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Chlorine in PDB 3q41: Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)

Protein crystallography data

The structure of Crystal Structure of the GLUN1 N-Terminal Domain (Ntd), PDB code: 3q41 was solved by A.N.Farina, K.Y.Blain, T.Maruo, W.Kwiatkowski, S.Choe, T.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.24 / 3.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.679, 164.679, 147.258, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 27.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd) (pdb code 3q41). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd), PDB code: 3q41:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3q41

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Chlorine binding site 1 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1

b:90.4
occ:1.00
 ND1 A:HIS146 3.7 59.3 1.0
CE2 A:TYR351 3.9 73.9 1.0
OH A:TYR351 3.9 75.1 1.0
CB A:HIS146 3.9 58.2 1.0
O A:LYS347 4.0 79.0 1.0
CB A:PRO142 4.0 53.7 1.0
CG A:HIS146 4.2 58.7 1.0
CZ A:TYR351 4.4 74.4 1.0
CG A:PRO142 4.5 53.5 1.0
CA A:PHE348 4.6 78.8 1.0
CB A:PHE348 4.7 79.2 1.0
O A:ALA349 4.7 76.6 1.0
CE1 A:HIS146 4.8 59.4 1.0
O A:HIS146 4.8 58.7 1.0
N A:ALA349 4.9 77.8 1.0
CD2 A:TYR351 5.0 74.2 1.0

Chlorine binding site 2 out of 8 in 3q41

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Chlorine binding site 2 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3

b:83.7
occ:1.00
 N A:ASN70 3.1 62.6 1.0
CD A:PRO69 3.3 64.0 1.0
N A:PRO69 3.4 64.0 1.0
CB A:ASN70 3.6 62.2 1.0
CB A:PRO69 3.8 63.8 1.0
CG A:PRO69 3.8 64.0 1.0
CG A:LYS68 3.9 63.7 1.0
CA A:ASN70 3.9 62.0 1.0
C A:LYS68 4.0 64.1 1.0
CA A:PRO69 4.0 63.7 1.0
C A:PRO69 4.0 63.3 1.0
CA A:LYS68 4.1 64.2 1.0
CB A:LYS68 4.1 64.1 1.0
O A:ASN70 4.6 61.3 1.0
C A:ASN70 4.8 61.3 1.0
CB A:GLN73 4.8 57.7 1.0
O A:LYS68 4.8 64.2 1.0
CG A:ASN70 5.0 63.0 1.0

Chlorine binding site 3 out of 8 in 3q41

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Chlorine binding site 3 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl4

b:0.3
occ:1.00
 CB A:PHE197 3.7 74.3 1.0
N A:ASP198 3.7 74.1 1.0
CA A:PHE197 3.7 74.4 1.0
O A:ASN203 4.0 71.3 1.0
CG2 A:THR201 4.2 72.2 1.0
C A:PHE197 4.3 74.3 1.0
OG1 A:THR201 4.6 72.3 1.0
CB A:THR201 4.7 72.2 1.0
CB A:ASP198 4.8 74.4 1.0
O A:GLN196 4.8 75.1 1.0
CA A:ASP198 4.8 74.2 1.0
CG2 A:VAL204 4.9 70.8 1.0
CD2 A:LEU207 4.9 69.1 1.0
N A:PHE197 5.0 74.7 1.0

Chlorine binding site 4 out of 8 in 3q41

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Chlorine binding site 4 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5

b:88.2
occ:1.00
 N2 A:NAG407 4.0 85.8 1.0
NH1 A:ARG212 4.1 72.4 1.0
C8 A:NAG407 4.2 86.5 1.0
CD A:ARG212 4.4 72.2 1.0
CZ A:ARG212 4.4 72.5 1.0
NE A:ARG212 4.5 72.2 1.0
C7 A:NAG407 4.6 86.4 1.0
O A:LEU238 4.9 71.0 1.0
CB A:ASN239 4.9 72.3 1.0
C2 A:NAG407 4.9 85.3 1.0
O A:ASN239 5.0 71.4 1.0
ND2 A:ASN239 5.0 79.0 1.0

Chlorine binding site 5 out of 8 in 3q41

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Chlorine binding site 5 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:84.2
occ:1.00
 N B:ASP198 3.9 76.5 1.0
CB B:PHE197 4.0 76.7 1.0
OG1 B:THR201 4.0 74.6 1.0
CA B:PHE197 4.1 76.8 1.0
O B:ASN203 4.1 74.8 1.0
CG2 B:THR201 4.4 75.0 1.0
C B:PHE197 4.5 76.7 1.0
CB B:THR201 4.6 74.8 1.0
CB B:ASP198 4.8 76.6 1.0
CA B:VAL204 4.9 74.3 1.0
CA B:ASP198 4.9 76.4 1.0

Chlorine binding site 6 out of 8 in 3q41

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Chlorine binding site 6 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl7

b:95.3
occ:1.00
 ND2 B:ASN239 3.6 79.8 1.0
O5 B:NAG407 4.0 84.1 1.0
C1 B:NAG407 4.2 83.0 1.0
NH1 B:ARG212 4.2 73.4 1.0
CB B:ASN239 4.3 74.9 1.0
CG B:ASN239 4.4 76.9 1.0
CZ B:ARG212 4.5 73.8 1.0
O B:ASN239 4.5 74.4 1.0
O B:LEU238 4.7 73.3 1.0
O7 B:NAG407 4.7 84.7 1.0
CD B:ARG212 4.8 74.1 1.0
NE B:ARG212 4.8 73.8 1.0

Chlorine binding site 7 out of 8 in 3q41

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Chlorine binding site 7 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2

b:75.3
occ:0.75
 O C:TYR128 2.8 62.6 1.0
O C:HIS134 3.0 65.3 1.0
O C:ASP130 3.2 64.2 1.0
O C:ILE133 3.3 65.1 1.0
CA C:GLY344 3.5 86.0 1.0
C C:HIS134 3.8 65.3 1.0
O C:SER129 3.8 63.5 1.0
C C:TYR128 4.0 62.4 1.0
C C:SER129 4.0 63.5 1.0
CA C:LEU135 4.1 65.1 1.0
CD2 C:LEU135 4.1 64.9 1.0
C C:ASP130 4.2 64.3 1.0
N C:LEU135 4.3 65.3 1.0
O C:PHE137 4.3 64.1 1.0
CA C:SER129 4.4 63.2 1.0
N C:GLY344 4.4 86.2 1.0
C C:ILE133 4.5 65.2 1.0
N C:ASP130 4.6 63.8 1.0
N C:SER129 4.6 62.8 1.0
CB C:HIS134 4.6 65.4 1.0
CA C:HIS134 4.7 65.4 1.0
C C:GLY344 4.8 85.9 1.0
CG C:LEU135 4.9 65.2 1.0
C C:LEU135 4.9 64.9 1.0
NZ C:LYS322 5.0 82.9 1.0

Chlorine binding site 8 out of 8 in 3q41

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Chlorine binding site 8 out of 8 in the Crystal Structure of the GLUN1 N-Terminal Domain (Ntd)


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 the GLUN1 N-Terminal Domain (Ntd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl8

b:87.8
occ:1.00
 N C:ASP198 3.6 76.1 1.0
CB C:ASP198 3.7 76.2 1.0
OG1 C:THR201 3.9 74.6 1.0
O C:ASN203 4.3 72.5 1.0
CA C:ASP198 4.3 76.0 1.0
CG2 C:THR201 4.3 74.4 1.0
CA C:PHE197 4.5 76.5 1.0
C C:PHE197 4.6 76.3 1.0
CB C:PHE197 4.6 76.2 1.0
CB C:THR201 4.6 74.5 1.0
CG C:ASP198 4.8 76.9 1.0
OD1 C:ASP198 4.9 77.8 1.0

Reference:

A.N.Farina, K.Y.Blain, T.Maruo, W.Kwiatkowski, S.Choe, T.Nakagawa. Separation of Domain Contacts Is Required For Heterotetrameric Assembly of Functional Nmda Receptors. J.Neurosci. V. 31 3565 2011.
ISSN: ISSN 0270-6474
PubMed: 21389213
DOI: 10.1523/JNEUROSCI.6041-10.2011
Page generated: Fri Jul 11 09:17:42 2025

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