Chlorine 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:

Calcium

(Ca)

7 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl905 b:37.9 occ:1.00 HZ2 A:LYS534 2.3 44.9 1.0 HZ2 B:LYS534 2.4 38.1 1.0 O B:HOH1054 2.9 40.2 1.0 HG3 B:LYS534 2.9 39.1 1.0 O A:HOH1067 3.0 37.0 1.0 HG3 A:LYS534 3.1 34.8 1.0 NZ A:LYS534 3.2 37.3 1.0 NZ B:LYS534 3.2 31.7 1.0 HZ1 A:LYS534 3.4 44.9 1.0 HZ3 B:LYS534 3.4 38.1 1.0 HZ3 A:LYS534 3.5 44.9 1.0 HG2 A:LYS534 3.5 34.8 1.0 HZ1 B:LYS534 3.5 38.1 1.0 HD3 A:ARG781 3.6 43.8 1.0 CG A:LYS534 3.7 29.0 1.0 CG B:LYS534 3.8 32.5 1.0 HD3 B:ARG781 3.8 46.4 1.0 HG2 B:LYS534 3.8 39.1 1.0 O B:HOH1082 4.2 37.6 1.0 CE B:LYS534 4.2 35.8 1.0 CE A:LYS534 4.2 37.3 1.0 OG B:SER785 4.3 35.0 1.0 H B:LYS534 4.3 34.7 1.0 O A:HOH1050 4.3 39.7 1.0 HE3 A:LYS534 4.3 44.8 1.0 HD2 A:ARG781 4.3 43.8 1.0 CD A:ARG781 4.3 36.4 1.0 HE3 B:LYS534 4.3 43.0 1.0 H A:LYS534 4.3 32.2 1.0 OG A:SER785 4.4 33.5 1.0 HD2 B:ARG781 4.4 46.4 1.0 HH11 A:ARG781 4.4 48.0 1.0 O A:PHE532 4.4 30.0 1.0 CD B:LYS534 4.5 34.2 1.0 CD B:ARG781 4.5 38.6 1.0 O B:PHE532 4.5 30.8 1.0 HH11 B:ARG781 4.5 46.0 1.0 N B:LYS534 4.5 28.8 1.0 N A:LYS534 4.6 26.8 1.0 CD A:LYS534 4.6 35.4 1.0 HD2 B:LYS534 4.6 41.1 1.0 HA B:LYS534 4.6 38.0 1.0 HA A:LYS534 4.7 31.6 1.0 HG B:SER785 4.7 42.1 1.0 NH1 A:ARG781 4.7 40.0 1.0 NE A:ARG781 4.8 41.9 1.0 NH1 B:ARG781 4.8 38.3 1.0 NE B:ARG781 4.8 42.1 1.0 CB B:LYS534 4.9 32.2 1.0 HB3 B:SER785 4.9 37.0 1.0 HG A:SER785 4.9 40.3 1.0 CZ A:ARG781 4.9 43.9 1.0 CA B:LYS534 4.9 31.6 1.0 CB A:LYS534 4.9 30.6 1.0 HD2 A:LYS534 4.9 42.6 1.0 CA A:LYS534 5.0 26.3 1.0 CZ B:ARG781 5.0 38.0 1.0 HB3 A:SER785 5.0 40.9 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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 B:Cl904 b:34.6 occ:1.00 H B:ARG535 2.4 35.0 1.0 HE B:ARG535 2.6 31.9 1.0 O B:HOH1100 3.0 28.4 1.0 HG2 B:ARG535 3.0 32.6 1.0 O A:HOH1107 3.0 24.3 1.0 HB3 B:ARG535 3.0 30.4 1.0 HA B:LYS534 3.1 38.0 1.0 N B:ARG535 3.2 29.1 1.0 HD13 B:ILE522 3.3 38.0 1.0 NE B:ARG535 3.4 26.5 1.0 HD3 A:LYS534 3.4 42.6 1.0 HG2 A:LYS534 3.5 34.8 1.0 CG B:ARG535 3.6 27.1 1.0 CB B:ARG535 3.6 25.3 1.0 HH21 B:ARG535 3.6 34.5 1.0 HE3 A:LYS534 3.7 44.8 1.0 HB3 A:LYS534 3.7 36.7 1.0 HD12 B:ILE522 3.7 38.0 1.0 HG2 B:LYS534 3.8 39.1 1.0 CA B:LYS534 3.9 31.6 1.0 CD1 B:ILE522 3.9 31.6 1.0 CA B:ARG535 4.0 28.1 1.0 C B:LYS534 4.0 28.8 1.0 HB3 B:LYS534 4.0 38.7 1.0 H A:ARG535 4.0 32.6 1.0 HG2 A:ARG535 4.0 31.4 1.0 CG A:LYS534 4.1 29.0 1.0 CD A:LYS534 4.1 35.4 1.0 CD B:ARG535 4.1 28.1 1.0 HD11 B:ILE522 4.2 38.0 1.0 NH2 B:ARG535 4.3 28.7 1.0 CB A:LYS534 4.3 30.6 1.0 HA A:LYS534 4.3 31.6 1.0 CZ B:ARG535 4.3 28.8 1.0 HE A:ARG535 4.3 30.1 1.0 CE A:LYS534 4.3 37.3 1.0 CB B:LYS534 4.3 32.2 1.0 HG21 B:ILE522 4.4 39.8 1.0 HA B:ARG535 4.5 33.8 1.0 HG3 B:ARG535 4.5 32.6 1.0 CG B:LYS534 4.5 32.5 1.0 HB2 B:ARG535 4.5 30.4 1.0 HA3 B:GLY769 4.6 35.8 1.0 HD2 B:ARG535 4.6 33.8 1.0 O B:SER533 4.8 31.5 1.0 HE2 A:LYS534 4.8 44.8 1.0 NE A:ARG535 4.8 25.1 1.0 N A:ARG535 4.8 27.1 1.0 O A:HOH1015 4.8 34.7 1.0 CA A:LYS534 4.8 26.3 1.0 HD3 B:ARG535 4.9 33.8 1.0 O A:HOH1108 4.9 30.4 1.0 HD2 A:LYS534 5.0 42.6 1.0 HG3 A:LYS534 5.0 34.8 1.0 CG A:ARG535 5.0 26.1 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.