Calcium in PDB 5kc8: Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2)

The structure of Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2), PDB code: 5kc8 was solved by J.Elegheert, J.E.Clay, C.Siebold, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.87 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	45.100, 79.160, 246.690, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.8

The binding sites of Calcium atom in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2) (pdb code 5kc8). 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 the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2), PDB code: 5kc8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2)


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 the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:34.2 occ:1.00 O A:HOH622 2.3 27.7 1.0 O A:HOH777 2.3 43.8 1.0 O A:HOH677 2.4 44.2 1.0 OE2 A:GLU81 2.4 28.0 1.0 O A:HOH805 2.5 44.0 1.0 OE1 A:GLU84 2.5 31.9 1.0 OE2 A:GLU84 2.5 32.6 1.0 OE1 A:GLU81 2.6 27.3 1.0 CD A:GLU84 2.8 30.0 1.0 CD A:GLU81 2.8 26.5 1.0 O A:HOH619 4.3 44.8 1.0 CG A:GLU84 4.3 24.9 1.0 O A:HOH660 4.3 34.0 1.0 CG A:GLU81 4.4 22.8 1.0 NE2 A:GLN80 4.4 39.7 1.0 O A:HOH798 4.5 44.1 1.0 O A:HOH656 4.7 20.2 1.0 CB A:GLU84 4.9 21.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2)


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 the Amino-Terminal Domain (Atd) of Iglur Delta-2 (GLUD2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:54.5 occ:1.00 O A:HOH669 2.4 58.5 1.0 O A:HOH686 2.4 52.0 1.0 O A:HOH639 2.4 47.1 1.0 O A:HOH799 4.0 47.6 1.0 OE1 A:GLU183 4.4 57.1 1.0 OD2 A:ASP154 4.4 37.7 1.0 NE2 A:HIS153 4.4 31.3 1.0 OE2 A:GLU183 4.5 55.9 1.0 O A:HOH817 4.5 48.4 1.0 CD A:GLU183 4.9 54.4 1.0 OD1 A:ASP154 4.9 36.0 1.0

J.Elegheert, W.Kakegawa, J.E.Clay, N.F.Shanks, E.Behiels, K.Matsuda, K.Kohda, E.Miura, M.Rossmann, N.Mitakidis, J.Motohashi, V.T.Chang, C.Siebold, I.H.Greger, T.Nakagawa, M.Yuzaki, A.R.Aricescu. Structural Basis For Integration of Glud Receptors Within Synaptic Organizer Complexes. Science V. 353 295 2016.
ISSN: ESSN 1095-9203
PubMed: 27418511
DOI: 10.1126/SCIENCE.AAE0104