Calcium in PDB 2ydx: Crystal Structure of Human S-Adenosylmethionine Synthetase 2, Beta Subunit

The structure of Crystal Structure of Human S-Adenosylmethionine Synthetase 2, Beta Subunit, PDB code: 2ydx was solved by J.R.C.Muniz, N.Shafqat, A.C.W.Pike, W.W.Yue, M.Vollmar, V.Papagriogriou, A.Roos, O.Gileadi, F.Von Delft, K.L.Kavanagh, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.96 / 2.80
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	163.389, 163.389, 252.882, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 18.8

The binding sites of Calcium atom in the Crystal Structure of Human S-Adenosylmethionine Synthetase 2, Beta Subunit (pdb code 2ydx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Human S-Adenosylmethionine Synthetase 2, Beta Subunit, PDB code: 2ydx:

Calcium binding site 1 out of 1 in the Crystal Structure of Human S-Adenosylmethionine Synthetase 2, Beta Subunit


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 Human S-Adenosylmethionine Synthetase 2, Beta Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1344 b:85.5 occ:1.00 OD2 A:ASP137 2.5 53.0 1.0 O A:HOH2125 2.8 33.5 1.0 O A:HOH2086 2.9 27.1 1.0 O A:HOH2098 3.0 29.8 1.0 CB A:PRO183 3.4 36.6 1.0 CG A:ASP137 3.6 51.8 1.0 CD1 A:PHE220 3.6 38.6 1.0 O A:HOH2052 3.7 39.8 1.0 O A:ALA293 3.7 36.3 1.0 C A:ALA293 3.8 36.0 1.0 CB A:PHE220 3.9 35.3 1.0 N A:GLN294 4.1 33.1 1.0 N A:PHE220 4.1 35.3 1.0 CG A:PHE220 4.2 36.1 1.0 CA A:GLN294 4.2 32.7 1.0 CB A:ASP137 4.2 40.3 1.0 CG A:PRO183 4.2 40.9 1.0 CB A:ALA293 4.4 29.7 1.0 CA A:ALA293 4.5 29.4 1.0 N A:ALA293 4.6 30.1 1.0 CA A:PRO183 4.6 34.7 1.0 O A:HOH2085 4.6 26.3 1.0 OD1 A:ASP137 4.6 53.6 1.0 CA A:PHE220 4.6 34.1 1.0 CE1 A:PHE220 4.7 38.9 1.0 C A:ARG219 4.7 37.7 1.0 CA A:ARG219 4.8 33.6 1.0 N A:LEU295 4.8 36.0 1.0 C A:GLN294 5.0 38.1 1.0 O A:GLN218 5.0 39.6 1.0

N.Shafqat, J.R.C.Muniz, E.S.Pilka, E.Papagrigoriou, F.Von Delft, U.Oppermann, W.W.Yue. Insight Into S-Adenosylmethionine Biosynthesis From the Crystal Structures of the Human Methionine Adenosyltransferase Catalytic and Regulatory Subunits. Biochem.J. V. 452 27 2013.
ISSN: ISSN 0264-6021
PubMed: 23425511
DOI: 10.1042/BJ20121580