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Chlorine in PDB 3jpw: Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B

Protein crystallography data

The structure of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpw 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) 28.93 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.975, 142.975, 89.263, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 23.1

Other elements in 3jpw:

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

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb code 3jpw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 3jpw

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Chlorine binding site 1 out of 17 in the Crystal Structure of 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 Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:73.6
occ:1.00
 N A:ILE133 3.4 69.4 1.0
NE2 A:GLN153 3.6 77.6 1.0
N A:LEU261 3.6 84.0 1.0
CG2 A:ILE133 3.6 67.7 1.0
CB A:SER260 3.8 64.3 1.0
CA A:MET132 3.9 64.5 1.0
CB A:LEU261 4.0 78.9 1.0
CG1 A:ILE133 4.1 73.2 1.0
NA A:NA701 4.1 84.9 1.0
OG A:SER260 4.1 72.1 1.0
C A:SER260 4.1 76.4 1.0
CA A:LEU261 4.2 81.8 1.0
C A:MET132 4.2 70.3 1.0
CB A:ILE133 4.2 75.0 1.0
O A:SER131 4.3 68.5 1.0
CA A:ILE133 4.3 71.9 1.0
CA A:SER260 4.3 67.1 1.0
CD A:GLN153 4.4 82.4 1.0
OE1 A:GLN153 4.5 85.4 1.0
N A:SER260 4.5 72.9 1.0
CB A:MET132 4.6 62.6 1.0
CD2 A:LEU261 4.6 71.3 1.0
CD1 A:ILE133 4.7 73.9 1.0
N A:MET132 4.8 62.9 1.0
CG A:LEU261 4.9 79.4 1.0
O A:PRO148 4.9 84.7 1.0
C A:SER131 5.0 66.0 1.0
O A:SER260 5.0 77.9 1.0

Chlorine binding site 2 out of 17 in 3jpw

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Chlorine binding site 2 out of 17 in the Crystal Structure of 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 Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:0.8
occ:1.00
 NH1 A:ARG292 3.1 77.3 1.0
O A:TYR282 3.2 90.8 1.0
OG A:SER131 3.2 72.3 1.0
ND1 A:HIS127 3.6 86.6 1.0
CD2 A:TYR282 3.7 79.7 1.0
CA A:HIS127 3.8 73.8 1.0
C A:TYR282 4.0 93.4 1.0
N A:GLY128 4.0 69.8 1.0
CB A:TYR282 4.1 81.3 1.0
CZ A:ARG292 4.1 79.9 1.0
O A:ILE126 4.2 70.4 1.0
CB A:SER131 4.4 67.5 1.0
CG A:TYR282 4.4 82.7 1.0
NH2 A:ARG292 4.4 81.3 1.0
CG A:HIS127 4.4 82.4 1.0
CB A:HIS127 4.4 82.8 1.0
C A:HIS127 4.4 73.6 1.0
CE1 A:HIS127 4.5 82.7 1.0
CE2 A:TYR282 4.6 81.8 1.0
N A:HIS127 4.7 73.6 1.0
CA A:TYR282 4.7 87.6 1.0
C A:ILE126 4.8 72.9 1.0
N A:ASP283 4.8 92.4 1.0
CA A:ASP283 4.9 90.1 1.0

Chlorine binding site 3 out of 17 in 3jpw

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Chlorine binding site 3 out of 17 in the Crystal Structure of 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 Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:94.3
occ:1.00
 N A:TRP285 3.0 97.1 1.0
N A:ASP286 3.5 90.5 1.0
N A:TYR287 3.6 93.7 1.0
NH2 A:ARG292 3.6 81.3 1.0
N A:GLU284 3.7 95.3 1.0
CA A:GLU284 3.8 94.1 1.0
CA A:TRP285 3.8 97.0 1.0
CB A:TYR287 3.8 83.0 1.0
C A:GLU284 3.8 98.4 1.0
CB A:TRP285 3.9 96.9 1.0
CD1 A:TRP285 4.0 96.8 1.0
C A:TRP285 4.1 0.7 1.0
C A:TYR282 4.2 93.4 1.0
O A:TYR282 4.2 90.8 1.0
CA A:TYR287 4.3 82.3 1.0
O A:TYR287 4.3 89.8 1.0
CA A:TYR282 4.3 87.6 1.0
CG A:TRP285 4.4 98.1 1.0
CA A:ASP286 4.4 95.2 1.0
C A:ASP286 4.5 96.0 1.0
N A:ASP283 4.6 92.4 1.0
CD1 A:TYR282 4.6 81.0 1.0
C A:ASP283 4.6 91.1 1.0
C A:TYR287 4.7 88.1 1.0
CB A:ASP286 4.8 1.0 1.0
O A:LYS361 4.9 88.8 1.0
CE1 A:TYR282 4.9 87.3 1.0
CZ A:ARG292 4.9 79.9 1.0
CG A:TYR282 4.9 82.7 1.0
OD2 A:ASP286 5.0 0.4 1.0
CG2 A:VAL363 5.0 79.5 1.0

Chlorine binding site 4 out of 17 in 3jpw

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Chlorine binding site 4 out of 17 in the Crystal Structure of 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 Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:84.1
occ:0.87
 O A:HOH12 2.9 76.6 1.0
NH1 A:ARG294 3.3 87.0 1.0
NH2 A:ARG294 3.6 88.4 1.0
CZ A:ARG294 3.9 96.8 1.0
CB A:ALA291 3.9 69.9 1.0
N A:ALA291 3.9 75.4 1.0
CB A:PRO290 4.0 77.0 1.0
CA A:ALA291 4.1 80.5 1.0
C A:PRO290 4.3 78.5 1.0
O A:HOH16 4.5 80.6 1.0
O A:PRO290 4.7 80.5 1.0
CA A:PRO290 4.8 82.4 1.0
CG A:PRO290 4.9 74.4 1.0

Chlorine binding site 5 out of 17 in 3jpw

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Chlorine binding site 5 out of 17 in the Crystal Structure of 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 Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:89.6
occ:0.91
 N A:GLN180 3.4 83.2 1.0
N A:GLY178 3.4 73.0 1.0
CB A:GLN180 3.5 89.9 1.0
N A:TYR179 3.7 81.4 1.0
CG A:GLN180 3.7 0.5 1.0
C A:GLY178 3.8 81.9 1.0
NE2 A:GLN180 3.8 0.3 1.0
CD A:GLN180 3.9 0.2 1.0
CA A:GLY178 3.9 71.5 1.0
CA A:GLN180 3.9 86.2 1.0
CD2 A:TYR179 4.1 87.1 1.0
N A:ASP181 4.2 86.3 1.0
CE2 A:TYR179 4.3 89.8 1.0
O A:GLY178 4.3 86.7 1.0
C A:TYR179 4.4 81.0 1.0
C A:PRO177 4.4 78.6 1.0
CA A:TYR179 4.5 84.4 1.0
CA A:PRO177 4.5 73.6 1.0
CG A:TYR179 4.5 90.4 1.0
OE1 A:GLN180 4.6 0.8 1.0
C A:GLN180 4.6 84.1 1.0
CZ A:TYR179 4.9 97.7 1.0
OD2 A:ASP181 4.9 0.1 1.0
CG A:ASP181 5.0 0.5 1.0

Chlorine binding site 6 out of 17 in 3jpw

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Chlorine binding site 6 out of 17 in the Crystal Structure of 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 6 of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:0.4
occ:0.79
 CG A:GLN180 3.0 0.5 1.0
CB A:GLN180 3.1 89.9 1.0
CA A:GLN180 3.4 86.2 1.0
OD1 A:ASN184 3.8 0.1 1.0
ND2 A:ASN184 3.9 91.5 1.0
CD A:GLN180 3.9 0.2 1.0
O A:GLN180 4.1 81.7 1.0
OE1 A:GLN180 4.1 0.8 1.0
CG A:ASN184 4.2 94.7 1.0
C A:GLN180 4.2 84.1 1.0
N A:GLN180 4.6 83.2 1.0
CB A:VAL183 4.7 72.4 1.0
CE1 A:TYR179 4.7 92.0 1.0
CG1 A:VAL183 4.9 76.3 1.0

Chlorine binding site 7 out of 17 in 3jpw

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Chlorine binding site 7 out of 17 in the Crystal Structure of 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 7 of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:93.5
occ:0.69
 N A:ARG375 3.0 82.9 1.0
CG A:ARG375 3.3 95.1 1.0
CA A:GLU374 3.6 89.5 1.0
C A:GLU374 3.7 89.9 1.0
CB A:ARG375 3.8 71.8 1.0
CA A:ARG375 4.0 82.7 1.0
CD A:ARG375 4.0 96.9 1.0
CG A:GLU374 4.0 0.0 1.0
O A:TRP373 4.3 77.2 1.0
CB A:GLU374 4.3 86.3 1.0
CZ3 A:TRP285 4.7 86.2 1.0
N A:GLU374 4.7 86.4 1.0
O A:ARG375 4.8 91.5 1.0
C A:ARG375 4.9 86.6 1.0
C A:TRP373 4.9 86.7 1.0
O A:GLU374 5.0 85.2 1.0

Chlorine binding site 8 out of 17 in 3jpw

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Chlorine binding site 8 out of 17 in the Crystal Structure of 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 8 of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:0.4
occ:1.00
 O A:GLN385 3.2 94.8 1.0
CG A:GLN385 3.7 0.6 1.0
CA A:GLY377 3.9 86.8 1.0
CB A:LYS387 4.0 84.3 1.0
N A:LYS387 4.1 88.5 1.0
C A:GLN385 4.1 93.8 1.0
C A:GLY377 4.1 81.2 1.0
C A:MET386 4.2 95.4 1.0
N A:GLY377 4.2 84.9 1.0
CA A:LYS387 4.2 89.8 1.0
O A:MET386 4.4 0.3 1.0
N A:LYS378 4.4 87.4 1.0
CG A:LYS378 4.4 78.3 1.0
O A:GLY377 4.6 80.4 1.0
CB A:LYS378 4.6 77.2 1.0
CB A:GLN385 4.7 92.7 1.0
CA A:MET386 4.7 95.5 1.0
CD A:GLN385 4.7 0.2 1.0
NE2 A:GLN385 4.7 0.6 1.0
N A:MET386 4.8 94.5 1.0
C A:VAL376 4.9 82.9 1.0

Chlorine binding site 9 out of 17 in 3jpw

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Chlorine binding site 9 out of 17 in the Crystal Structure of 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 9 of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:0.3
occ:0.85
 CG A:MET73 3.7 90.9 1.0
N A:ASN74 3.7 0.2 1.0
CE A:MET73 3.8 79.4 1.0
N A:GLU75 3.8 0.6 1.0
CB A:MET73 3.9 94.4 1.0
CA A:MET73 4.0 94.7 1.0
CB A:GLU75 4.2 0.0 1.0
C A:MET73 4.3 0.4 1.0
CB A:ASN74 4.4 0.8 1.0
SD A:MET73 4.5 91.9 1.0
CD A:ARG84 4.5 87.8 1.0
CA A:ASN74 4.5 0.5 1.0
CG A:GLU75 4.6 0.7 1.0
CA A:GLU75 4.6 99.9 1.0
O A:ALA72 4.6 88.1 1.0
C A:ASN74 4.7 0.8 1.0
NE A:ARG84 4.9 0.4 1.0

Chlorine binding site 10 out of 17 in 3jpw

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Chlorine binding site 10 out of 17 in the Crystal Structure of 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 10 of Crystal Structure of Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:89.5
occ:0.80
 CB A:SER320 2.9 81.9 1.0
N A:ASN323 3.2 96.0 1.0
CA A:SER320 3.4 82.1 1.0
N A:TYR322 3.5 77.0 1.0
CG A:ASN323 3.7 93.7 1.0
ND2 A:ASN323 3.7 95.4 1.0
CB A:TYR322 3.7 79.7 1.0
OG A:SER320 3.7 95.9 1.0
CB A:ASN323 3.8 73.6 1.0
CD1 A:TYR322 3.8 82.3 1.0
N A:CYS321 3.9 81.7 1.0
CA A:TYR322 3.9 81.8 1.0
C A:SER320 3.9 79.2 1.0
CA A:ASN323 4.0 90.3 1.0
C A:TYR322 4.0 86.6 1.0
OD1 A:ASN323 4.2 87.8 1.0
CG A:TYR322 4.3 85.2 1.0
C A:ASN323 4.5 97.2 1.0
O A:ASN323 4.5 98.1 1.0
C A:CYS321 4.6 77.9 1.0
N A:SER320 4.8 83.5 1.0
O A:SER320 4.8 85.8 1.0
CA A:CYS321 4.8 80.6 1.0
O A:SER319 4.9 93.2 1.0
CE1 A:TYR322 4.9 90.1 1.0

Reference:

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
Page generated: Sat Jul 20 22:07:10 2024

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