Magnesium in PDB 2p51: Crystal Structure of the S. Pombe POP2P Deadenylation Subunit

The structure of Crystal Structure of the S. Pombe POP2P Deadenylation Subunit, PDB code: 2p51 was solved by A.Thyssen Jonstrup, K.R.Andersen, L.B.Van, D.E.Brodersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.47 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.370, 54.089, 90.959, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of the S. Pombe POP2P Deadenylation Subunit (pdb code 2p51). 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 the S. Pombe POP2P Deadenylation Subunit, PDB code: 2p51:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the S. Pombe POP2P Deadenylation Subunit


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 the S. Pombe POP2P Deadenylation Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:14.7 occ:1.00 O A:HOH3003 2.0 18.1 1.0 OD1 A:ASP50 2.0 13.5 1.0 O A:HOH3002 2.1 13.0 0.9 O A:HOH3001 2.1 14.4 1.0 OD2 A:ASP171 2.1 13.8 1.0 O A:HOH3004 2.1 14.6 0.9 CG A:ASP171 3.1 13.1 1.0 CG A:ASP50 3.2 13.7 1.0 OD1 A:ASP171 3.3 13.7 1.0 O A:HOH3006 3.6 15.1 0.8 O A:PHE166 3.8 15.2 1.0 O A:HOH3185 3.9 35.9 1.0 OD2 A:ASP50 3.9 16.3 1.0 O A:HOH3007 4.0 21.8 0.9 O A:HOH3019 4.0 14.4 1.0 O A:HOH3017 4.2 14.7 0.8 CB A:ASP50 4.3 13.2 1.0 N A:THR51 4.4 12.1 1.0 O A:HOH3102 4.5 15.0 1.0 O A:THR51 4.5 14.1 1.0 CB A:ASP171 4.5 13.2 1.0 CA A:ASP50 4.5 11.2 1.0 MG A:MG2002 4.6 15.8 0.9 O A:HIS167 4.8 15.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the S. Pombe POP2P Deadenylation Subunit


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 the S. Pombe POP2P Deadenylation Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:15.8 occ:0.86 OD2 A:ASP240 2.0 16.2 1.0 OD2 A:ASP50 2.1 16.3 1.0 O A:HOH3005 2.1 17.2 0.9 OE2 A:GLU52 2.1 16.4 1.0 O A:HOH3007 2.1 21.8 0.9 O A:HOH3006 2.1 15.1 0.8 CD A:GLU52 3.1 14.8 1.0 CG A:ASP240 3.1 19.0 1.0 CG A:ASP50 3.2 13.7 1.0 OE1 A:GLU52 3.3 16.3 1.0 O A:HOH3003 3.4 18.1 1.0 CB A:ASP240 3.6 14.4 1.0 OD1 A:ASP50 3.6 13.5 1.0 O A:HOH3203 3.8 35.7 1.0 O A:THR51 4.0 14.1 1.0 OD1 A:ASP240 4.2 18.8 1.0 O A:HOH3151 4.2 31.3 1.0 O A:HOH3185 4.3 35.9 1.0 CA A:HIS235 4.3 21.2 1.0 CG A:GLU52 4.4 14.0 1.0 CB A:ASP50 4.4 13.2 1.0 MG A:MG2001 4.6 14.7 1.0 O A:HOH3001 4.6 14.4 1.0 C A:HIS235 4.6 20.0 1.0 O A:GLN236 4.7 16.7 1.0 CA A:ALA237 4.7 13.0 1.0 C A:GLN236 4.8 12.4 1.0 O A:HOH3181 4.8 40.5 0.8 N A:GLN236 4.8 18.0 1.0 C A:THR51 4.8 10.3 1.0 N A:ALA237 4.9 12.9 1.0 N A:HIS235 5.0 21.6 1.0

A.Thyssen Jonstrup, K.R.Andersen, L.B.Van, D.E.Brodersen. The 1.4-A Crystal Structure of the S. Pombe POP2P Deadenylase Subunit Unveils the Configuration of An Active Enzyme Nucleic Acids Res. V. 35 3153 2007.
ISSN: ISSN 0305-1048
PubMed: 17452359
DOI: 10.1093/NAR/GKM178