Calcium in PDB 1rk8: Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex

The structure of Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex, PDB code: 1rk8 was solved by F.Bono, J.Ebert, T.Guettler, E.Izaurralde, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.357, 106.357, 58.139, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 24.9

The binding sites of Calcium atom in the Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex (pdb code 1rk8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex, PDB code: 1rk8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca9001 b:25.7 occ:1.00 OE2 A:GLU138 2.5 28.1 1.0 O A:HOH9028 2.8 23.6 1.0 O A:HOH9029 2.8 21.3 1.0 CD A:GLU138 3.5 26.9 1.0 CG A:GLU138 3.9 22.0 1.0 O A:GLY136 4.5 20.0 1.0 OG1 A:THR143 4.5 16.6 1.0 OE1 A:GLU138 4.6 28.0 1.0

Calcium binding site 2 out of 3 in the Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca9002 b:23.0 occ:1.00 OD2 A:ASP87 2.5 17.5 1.0 OE2 A:GLU91 2.6 31.5 1.0 O A:HOH9019 2.7 17.8 1.0 O A:HOH9020 2.8 29.4 1.0 O A:HOH9018 2.8 19.0 1.0 OE1 A:GLU91 2.9 33.4 1.0 CD A:GLU91 3.0 30.3 1.0 OE2 A:GLU88 3.5 16.7 1.0 CG A:ASP87 3.7 17.7 1.0 CA A:CA9003 3.9 17.5 1.0 CB A:ASP87 4.3 17.4 1.0 CG A:GLU91 4.4 27.4 1.0 O A:HOH9017 4.5 18.6 1.0 O A:ASP87 4.5 17.9 1.0 CD A:GLU88 4.5 17.9 1.0 C A:ASP87 4.6 16.6 1.0 OD1 A:ASP87 4.6 16.8 1.0 O A:HOH9057 4.8 44.2 1.0 O A:HOH9039 4.8 34.0 1.0 N A:GLU88 4.8 16.8 1.0 CB A:GLU91 5.0 24.3 1.0

Calcium binding site 3 out of 3 in the Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Cytosolic Protein Pym Bound to the Mago- Y14 Core of the Exon Junction Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca9003 b:17.5 occ:1.00 OE2 A:GLU88 2.5 16.7 1.0 OD2 A:ASP87 2.5 17.5 1.0 OE1 A:GLU88 2.6 15.2 1.0 OD1 A:ASP87 2.7 16.8 1.0 O A:HOH9077 2.8 25.3 1.0 O A:HOH9017 2.8 18.6 1.0 O A:HOH9018 2.8 19.0 1.0 CD A:GLU88 2.9 17.9 1.0 CG A:ASP87 3.0 17.7 1.0 CA A:CA9002 3.9 23.0 1.0 CB A:GLN85 4.4 23.2 1.0 CG A:GLU88 4.4 17.9 1.0 CB A:ASP87 4.5 17.4 1.0 O A:HOH9079 4.5 50.8 1.0 O A:HOH9039 4.6 34.0 1.0 N A:GLU88 4.7 16.8 1.0 O A:HOH9020 4.7 29.4 1.0 CG A:GLN85 4.8 30.3 1.0 N A:GLN85 4.8 18.2 1.0

F.Bono, J.Ebert, L.Unterholzner, T.Guettler, E.Izaurralde, E.Conti. Molecular Insights Into the Interaction of Pym with the Mago-Y14 Core of the Exon Junction Complex Embo Rep. V. 5 304 2004.
ISSN: ISSN 1469-221X
PubMed: 14968132
DOI: 10.1038/SJ.EMBOR.7400091