Calcium in PDB 5ulj: Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion

The structure of Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion, PDB code: 5ulj was solved by S.K.Doamekpor, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.68 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.350, 102.476, 101.194, 90.00, 112.85, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Calcium atom in the Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion (pdb code 5ulj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion, PDB code: 5ulj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:42.2 occ:1.00 OD2 A:ASP230 2.6 25.6 1.0 O A:HOH505 2.6 38.9 1.0 O A:LEU250 2.6 21.6 1.0 OP2 A:0WD402 2.7 52.9 1.0 O A:HOH512 2.8 41.5 1.0 OE2 A:GLU249 2.9 39.9 1.0 O A:HOH504 3.0 44.5 1.0 OE2 A:GLU179 3.1 39.3 1.0 OD1 A:ASP230 3.2 26.9 1.0 CG A:ASP230 3.2 25.9 1.0 C A:LEU250 3.8 19.1 1.0 CD A:GLU249 3.8 35.3 1.0 P2' A:0WD402 3.9 61.1 1.0 O3B A:0WD402 4.0 61.1 1.0 NZ A:LYS251 4.0 33.0 1.0 CD A:LYS251 4.0 25.1 1.0 CE A:LYS251 4.1 31.7 1.0 N A:LEU250 4.1 16.4 1.0 CD A:GLU179 4.3 39.7 1.0 OP3 A:0WD402 4.4 51.8 1.0 CG A:GLU249 4.4 31.1 1.0 CA A:LEU250 4.5 19.4 1.0 CB A:ASP230 4.7 20.5 1.0 OE1 A:GLU249 4.7 40.0 1.0 O A:HOH645 4.7 24.1 1.0 OE1 A:GLU228 4.7 33.5 1.0 N A:LYS251 4.8 15.8 1.0 CB A:LEU250 4.8 19.2 1.0 CG A:LYS251 4.9 22.0 1.0 O A:HOH765 5.0 36.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Scheffersomyces Stipitis RAI1 in Complex with (3'-Nadp)+ and Calcium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:23.9 occ:1.00 OE2 B:GLU249 2.4 27.9 1.0 OD2 B:ASP230 2.4 18.7 1.0 O B:HOH540 2.5 31.9 1.0 O B:HOH604 2.5 25.7 1.0 O B:LEU250 2.5 18.3 1.0 OP2 B:0WD402 2.5 26.0 1.0 O B:HOH521 2.6 26.1 1.0 CG B:ASP230 3.2 22.3 1.0 OD1 B:ASP230 3.3 20.7 1.0 CD B:GLU249 3.4 25.4 1.0 O B:HOH707 3.4 36.3 1.0 C B:LEU250 3.6 20.2 1.0 O3B B:0WD402 3.7 28.9 1.0 P2' B:0WD402 3.8 35.1 1.0 OE1 B:GLU249 4.0 26.9 1.0 N B:LEU250 4.1 18.0 1.0 CD B:LYS251 4.2 19.8 1.0 NZ B:LYS251 4.3 22.6 1.0 CA B:LEU250 4.3 17.3 1.0 CG B:GLU249 4.4 22.9 1.0 CE B:LYS251 4.4 21.1 1.0 OP3 B:0WD402 4.6 36.3 1.0 O B:HOH640 4.6 20.9 1.0 CB B:LEU250 4.7 16.8 1.0 CB B:ASP230 4.7 15.1 1.0 N B:LYS251 4.7 16.6 1.0 OP1 B:0WD402 4.8 33.8 1.0 OE1 B:GLU228 4.8 25.0 1.0 O2B B:0WD402 4.8 25.9 1.0 CG B:LYS251 4.9 16.2 1.0 CA B:LYS251 5.0 16.1 1.0

X.Jiao, S.K.Doamekpor, J.G.Bird, B.E.Nickels, L.Tong, R.P.Hart, M.Kiledjian. 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes Rna Decay Through Dxo-Mediated Denadding. Cell V. 168 1015 2017.
ISSN: ISSN 1097-4172
PubMed: 28283058
DOI: 10.1016/J.CELL.2017.02.019