Calcium in PDB 8bn2: Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine, PDB code: 8bn2 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)	37.45 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.209, 66.845, 175.901, 90, 90, 90
R / Rfree (%)	18.2 / 21.4

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine 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 D-Serine (pdb code 8bn2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 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 D-Serine, PDB code: 8bn2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


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 D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:36.0 occ:1.00 O A:GLU527 2.3 39.8 1.0 OD1 A:ASP531 2.3 39.5 1.0 OE2 A:GLU527 2.3 33.5 1.0 O A:VAL530 2.4 35.8 1.0 O A:HOH1045 2.4 41.0 1.0 O A:HOH1073 2.5 41.4 1.0 O B:HOH1063 2.6 36.9 1.0 HA A:ASP531 3.1 43.2 1.0 HG3 A:GLU527 3.2 43.8 1.0 CD A:GLU527 3.2 39.6 1.0 C A:VAL530 3.4 36.0 1.0 C A:GLU527 3.4 33.1 1.0 CG A:ASP531 3.5 36.5 1.0 HH22 A:ARG781 3.7 50.5 1.0 CG A:GLU527 3.7 36.5 1.0 HA A:GLU527 3.8 38.9 1.0 CA A:ASP531 3.9 35.9 1.0 HH12 A:ARG781 4.0 48.0 1.0 O B:HOH1077 4.0 43.6 1.0 N A:ASP531 4.0 36.1 1.0 CA A:GLU527 4.1 32.4 1.0 OE1 A:GLU527 4.2 33.1 1.0 HA A:SER528 4.2 46.8 1.0 CB A:ASP531 4.3 38.7 1.0 H A:VAL530 4.4 43.3 1.0 NH2 A:ARG781 4.4 42.1 1.0 OD2 A:ASP531 4.4 42.9 1.0 HG2 A:GLU527 4.4 43.8 1.0 N A:VAL530 4.5 36.1 1.0 N A:SER528 4.5 33.4 1.0 C A:SER528 4.5 41.5 1.0 ND1 A:HIS776 4.5 46.8 1.0 CB A:GLU527 4.5 35.3 1.0 CA A:VAL530 4.5 39.4 1.0 O A:HOH1040 4.6 50.0 1.0 OE1 B:GLN786 4.6 37.7 1.0 CA A:SER528 4.6 38.9 1.0 O A:SER528 4.7 39.8 1.0 HB3 A:ASP531 4.7 46.5 1.0 NH1 A:ARG781 4.7 40.0 1.0 HA A:HIS776 4.8 54.8 1.0 H A:PHE532 4.8 39.0 1.0 N A:VAL529 4.8 36.6 1.0 HA A:VAL530 4.8 47.3 1.0 H A:ASP531 4.9 43.4 1.0 O B:HOH1131 4.9 38.7 1.0 HH21 A:ARG781 4.9 50.5 1.0 H A:VAL529 4.9 44.0 1.0 HE1 A:HIS776 5.0 67.4 1.0 C A:VAL529 5.0 40.7 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


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 D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:83.3 occ:1.00 O B:HOH1112 2.9 58.2 1.0 O B:HOH1014 3.1 52.6 1.0 OD2 A:ASP782 3.1 58.1 1.0 OD2 B:ASP782 3.8 48.0 1.0 O A:HOH1068 3.8 44.2 1.0 CG A:ASP782 4.1 54.7 1.0 OD1 A:ASP782 4.4 43.7 1.0 HH21 B:ARG781 4.4 50.0 1.0 O A:HOH1025 4.5 45.4 1.0 O B:HOH1117 4.5 53.9 1.0 HE A:ARG781 4.6 50.3 1.0 CG B:ASP782 4.7 50.2 1.0 HE B:ARG781 4.7 50.6 1.0 OD1 B:ASP782 4.8 47.3 1.0 O B:HOH1030 4.9 46.9 1.0 HH21 A:ARG781 4.9 50.5 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


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 D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:85.2 occ:1.00 O A:GLY548 2.5 49.1 1.0 C A:GLY548 3.6 51.2 1.0 HA A:THR549 4.1 51.6 1.0 HA3 A:GLY548 4.2 56.4 1.0 HA2 A:GLY548 4.2 56.4 1.0 CA A:GLY548 4.3 46.9 1.0 N A:THR549 4.6 44.7 1.0 HD3 A:PRO664 4.7 48.5 1.0 CA A:THR549 4.8 42.9 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:96.2 occ:1.00 O A:HOH1074 2.6 68.0 1.0 O A:HOH1006 2.7 59.1 1.0 O A:HOH1130 3.1 66.7 1.0 HB A:THR752 4.1 56.7 1.0 OG1 A:THR752 4.4 44.3 1.0 O A:THR752 4.5 47.5 1.0 O A:HOH1021 4.5 43.9 1.0 O A:HOH1016 4.7 64.0 1.0 CB A:THR752 4.7 47.2 1.0 OE1 A:GLU447 4.8 48.0 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:38.7 occ:1.00 O B:GLU527 2.2 43.2 1.0 OE2 B:GLU527 2.3 35.5 1.0 OD1 B:ASP531 2.4 45.5 1.0 O B:VAL530 2.4 45.3 1.0 O B:HOH1019 2.4 43.9 1.0 O B:HOH1043 2.6 45.1 1.0 O B:HOH1109 2.6 47.5 1.0 HA B:ASP531 3.1 49.2 1.0 CD B:GLU527 3.3 40.6 1.0 HG3 B:GLU527 3.3 48.4 1.0 C B:GLU527 3.4 42.5 1.0 C B:VAL530 3.4 44.0 1.0 CG B:ASP531 3.5 45.4 1.0 HH22 B:ARG781 3.7 50.0 1.0 CG B:GLU527 3.8 40.3 1.0 CA B:ASP531 3.8 41.0 1.0 HA B:GLU527 3.8 48.5 1.0 N B:ASP531 4.0 42.2 1.0 HH12 B:ARG781 4.0 46.0 1.0 HA B:SER528 4.1 56.5 1.0 CA B:GLU527 4.1 40.3 1.0 OE1 B:GLU527 4.2 39.2 1.0 O A:HOH1038 4.2 44.0 1.0 CB B:ASP531 4.2 43.8 1.0 H B:VAL530 4.4 55.1 1.0 N B:SER528 4.4 43.5 1.0 OD2 B:ASP531 4.4 49.0 1.0 C B:SER528 4.4 48.4 1.0 N B:VAL530 4.5 45.8 1.0 NH2 B:ARG781 4.5 41.6 1.0 ND1 B:HIS776 4.5 56.4 1.0 CA B:VAL530 4.5 53.9 1.0 CA B:SER528 4.5 47.0 1.0 O B:HOH1004 4.5 47.4 1.0 O B:SER528 4.5 50.8 1.0 CB B:GLU527 4.6 40.1 1.0 HG2 B:GLU527 4.6 48.4 1.0 HB3 B:ASP531 4.7 52.6 1.0 H B:PHE532 4.7 44.9 1.0 OE1 A:GLN786 4.7 45.8 1.0 NH1 B:ARG781 4.7 38.3 1.0 HA B:VAL530 4.8 64.8 1.0 HA B:HIS776 4.8 57.8 1.0 O A:HOH1120 4.8 43.3 1.0 H B:ASP531 4.8 50.7 1.0 N B:VAL529 4.8 45.7 1.0 HE1 B:HIS776 4.8 64.0 1.0 C B:VAL529 5.0 51.6 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:85.2 occ:1.00 O B:HOH1010 2.2 66.9 1.0 O B:HOH1116 2.5 61.9 1.0 O B:GLY548 2.5 45.0 1.0 O B:HOH1135 3.2 62.0 1.0 C B:GLY548 3.5 44.0 1.0 HA2 B:GLY548 3.8 46.9 1.0 CA B:GLY548 4.1 39.0 1.0 HA3 B:GLY548 4.1 46.9 1.0 HA B:THR549 4.3 48.8 1.0 N B:THR549 4.6 36.3 1.0 HD3 B:PRO664 4.6 49.9 1.0 HD2 B:HIS816 4.6 73.3 1.0 CA B:THR549 4.8 40.6 1.0 C B:THR549 4.9 38.7 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1) in Complex with D-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:89.3 occ:1.00 OD2 B:ASP742 3.1 38.8 1.0 HB2 B:ASP742 3.6 33.4 1.0 HE2 B:TYR539 3.7 36.7 1.0 O B:ALA519 3.7 35.2 1.0 HE1 B:TYR770 3.8 35.9 1.0 O B:HOH1129 3.8 66.9 1.0 HB3 B:ALA519 3.8 40.6 1.0 O B:HOH1072 3.9 41.8 1.0 HB1 B:ALA519 4.0 40.6 1.0 CG B:ASP742 4.0 36.9 1.0 O B:HOH1105 4.2 42.5 1.0 CB B:ASP742 4.2 27.8 1.0 HG21 B:VAL745 4.2 36.0 1.0 HH B:TYR770 4.3 36.9 1.0 HB3 B:ASP742 4.3 33.4 1.0 HH B:TYR492 4.4 65.5 1.0 HG23 B:THR521 4.4 40.8 1.0 CB B:ALA519 4.4 33.8 1.0 OH B:TYR492 4.4 54.5 1.0 HG23 B:VAL745 4.5 36.0 1.0 CE2 B:TYR539 4.5 30.5 1.0 O B:HOH1011 4.6 42.9 1.0 CE1 B:TYR770 4.7 29.9 1.0 HE2 B:TYR492 4.7 85.7 1.0 HZ2 B:TRP741 4.7 39.1 1.0 CZ B:TYR492 4.7 62.7 1.0 HE1 B:TRP741 4.7 35.5 1.0 HD2 B:TYR539 4.7 33.3 1.0 OE1 B:GLU446 4.8 66.0 1.0 CE2 B:TYR492 4.8 71.4 1.0 C B:ALA519 4.8 37.4 1.0 CG2 B:VAL745 4.8 29.9 1.0 HG2 B:GLU446 4.8 46.6 1.0 OH B:TYR770 4.9 30.7 1.0 O B:HOH1071 5.0 53.7 1.0 HH B:TYR539 5.0 42.5 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 D-Serine To Be Published.