Chlorine in PDB 8blj: Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State, PDB code: 8blj 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)	62.59 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.29, 107.569, 98.559, 90, 94.08, 90
R / Rfree (%)	20.6 / 24.4

The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State also contains other interesting chemical elements:

Calcium

(Ca)

11 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State (pdb code 8blj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State, PDB code: 8blj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State


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), Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl904 b:32.7 occ:1.00 HZ1 B:LYS534 2.3 27.3 1.0 HZ2 A:LYS534 2.5 34.8 1.0 O B:HOH1025 2.9 25.4 1.0 O A:HOH1048 3.0 28.4 1.0 HG3 B:LYS534 3.0 26.2 1.0 NZ B:LYS534 3.0 22.0 1.0 HZ2 B:LYS534 3.1 27.3 1.0 NZ A:LYS534 3.3 28.2 1.0 HG3 A:LYS534 3.3 29.8 1.0 HZ3 B:LYS534 3.3 27.3 1.0 HZ3 A:LYS534 3.3 34.8 1.0 HZ1 A:LYS534 3.5 34.8 1.0 HD3 B:ARG781 3.6 40.4 1.0 HD3 A:ARG781 3.7 30.9 1.0 CG B:LYS534 3.9 21.1 1.0 HG2 B:LYS534 4.0 26.2 1.0 HG2 A:LYS534 4.1 29.8 1.0 CG A:LYS534 4.1 24.0 1.0 HH11 A:ARG781 4.2 41.8 1.0 CE B:LYS534 4.3 22.5 1.0 HD2 B:ARG781 4.3 40.4 1.0 CD B:ARG781 4.3 32.9 1.0 NH1 A:ARG781 4.4 34.0 1.0 H B:LYS534 4.4 37.5 1.0 O B:PHE532 4.4 30.4 1.0 HH11 B:ARG781 4.4 42.4 1.0 CD A:ARG781 4.5 25.0 1.0 HE3 B:LYS534 4.5 27.9 1.0 OG B:SER785 4.5 25.8 1.0 O A:PHE532 4.5 26.5 1.0 CE A:LYS534 4.5 27.9 1.0 O A:HOH1011 4.5 33.6 1.0 CD B:LYS534 4.6 16.3 1.0 NE B:ARG781 4.6 39.8 1.0 HD2 A:ARG781 4.6 30.9 1.0 OG A:SER785 4.6 29.8 1.0 H A:LYS534 4.6 26.3 1.0 N B:LYS534 4.7 30.5 1.0 NH1 B:ARG781 4.7 34.5 1.0 HE3 A:LYS534 4.7 34.3 1.0 HD2 B:LYS534 4.7 20.5 1.0 CZ A:ARG781 4.7 36.8 1.0 NE A:ARG781 4.7 29.8 1.0 HA B:LYS534 4.7 26.9 1.0 HH12 A:ARG781 4.8 41.8 1.0 HA B:SER533 4.8 35.8 1.0 CZ B:ARG781 4.8 43.0 1.0 N A:LYS534 4.8 21.2 1.0 HA A:LYS534 4.8 23.6 1.0 CD A:LYS534 4.9 26.1 1.0 HG B:SER785 5.0 31.9 1.0 HA A:SER533 5.0 26.2 1.0 CB B:LYS534 5.0 20.6 1.0 HE B:ARG781 5.0 48.7 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State


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), Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl905 b:51.6 occ:1.00 HH22 A:ARG535 2.3 30.1 1.0 HH12 A:ARG535 3.0 24.1 1.0 NH2 A:ARG535 3.2 24.3 1.0 HE22 B:GLN792 3.2 38.9 1.0 OE1 B:GLN792 3.4 47.6 1.0 OG A:SER766 3.6 26.1 1.0 NE2 B:GLN792 3.6 31.6 1.0 O A:SER766 3.6 28.6 1.0 NH1 A:ARG535 3.7 19.3 1.0 HA A:LYS768 3.7 24.5 1.0 HH21 A:ARG535 3.7 30.1 1.0 CD B:GLN792 3.8 37.5 1.0 HG A:SER766 3.8 32.3 1.0 HD2 B:ARG535 3.8 25.4 1.0 OD1 B:ASP538 3.8 24.2 1.0 O A:SER767 3.9 39.9 1.0 CZ A:ARG535 3.9 20.3 1.0 HG3 B:ARG535 4.0 22.3 1.0 C A:SER767 4.0 31.8 1.0 HE21 B:GLN792 4.2 38.9 1.0 N A:LYS768 4.3 22.8 1.0 C A:SER766 4.3 28.6 1.0 HA A:SER767 4.4 32.0 1.0 CA A:LYS768 4.4 19.7 1.0 O B:HOH1001 4.4 23.7 1.0 HH11 A:ARG535 4.5 24.1 1.0 CD B:ARG535 4.6 20.4 1.0 CG B:ASP538 4.6 25.4 1.0 HB2 A:SER766 4.6 29.5 1.0 CA A:SER767 4.6 25.9 1.0 CB A:SER766 4.6 23.8 1.0 CG B:ARG535 4.7 17.8 1.0 OD2 B:ASP538 4.7 21.8 1.0 C A:LYS768 4.7 17.6 1.0 O B:HOH1039 4.7 29.4 1.0 H A:LYS768 4.8 28.2 1.0 O B:HOH1011 4.8 12.8 1.0 N A:SER767 4.8 25.7 1.0 HG2 B:ARG535 4.8 22.3 1.0 HD3 B:ARG535 4.8 25.4 1.0 O A:LYS768 4.9 21.4 1.0 CG B:GLN792 5.0 28.6 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl903 b:49.7 occ:1.00 HZ2 C:LYS534 2.4 63.1 1.0 HZ1 D:LYS534 2.5 48.2 1.0 NZ D:LYS534 3.2 39.4 1.0 NZ C:LYS534 3.2 51.8 1.0 HG3 D:LYS534 3.3 43.1 1.0 HD3 C:ARG781 3.3 59.1 1.0 HZ2 D:LYS534 3.3 48.2 1.0 HG3 C:LYS534 3.3 43.3 1.0 HZ1 C:LYS534 3.4 63.1 1.0 HZ3 D:LYS534 3.4 48.2 1.0 HZ3 C:LYS534 3.5 63.1 1.0 HD3 D:ARG781 3.5 46.5 1.0 HG2 C:LYS534 3.9 43.3 1.0 HH11 C:ARG781 4.0 57.3 1.0 HG2 D:LYS534 4.0 43.1 1.0 CG C:LYS534 4.0 35.3 1.0 CG D:LYS534 4.1 35.2 1.0 HH11 D:ARG781 4.1 60.9 1.0 CD C:ARG781 4.1 48.5 1.0 HD2 C:ARG781 4.2 59.1 1.0 NH1 D:ARG781 4.3 50.0 1.0 CD D:ARG781 4.3 38.0 1.0 NH1 C:ARG781 4.3 47.0 1.0 O C:PHE532 4.4 43.8 1.0 CE C:LYS534 4.4 42.0 1.0 O D:HOH1010 4.4 33.6 1.0 HD2 D:ARG781 4.4 46.5 1.0 CE D:LYS534 4.4 39.4 1.0 O D:PHE532 4.4 38.8 1.0 HE3 C:LYS534 4.5 51.3 1.0 OG C:SER785 4.5 38.7 1.0 NE D:ARG781 4.5 45.3 1.0 NE C:ARG781 4.5 52.1 1.0 CZ D:ARG781 4.5 48.5 1.0 H C:LYS534 4.5 42.1 1.0 CZ C:ARG781 4.6 58.0 1.0 OG D:SER785 4.6 34.0 1.0 HE3 D:LYS534 4.6 48.2 1.0 HH12 D:ARG781 4.6 60.9 1.0 HA C:SER533 4.7 40.0 1.0 H D:LYS534 4.7 45.3 1.0 HH12 C:ARG781 4.7 57.3 1.0 N C:LYS534 4.8 34.3 1.0 CD C:LYS534 4.8 35.1 1.0 CD D:LYS534 4.8 33.3 1.0 HA D:LYS534 4.8 38.2 1.0 N D:LYS534 4.9 37.0 1.0 HG C:SER785 4.9 47.3 1.0 HA C:LYS534 4.9 34.3 1.0 HE D:ARG781 5.0 55.2 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl904 b:47.5 occ:1.00 H C:ARG535 2.2 32.6 1.0 HE C:ARG535 2.6 29.9 1.0 HB3 C:ARG535 2.7 27.6 1.0 N C:ARG535 3.0 26.4 1.0 O C:HOH1037 3.0 22.8 1.0 O D:HOH1032 3.0 17.1 1.0 HA C:LYS534 3.1 34.3 1.0 HG2 C:ARG535 3.1 30.9 1.0 HD12 C:ILE522 3.1 35.7 1.0 CB C:ARG535 3.4 22.2 1.0 NE C:ARG535 3.4 24.2 1.0 HD13 C:ILE522 3.5 35.7 1.0 HG2 D:LYS534 3.5 43.1 1.0 CG C:ARG535 3.7 25.0 1.0 HH21 C:ARG535 3.7 42.9 1.0 CD1 C:ILE522 3.7 29.0 1.0 CA C:ARG535 3.8 22.4 1.0 HE3 D:LYS534 3.8 48.2 1.0 CA C:LYS534 3.9 27.9 1.0 HG2 D:ARG535 3.9 33.3 1.0 C C:LYS534 3.9 30.3 1.0 HD11 C:ILE522 4.0 35.7 1.0 HD3 D:LYS534 4.1 40.9 1.0 HB3 C:LYS534 4.1 37.6 1.0 CD C:ARG535 4.2 26.3 1.0 HG2 C:LYS534 4.2 43.3 1.0 HB3 D:LYS534 4.2 44.2 1.0 HA C:ARG535 4.2 27.8 1.0 H D:ARG535 4.3 31.7 1.0 HB2 C:ARG535 4.3 27.6 1.0 NH2 C:ARG535 4.3 35.0 1.0 CG D:LYS534 4.3 35.2 1.0 CZ C:ARG535 4.3 29.2 1.0 HE D:ARG535 4.4 39.3 1.0 CB C:LYS534 4.5 30.6 1.0 HG21 C:ILE522 4.5 42.5 1.0 CD D:LYS534 4.5 33.3 1.0 HG3 C:ARG535 4.5 30.9 1.0 HA3 C:GLY769 4.6 31.4 1.0 CE D:LYS534 4.6 39.4 1.0 HA D:LYS534 4.6 38.2 1.0 O C:SER533 4.7 38.5 1.0 O D:HOH1005 4.7 27.8 1.0 HD2 C:ARG535 4.7 32.4 1.0 CB D:LYS534 4.7 36.1 1.0 NE D:ARG535 4.8 32.0 1.0 CG D:ARG535 4.8 27.0 1.0 CG C:LYS534 4.8 35.3 1.0 HD3 C:ARG535 4.8 32.4 1.0 HB C:ILE522 4.9 33.0 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl902 b:44.5 occ:1.00 HZ2 F:LYS534 2.1 43.4 1.0 HZ1 E:LYS534 2.6 51.5 1.0 O F:HOH1027 2.8 28.7 1.0 NZ F:LYS534 2.9 35.4 1.0 HZ3 F:LYS534 3.0 43.4 1.0 HG3 F:LYS534 3.1 43.8 1.0 HZ1 F:LYS534 3.1 43.4 1.0 O E:HOH1020 3.3 35.8 1.0 HG3 E:LYS534 3.3 38.6 1.0 NZ E:LYS534 3.4 42.1 1.0 HD3 F:ARG781 3.5 45.0 1.0 HD3 E:ARG781 3.5 55.0 1.0 HZ2 E:LYS534 3.6 51.5 1.0 HZ3 E:LYS534 3.7 51.5 1.0 HG E:SER785 3.7 44.8 1.0 HG2 F:LYS534 3.8 43.8 1.0 CG F:LYS534 3.9 35.7 1.0 HG2 E:LYS534 4.0 38.6 1.0 HH11 E:ARG781 4.0 59.5 1.0 HH11 F:ARG781 4.1 58.2 1.0 CG E:LYS534 4.1 31.4 1.0 CE F:LYS534 4.1 36.9 1.0 O E:PHE532 4.1 41.0 1.0 CD F:ARG781 4.3 36.8 1.0 NH1 E:ARG781 4.3 48.8 1.0 CD E:ARG781 4.3 45.1 1.0 HE3 F:LYS534 4.3 45.2 1.0 HD2 F:ARG781 4.3 45.0 1.0 NH1 F:ARG781 4.4 47.8 1.0 HD2 E:ARG781 4.4 55.0 1.0 OG F:SER785 4.5 31.5 1.0 NE E:ARG781 4.5 41.9 1.0 CZ E:ARG781 4.5 46.1 1.0 CD F:LYS534 4.5 34.4 1.0 OG E:SER785 4.5 36.5 1.0 NE F:ARG781 4.6 36.9 1.0 CE E:LYS534 4.6 38.2 1.0 CZ F:ARG781 4.6 44.4 1.0 HH12 E:ARG781 4.6 59.5 1.0 H E:LYS534 4.6 45.9 1.0 H F:LYS534 4.7 36.1 1.0 O F:PHE532 4.7 29.7 1.0 HE3 E:LYS534 4.7 46.8 1.0 HD2 F:LYS534 4.7 42.2 1.0 HH12 F:ARG781 4.7 58.2 1.0 HA E:SER533 4.7 46.2 1.0 N E:LYS534 4.8 37.5 1.0 HA E:LYS534 4.8 34.4 1.0 HE2 F:LYS534 4.8 45.2 1.0 N F:LYS534 4.8 29.4 1.0 HA F:LYS534 4.8 30.7 1.0 CD E:LYS534 4.9 33.3 1.0 HB3 F:SER785 4.9 25.9 1.0 HG F:SER785 5.0 38.8 1.0 HE E:ARG781 5.0 51.2 1.0

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