Chlorine in PDB 3jpy: Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy was solved by E.Karakas, N.Simorowski, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 3.21
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.368, 143.368, 88.467, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.3

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B also contains other interesting chemical elements:

Zinc	(Zn)	5 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb code 3jpy). 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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:0.1 occ:1.00 NE2 A:GLN153 3.2 0.0 1.0 N A:ILE133 3.5 0.0 1.0 CB A:SER260 3.5 0.5 1.0 CG2 A:ILE133 3.8 0.8 1.0 N A:LEU261 3.8 0.6 1.0 NA A:NA701 3.8 0.1 1.0 OG A:SER260 3.9 0.5 1.0 CG1 A:ILE133 3.9 0.7 1.0 CB A:LEU261 4.0 0.7 1.0 CA A:MET132 4.0 94.0 1.0 C A:SER260 4.2 99.5 1.0 CB A:ILE133 4.2 99.4 1.0 CD A:GLN153 4.2 99.9 1.0 CA A:SER260 4.3 0.2 1.0 CA A:LEU261 4.3 0.1 1.0 C A:MET132 4.3 0.8 1.0 CA A:ILE133 4.4 97.8 1.0 O A:SER131 4.4 1.0 1.0 OE1 A:GLN153 4.5 99.0 1.0 N A:SER260 4.5 99.4 1.0 O A:PRO148 4.7 0.6 1.0 CB A:MET132 4.7 94.5 1.0 CD1 A:ILE133 4.8 0.1 1.0 CD2 A:LEU261 4.8 98.5 1.0 CG A:MET132 4.9 0.3 1.0 CG A:LEU261 5.0 96.4 1.0 CD A:PRO148 5.0 0.2 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:0.3 occ:1.00 NE A:ARG294 3.1 0.8 1.0 NE2 A:HIS60 3.6 0.2 1.0 NH2 A:ARG294 3.9 0.7 1.0 CD A:ARG294 3.9 0.9 1.0 CZ A:ARG294 3.9 0.8 1.0 CG A:ARG294 4.0 0.6 1.0 CD2 A:HIS60 4.1 0.3 1.0 CE1 A:PHE59 4.2 0.6 1.0 CB A:ARG294 4.4 98.4 1.0 CZ A:PHE59 4.8 0.2 1.0 CD1 A:PHE59 4.8 0.8 1.0 CE1 A:HIS60 4.8 1.0 1.0 CA A:ARG294 5.0 96.2 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:0.1 occ:0.68 N A:GLY178 3.2 98.8 1.0 CB A:GLN180 3.2 0.1 1.0 N A:GLN180 3.4 0.1 1.0 C A:GLY178 3.7 0.4 1.0 CA A:GLY178 3.7 0.3 1.0 CA A:GLN180 3.8 0.1 1.0 N A:TYR179 3.9 0.3 1.0 N A:ASP181 3.9 0.3 1.0 O A:GLY178 4.1 0.1 1.0 CD2 A:TYR179 4.2 0.8 1.0 C A:PRO177 4.3 0.7 1.0 CE2 A:TYR179 4.4 0.3 1.0 C A:GLN180 4.4 0.9 1.0 C A:TYR179 4.4 0.0 1.0 CA A:PRO177 4.5 0.4 1.0 CA A:TYR179 4.7 0.9 1.0 CG A:TYR179 4.8 0.4 1.0 CB A:ASP181 5.0 95.3 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:0.6 occ:0.85 N A:GLY377 3.1 0.6 1.0 CA A:GLY377 3.6 0.9 1.0 C A:GLY377 3.6 0.7 1.0 O A:GLY377 3.8 0.7 1.0 C A:VAL376 3.8 0.1 1.0 N A:VAL376 4.1 95.3 1.0 CA A:VAL376 4.2 96.6 1.0 N A:LYS378 4.2 0.8 1.0 C A:ARG375 4.3 97.4 1.0 CB A:LYS387 4.4 0.3 1.0 O A:ARG375 4.5 98.4 1.0 CB A:ARG375 4.5 81.7 1.0 O A:VAL376 4.7 0.7 1.0 CB A:LYS378 4.8 91.2 1.0 O A:GLN385 5.0 0.1 1.0 CA A:ARG375 5.0 94.3 1.0 CA A:LYS378 5.0 0.0 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:0.9 occ:0.76 N A:ASP104 3.2 0.2 1.0 CG A:GLN105 3.9 1.0 1.0 CB A:THR103 3.9 0.2 1.0 CB A:ASP104 3.9 0.4 1.0 CA A:ASP104 4.0 0.8 1.0 CA A:THR103 4.1 0.7 1.0 C A:THR103 4.1 0.7 1.0 C A:ASP104 4.2 0.1 1.0 NE2 A:GLN105 4.4 0.5 1.0 N A:GLN105 4.5 0.9 1.0 CD A:GLN105 4.5 0.3 1.0 OG1 A:THR103 4.7 0.3 1.0 O A:ASP104 4.8 0.3 1.0 CG2 A:THR103 4.9 0.6 1.0

E.Karakas, N.Simorowski, H.Furukawa. Structure of the Zinc-Bound Amino-Terminal Domain of the Nmda Receptor NR2B Subunit. Embo J. V. 28 3910 2009.
ISSN: ISSN 0261-4189
PubMed: 19910922
DOI: 10.1038/EMBOJ.2009.338