A:LYS111 3.6 62.1 1.0 OE2 A:GLU209 3.6 92.1 1.0 OE1 A:GLU211 3.7 66.3 1.0 OD1 A:ASP104 3.7 70.4 1.0 CG A:GLU209 3.8 57.5 1.0 MG A:MG902 3.8 47.2 1.0 CG A:ASP104 3.9 70.8 1.0 CE A:LYS111 4.1 59.7 1.0 CG A:GLU211 4.1 83.9 1.0 CD A:GLU209 4.2 73.3 1.0 OD2 A:ASP239 4.4 67.0 1.0 OD2 A:ASP55 4.6 65.7 1.0 NH2 A:ARG118 4.6 61.7 1.0 OD1 A:ASP55 4.9 84.5 1.0 N A:GLY210 4.9 42.3 1.0 NH1 A:ARG118 5.0 57.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of C. Thermophilum XRN2


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 C. Thermophilum XRN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:47.2 occ:1.00 OE1 A:GLU211 2.2 66.3 1.0 OD2 A:ASP239 2.3 67.0 1.0 OD2 A:ASP241 2.6 68.5 1.0 CD A:GLU211 3.0 74.8 1.0 OD2 A:ASP351 3.0 80.0 1.0 OE2 A:GLU209 3.0 92.1 1.0 OE2 A:GLU211 3.3 58.1 1.0 CG A:ASP239 3.3 64.3 1.0 OD1 A:ASP239 3.6 68.6 1.0 CG A:ASP241 3.7 67.8 1.0 NZ A:LYS111 3.7 62.1 1.0 N A:GLY2 3.8 60.1 1.0 MG A:MG901 3.8 51.0 1.0 CB A:ASP241 4.1 57.6 1.0 CG A:ASP351 4.1 68.8 1.0 CD A:GLU209 4.2 73.3 1.0 CG A:GLU211 4.2 83.9 1.0 CB A:ASP239 4.6 57.6 1.0 OD1 A:ASP241 4.7 73.4 1.0 CE A:LYS111 4.8 59.7 1.0 OD1 A:ASP351 4.9 68.3 1.0 CA A:GLY2 4.9 61.7 1.0 CG A:GLU209 5.0 57.5 1.0

J.H.Overbeck, D.Stelzig, A.L.Fuchs, J.P.Wurm, R.Sprangers. Observation of Conformational Changes That Underlie the Catalytic Cycle of XRN2. Nat.Chem.Biol. V. 18 1152 2022.
ISSN: ESSN 1552-4469
PubMed: 36008487
DOI: 10.1038/S41589-022-01111-6