Chlorine in PDB 5x2q: Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine

Protein crystallography data

The structure of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine, PDB code: 5x2q was solved by N.Nuemket, N.Yasui, N.Atsumi, A.Yamashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.517, 112.724, 128.685, 90.00, 92.16, 90.00
R / Rfree (%) 15.4 / 23

Other elements in 5x2q:

The structure of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine (pdb code 5x2q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine, PDB code: 5x2q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5x2q

Go back to Chlorine Binding Sites List in 5x2q
Chlorine binding site 1 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine


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 Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl971

b:46.9
occ:1.00
OG1 B:THR105 3.1 31.3 1.0
N B:SER149 3.3 40.1 1.0
N B:GLN148 3.4 48.5 1.0
CB B:SER149 3.6 33.7 1.0
CD B:PRO45 3.6 38.9 1.0
CB B:GLN148 3.6 37.5 1.0
CG B:MET152 3.7 37.2 1.0
CB B:THR105 3.8 29.7 1.0
CA B:GLN148 3.9 44.0 1.0
CG2 B:THR105 3.9 39.7 1.0
CB B:PRO147 3.9 29.4 1.0
CG B:PRO45 4.0 40.1 1.0
CB B:PRO45 4.0 34.5 1.0
C B:GLN148 4.1 39.3 1.0
N B:PRO45 4.1 37.6 1.0
CA B:SER149 4.1 33.2 1.0
CG B:ARG107 4.2 56.4 1.0
CB B:MET152 4.3 33.4 1.0
C B:PRO147 4.3 42.2 1.0
CA B:PRO45 4.5 36.6 1.0
CA B:PRO147 4.5 33.0 1.0
C B:PHE44 4.6 35.1 1.0
OG B:SER149 4.8 42.0 1.0
CG B:GLN148 4.8 38.4 1.0
CA B:ARG107 4.9 38.3 1.0
CD B:ARG107 4.9 62.7 1.0
NE B:ARG107 4.9 71.7 1.0
N B:ARG107 5.0 37.6 1.0

Chlorine binding site 2 out of 3 in 5x2q

Go back to Chlorine Binding Sites List in 5x2q
Chlorine binding site 2 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine


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 Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl971

b:41.3
occ:1.00
O C:HOH1047 3.0 25.4 1.0
O C:HOH1024 3.0 24.1 1.0
N C:LYS295 3.1 26.9 1.0
CE C:LYS265 3.5 32.9 1.0
ND2 C:ASN294 3.7 27.6 1.0
CA C:ASN294 3.8 22.6 1.0
CG C:ASN294 3.9 30.8 1.0
NZ C:LYS265 3.9 40.7 1.0
C C:ASN294 3.9 19.4 1.0
CB C:LYS295 4.1 26.2 1.0
CB C:ASP362 4.1 29.3 1.0
CA C:LYS295 4.1 28.8 1.0
OD1 C:ASN294 4.3 18.7 1.0
N C:LYS296 4.3 25.2 1.0
CG C:PRO66 4.3 16.7 1.0
CB C:ASN294 4.4 29.4 1.0
CG C:LYS295 4.4 26.6 1.0
CD C:LYS265 4.5 25.8 1.0
O C:HOH1044 4.7 30.1 1.0
C C:LYS295 4.7 21.7 1.0
CD C:PRO66 4.7 21.3 1.0
OD2 C:ASP362 4.7 35.1 1.0
CG C:LYS265 4.8 23.3 1.0
OE2 C:GLU269 4.8 57.2 1.0
O C:LEU293 4.8 22.8 1.0
N C:ASP362 4.8 23.8 1.0
O C:HOH1076 4.9 23.8 1.0
CB C:PRO66 4.9 16.9 1.0
N C:ASN294 4.9 18.8 1.0
CG C:ASP362 4.9 32.5 1.0

Chlorine binding site 3 out of 3 in 5x2q

Go back to Chlorine Binding Sites List in 5x2q
Chlorine binding site 3 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine


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 Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl971

b:43.1
occ:1.00
OG1 D:THR105 3.0 26.8 1.0
N D:GLN148 3.3 26.3 1.0
CD D:PRO45 3.6 20.4 1.0
CG2 D:THR105 3.6 35.4 1.0
CB D:PRO147 3.7 24.1 1.0
CB D:THR105 3.7 28.0 1.0
CB D:GLN148 3.8 23.4 1.0
CB D:PRO45 3.8 23.9 1.0
N D:PRO45 3.8 24.7 1.0
CG D:MET152 3.8 21.5 1.0
N D:SER149 3.8 24.7 1.0
CG D:PRO45 3.9 22.7 1.0
CA D:GLN148 4.0 21.4 1.0
CB D:MET152 4.2 20.7 1.0
C D:PRO147 4.2 24.1 1.0
CA D:PRO45 4.2 25.9 1.0
C D:PHE44 4.2 29.8 1.0
CA D:PRO147 4.3 19.3 1.0
OG D:SER149 4.4 38.5 1.0
C D:GLN148 4.4 24.0 1.0
CB D:SER149 4.6 31.1 1.0
CA D:PHE44 4.7 26.5 1.0
O D:PHE44 4.8 42.8 1.0
CA D:SER149 4.8 27.1 1.0
CG D:PRO147 4.9 27.2 1.0
O D:LEU43 4.9 28.6 1.0

Reference:

N.Nuemket, N.Yasui, Y.Kusakabe, Y.Nomura, N.Atsumi, S.Akiyama, E.Nango, Y.Kato, M.K.Kaneko, J.Takagi, M.Hosotani, A.Yamashita. Structural Basis For Perception of Diverse Chemical Substances By T1R Taste Receptors Nat Commun V. 8 15530 2017.
ISSN: ESSN 2041-1723
PubMed: 28534491
DOI: 10.1038/NCOMMS15530
Page generated: Sat Dec 12 12:38:24 2020

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