Calcium in PDB 8bn5: Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba, PDB code: 8bn5 was solved by C.Heroven, T.Malinauskas, A.R.Aricescu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.35 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.838, 66.967, 175.413, 90, 90, 90
R / Rfree (%)	18.4 / 22.8

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba (pdb code 8bn5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba, PDB code: 8bn5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba


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 Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:34.5 occ:1.00 O A:GLU527 2.2 32.9 1.0 OD1 A:ASP531 2.3 31.6 1.0 OE2 A:GLU527 2.3 31.3 1.0 O A:VAL530 2.5 34.9 1.0 O A:HOH1038 2.5 38.5 1.0 O A:HOH1058 2.6 42.8 1.0 O B:HOH1044 2.7 37.8 1.0 HA A:ASP531 3.1 42.3 1.0 HG3 A:GLU527 3.1 46.0 1.0 CD A:GLU527 3.2 38.2 1.0 C A:GLU527 3.4 33.2 1.0 C A:VAL530 3.4 35.6 1.0 CG A:ASP531 3.5 35.8 1.0 CG A:GLU527 3.7 38.2 1.0 HH22 A:ARG781 3.8 46.3 1.0 HA A:GLU527 3.8 41.6 1.0 CA A:ASP531 3.9 35.2 1.0 N A:ASP531 4.0 34.4 1.0 CA A:GLU527 4.1 34.6 1.0 O B:HOH1047 4.1 39.4 1.0 HH12 A:ARG781 4.1 45.7 1.0 OE1 A:GLU527 4.2 33.5 1.0 HA A:SER528 4.2 46.8 1.0 H A:VAL530 4.2 39.8 1.0 CB A:ASP531 4.2 32.5 1.0 N A:VAL530 4.4 33.1 1.0 OD2 A:ASP531 4.4 37.9 1.0 N A:SER528 4.4 34.0 1.0 O A:HOH1017 4.4 44.1 1.0 HG2 A:GLU527 4.4 46.0 1.0 C A:SER528 4.4 41.4 1.0 CA A:VAL530 4.5 33.6 1.0 CB A:GLU527 4.5 31.8 1.0 NH2 A:ARG781 4.5 38.5 1.0 O A:SER528 4.5 40.5 1.0 CA A:SER528 4.6 38.9 1.0 ND1 A:HIS776 4.6 46.3 1.0 OE1 B:GLN786 4.6 35.6 1.0 HB3 A:ASP531 4.7 39.1 1.0 HA A:VAL530 4.7 40.4 1.0 HA A:HIS776 4.8 58.3 1.0 H A:PHE532 4.8 37.9 1.0 N A:VAL529 4.8 38.2 1.0 H A:ASP531 4.8 41.4 1.0 NH1 A:ARG781 4.8 38.0 1.0 O B:HOH1108 4.8 39.5 1.0 H A:VAL529 5.0 46.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba


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 Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:33.5 occ:1.00 O B:GLU527 2.2 35.3 1.0 OE2 B:GLU527 2.3 36.2 1.0 OD1 B:ASP531 2.3 41.4 1.0 O B:HOH1075 2.4 38.4 1.0 O B:VAL530 2.4 37.6 1.0 O B:HOH1060 2.5 36.8 1.0 O B:HOH1038 2.5 40.9 1.0 HA B:ASP531 3.1 42.8 1.0 HG3 B:GLU527 3.2 45.0 1.0 CD B:GLU527 3.2 36.0 1.0 C B:GLU527 3.4 34.5 1.0 C B:VAL530 3.4 43.0 1.0 CG B:ASP531 3.5 41.4 1.0 CG B:GLU527 3.7 37.4 1.0 HH22 B:ARG781 3.8 45.8 1.0 CA B:ASP531 3.8 35.6 1.0 HA B:GLU527 3.8 46.0 1.0 HH12 B:ARG781 4.0 44.7 1.0 N B:ASP531 4.0 39.7 1.0 HA B:SER528 4.0 50.6 1.0 O A:HOH1042 4.1 42.3 1.0 CA B:GLU527 4.1 38.3 1.0 CB B:ASP531 4.2 36.6 1.0 OE1 B:GLU527 4.2 37.6 1.0 H B:VAL530 4.4 44.6 1.0 N B:SER528 4.4 37.0 1.0 C B:SER528 4.4 39.1 1.0 OD2 B:ASP531 4.4 42.8 1.0 N B:VAL530 4.5 37.1 1.0 CA B:SER528 4.5 42.1 1.0 HG2 B:GLU527 4.5 45.0 1.0 CA B:VAL530 4.5 38.2 1.0 CB B:GLU527 4.5 37.9 1.0 NH2 B:ARG781 4.5 38.1 1.0 O B:SER528 4.6 40.8 1.0 O B:HOH1028 4.6 41.0 1.0 HB3 B:ASP531 4.6 44.1 1.0 OE1 A:GLN786 4.6 41.2 1.0 O A:HOH1099 4.7 37.4 1.0 ND1 B:HIS776 4.7 44.9 1.0 H B:PHE532 4.7 39.0 1.0 NH1 B:ARG781 4.7 37.2 1.0 N B:VAL529 4.8 41.8 1.0 HA B:VAL530 4.8 45.9 1.0 H B:ASP531 4.8 47.7 1.0 HA B:HIS776 4.9 51.0 1.0 H B:VAL529 4.9 50.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:85.0 occ:1.00 O A:HOH1107 2.4 59.9 1.0 O A:HOH1001 2.4 50.6 1.0 O B:HOH1002 2.9 60.2 1.0 OD2 B:ASP782 3.0 44.2 1.0 O A:HOH1106 3.7 59.0 1.0 O A:HOH1037 4.0 52.0 1.0 CG B:ASP782 4.0 44.3 1.0 HH21 A:ARG781 4.1 46.3 1.0 O A:HOH1061 4.2 45.1 1.0 O B:HOH1083 4.3 44.4 1.0 OD1 B:ASP782 4.4 39.3 1.0 OD2 A:ASP782 4.5 45.5 1.0 HE A:ARG781 4.5 47.0 1.0 O A:HOH1017 4.6 44.1 1.0 HA2 A:GLY777 4.9 54.0 1.0

C.Heroven, T.Malinauskas, A.R.Aricescu. Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with Gaba To Be Published.