Chlorine in PDB 2rc7: Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution

The structure of Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution, PDB code: 2rc7 was solved by Y.Yao, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.892, 97.568, 59.901, 90.00, 93.55, 90.00
R / Rfree (%)	14.8 / 17.7

The structure of Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution (pdb code 2rc7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution, PDB code: 2rc7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom 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 NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl296 b:12.3 occ:0.60 BR A:BR295 0.5 14.0 0.4 O A:HOH400 3.1 24.6 1.0 N A:ALA31 3.5 19.2 1.0 NH1 A:ARG21 3.5 12.2 1.0 C A:CYS29 3.7 16.1 1.0 CA A:CYS29 3.7 17.1 1.0 N A:PRO30 3.8 17.0 1.0 CD A:PRO30 3.8 17.3 1.0 CD A:ARG21 3.9 10.4 1.0 C A:ALA31 4.0 20.8 1.0 N A:GLY32 4.0 19.2 1.0 SG A:CYS67 4.0 15.0 1.0 CA A:ALA31 4.0 19.1 1.0 CB A:CYS67 4.1 12.6 1.0 CB A:ALA31 4.1 19.2 1.0 CB A:CYS29 4.1 14.9 1.0 O A:CYS29 4.3 17.3 1.0 CZ A:ARG21 4.5 12.4 1.0 CG A:ARG21 4.5 10.2 1.0 C A:PRO30 4.5 19.9 1.0 O A:ALA31 4.6 23.2 1.0 NE A:ARG21 4.6 11.4 1.0 CA A:PRO30 4.7 18.6 1.0 CA A:GLY32 4.7 19.1 1.0 CG A:PRO30 4.9 16.6 1.0 CB A:PRO30 5.0 16.8 1.0 SG A:CYS29 5.0 14.8 1.0

Chlorine binding site 2 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom 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 NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl297 b:25.8 occ:1.00 N A:PHE141 3.7 7.7 1.0 O A:HOH442 3.7 39.0 1.0 C A:PHE141 3.8 8.3 1.0 O A:PRO139 3.8 8.4 1.0 O A:PHE141 3.9 8.1 1.0 CA A:PHE141 3.9 8.5 1.0 NZ A:LYS274 3.9 17.4 1.0 C A:PHE140 4.0 9.2 1.0 O A:HOH588 4.1 40.5 1.0 C A:PRO139 4.2 8.0 1.0 CB A:PRO139 4.2 9.4 1.0 CG A:PRO139 4.2 9.9 1.0 N A:SER142 4.2 8.4 1.0 CD A:LYS274 4.3 13.7 1.0 CB A:SER142 4.4 13.5 1.0 O A:PHE140 4.4 9.1 1.0 CA A:PHE140 4.6 7.9 1.0 N A:PHE140 4.6 7.7 1.0 O A:HOH353 4.6 19.9 1.0 CE A:LYS274 4.8 17.5 1.0 O A:HOH497 4.8 26.4 1.0 O A:HOH564 4.8 42.3 1.0 CA A:PRO139 4.9 7.3 1.0 CA A:SER142 4.9 9.8 1.0

Chlorine binding site 3 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom 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 NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl298 b:28.0 occ:1.00 NH1 A:ARG177 2.9 17.0 1.0 NZ A:LYS96 3.1 11.0 1.0 CE A:LYS96 3.6 9.4 1.0 CB A:PRO202 3.6 9.7 1.0 CD A:ARG177 3.7 12.5 1.0 CG A:PRO202 3.9 10.6 1.0 CA A:PRO202 3.9 7.2 1.0 CZ A:ARG177 4.1 14.9 1.0 O A:HOH351 4.3 18.1 1.0 NE A:ARG177 4.4 13.2 1.0 N A:PRO202 4.7 7.5 1.0 O A:HOH527 4.7 42.5 1.0 O A:HOH357 4.8 18.4 1.0 CD A:PRO202 4.9 8.6 1.0 CB A:ARG177 4.9 7.1 1.0 CG A:ARG177 5.0 8.8 1.0

Chlorine binding site 4 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom 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 NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl299 b:36.4 occ:1.00 NE A:ARG152 3.3 21.6 1.0 NH2 A:ARG152 3.7 20.9 1.0 CZ A:ARG152 3.9 21.3 1.0 CG A:ARG152 4.1 19.7 1.0 CD A:ARG152 4.3 20.9 1.0

Chlorine binding site 5 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution


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 NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl295 b:37.7 occ:1.00 NH1 B:ARG21 2.9 22.4 1.0 O B:HOH1002 3.1 27.1 1.0 C B:CYS29 3.3 22.6 1.0 CB B:CYS67 3.4 9.3 1.0 CA B:CYS29 3.5 21.5 1.0 CD B:ARG21 3.5 19.2 1.0 N B:PRO30 3.6 23.3 1.0 N B:ALA31 3.6 22.6 1.0 O B:CYS29 3.7 22.4 1.0 N B:GLY32 3.7 19.3 1.0 SG B:CYS67 3.8 13.4 1.0 CD B:PRO30 3.8 23.5 1.0 CB B:CYS29 3.8 19.7 1.0 CG B:ARG21 3.8 16.2 1.0 C B:ALA31 3.9 21.4 1.0 CZ B:ARG21 3.9 21.0 1.0 CA B:GLY32 4.0 17.6 1.0 NE B:ARG21 4.2 20.7 1.0 O B:ALA31 4.2 23.1 1.0 CA B:ALA31 4.3 22.9 1.0 CA B:PRO30 4.4 24.6 1.0 C B:PRO30 4.4 26.0 1.0 O B:HOH1078 4.6 32.0 1.0 CB B:PRO30 4.6 24.5 1.0 SG B:CYS29 4.7 19.3 1.0 CG B:PRO30 4.7 24.4 1.0 CA B:CYS67 4.8 8.2 1.0 C B:GLY32 4.8 16.4 1.0 N B:CYS29 4.9 22.0 1.0 CB B:ALA31 5.0 23.8 1.0

Chlorine binding site 6 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl296 b:21.2 occ:1.00 NE B:ARG152 3.3 12.4 1.0 NH2 B:ARG152 3.6 12.1 1.0 CZ B:ARG152 3.9 12.6 1.0 CG B:ARG152 4.2 10.4 1.0 CD B:ARG152 4.3 11.4 1.0

Chlorine binding site 7 out of 7 in the Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the NR3A Ligand Binding Core Complex with Glycine at 1.58 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl297 b:25.9 occ:1.00 O A:HOH588 3.4 40.5 1.0 O A:HOH564 3.6 42.3 1.0 N B:PHE141 3.6 5.2 1.0 C B:PHE141 3.7 5.6 1.0 O B:PHE141 3.8 5.4 1.0 O A:HOH442 3.8 39.0 1.0 CA B:PHE141 3.9 6.7 1.0 O B:PRO139 3.9 7.3 1.0 NZ B:LYS274 4.0 15.2 1.0 C B:PHE140 4.0 5.8 1.0 N B:SER142 4.2 5.8 1.0 CB B:PRO139 4.2 6.8 1.0 C B:PRO139 4.2 6.2 1.0 CD B:LYS274 4.2 12.9 1.0 CG B:PRO139 4.3 7.7 1.0 CB B:SER142 4.4 10.9 1.0 O B:PHE140 4.4 7.7 1.0 CA B:PHE140 4.6 4.8 1.0 N B:PHE140 4.6 4.2 1.0 O B:HOH1033 4.7 24.9 1.0 O B:HOH992 4.7 18.6 1.0 CE B:LYS274 4.8 15.9 1.0 CA B:SER142 4.9 7.2 1.0 CA B:PRO139 4.9 6.0 1.0

Y.Yao, C.B.Harrison, P.L.Freddolino, K.Schulten, M.L.Mayer. Molecular Mechanism of Ligand Recognition By NR3 Subtype Glutamate Receptors. Embo J. V. 27 2158 2008.
ISSN: ISSN 0261-4189
PubMed: 18636091
DOI: 10.1038/EMBOJ.2008.140