Chlorine in PDB 1pbq: Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution

The structure of Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution, PDB code: 1pbq was solved by H.Furukawa, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.700, 65.300, 124.300, 90.00, 98.10, 90.00
R / Rfree (%)	23.1 / 27

The binding sites of Chlorine atom in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution (pdb code 1pbq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution, PDB code: 1pbq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution


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 NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:1.3 occ:1.00 CL2 A:DK11001 0.0 1.3 1.0 C8 A:DK11001 1.7 10.9 1.0 C7 A:DK11001 2.7 14.2 1.0 C9 A:DK11001 2.7 12.0 1.0 CE1 A:PHE16 3.4 18.5 1.0 CD1 A:PHE16 3.5 17.7 1.0 CG A:PRO124 3.6 14.5 1.0 CB A:PRO124 3.7 15.9 1.0 OD1 A:ASP224 3.7 18.9 1.0 CZ A:PHE250 3.8 18.0 1.0 CG A:ASP224 3.8 18.7 1.0 OD2 A:ASP224 3.8 17.9 1.0 CG A:GLN13 3.8 13.6 1.0 C6 A:DK11001 4.0 14.3 1.0 C10 A:DK11001 4.0 14.3 1.0 CG2 A:VAL227 4.2 15.9 1.0 CE2 A:PHE250 4.2 17.6 1.0 CD A:GLN13 4.3 14.8 1.0 CZ A:PHE16 4.3 19.6 1.0 NE2 A:GLN13 4.3 16.2 1.0 CE1 A:PHE250 4.5 15.4 1.0 CG A:PHE16 4.6 12.9 1.0 C5 A:DK11001 4.6 13.1 1.0 CB A:ASP224 4.6 17.1 1.0 O A:PRO124 4.9 15.0 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution


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 NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:6.2 occ:1.00 CL1 A:DK11001 0.0 6.2 1.0 C6 A:DK11001 1.7 14.3 1.0 C7 A:DK11001 2.6 14.2 1.0 C5 A:DK11001 2.8 13.1 1.0 O3 A:DK11001 3.0 19.0 1.0 CZ2 A:TRP223 3.2 19.3 1.0 C4 A:DK11001 3.3 16.1 1.0 CE2 A:TRP223 3.4 21.5 1.0 O A:HOH1111 3.6 38.2 1.0 O A:HOH1036 3.6 23.7 1.0 NE1 A:TRP223 3.6 19.9 1.0 O A:HOH1179 3.7 41.2 1.0 CH2 A:TRP223 3.8 21.1 1.0 C8 A:DK11001 3.9 10.9 1.0 OE1 A:GLN13 4.0 15.1 1.0 C10 A:DK11001 4.1 14.3 1.0 O A:HOH1002 4.2 11.8 1.0 CD2 A:TRP223 4.2 18.9 1.0 CB A:ASP224 4.3 17.1 1.0 CD A:GLN13 4.4 14.8 1.0 NE2 A:GLN13 4.5 16.2 1.0 CD1 A:TRP223 4.5 19.4 1.0 C9 A:DK11001 4.5 12.0 1.0 CZ3 A:TRP223 4.6 18.1 1.0 C3 A:DK11001 4.7 15.1 1.0 CE3 A:TRP223 4.8 19.3 1.0 CG A:TRP223 4.9 20.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution


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 NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1002 b:1.3 occ:1.00 CL2 B:DK11002 0.0 1.3 1.0 C8 B:DK11002 1.7 14.1 1.0 C9 B:DK11002 2.7 14.0 1.0 C7 B:DK11002 2.7 13.7 1.0 CE2 B:PHE16 3.3 15.3 1.0 CD2 B:PHE16 3.5 18.3 1.0 CB B:PRO124 3.5 16.0 1.0 CG B:PRO124 3.6 18.7 1.0 CZ B:PHE250 3.7 13.3 1.0 OD1 B:ASP224 3.7 15.0 1.0 CG B:ASP224 3.8 12.9 1.0 CG B:GLN13 3.9 26.1 1.0 OD2 B:ASP224 3.9 16.5 1.0 C6 B:DK11002 4.0 15.9 1.0 C10 B:DK11002 4.0 17.1 1.0 CG2 B:VAL227 4.1 17.4 1.0 CE2 B:PHE250 4.2 16.1 1.0 CZ B:PHE16 4.3 18.3 1.0 CE1 B:PHE250 4.5 18.0 1.0 C5 B:DK11002 4.6 17.2 1.0 CD B:GLN13 4.6 26.2 1.0 CB B:ASP224 4.6 14.5 1.0 CG B:PHE16 4.6 17.9 1.0 O B:PRO124 4.8 16.1 1.0 CA B:PRO124 5.0 17.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution


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 NR1 Ligand Binding Core in Complex with 5,7- Dichlorokynurenic Acid (Dcka) at 1.90 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1002 b:4.2 occ:1.00 CL1 B:DK11002 0.0 4.2 1.0 C6 B:DK11002 1.7 15.9 1.0 C7 B:DK11002 2.6 13.7 1.0 C5 B:DK11002 2.8 17.2 1.0 O3 B:DK11002 3.0 24.4 1.0 CZ2 B:TRP223 3.2 16.2 1.0 CE2 B:TRP223 3.3 15.8 1.0 C4 B:DK11002 3.3 19.4 1.0 O B:HOH1029 3.4 24.3 1.0 NE1 B:TRP223 3.5 13.6 1.0 O B:HOH1016 3.8 27.2 1.0 CH2 B:TRP223 3.9 17.8 1.0 C8 B:DK11002 3.9 14.1 1.0 C10 B:DK11002 4.1 17.1 1.0 CD2 B:TRP223 4.1 14.6 1.0 O B:HOH1004 4.2 15.8 1.0 CB B:ASP224 4.2 14.5 1.0 CD1 B:TRP223 4.3 16.2 1.0 OE1 B:GLN13 4.4 29.7 1.0 C9 B:DK11002 4.5 14.0 1.0 CZ3 B:TRP223 4.6 18.1 1.0 CG B:TRP223 4.7 14.8 1.0 CE3 B:TRP223 4.7 14.4 1.0 C3 B:DK11002 4.7 21.0 1.0 CG2 B:VAL227 4.9 17.4 1.0 N B:ASP224 4.9 12.2 1.0 O B:HOH1159 4.9 38.2 1.0

H.Furukawa, E.Gouaux. Mechanisms of Activation, Inhibition and Specificity: Crystal Structures of the Nmda Receptor NR1 Ligand-Binding Core Embo J. V. 22 2873 2003.
ISSN: ISSN 0261-4189
PubMed: 12805203
DOI: 10.1093/EMBOJ/CDG303