Sodium in PDB 5x2m: Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine

The structure of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine, PDB code: 5x2m 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)	49.89 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.656, 116.355, 129.476, 90.00, 92.20, 90.00
R / Rfree (%)	17.3 / 22.7

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

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine (pdb code 5x2m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine, PDB code: 5x2m:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na961 b:41.9 occ:1.00 O A:HOH1094 2.4 35.2 1.0 O A:LEU88 2.4 46.1 1.0 O A:LEU87 2.5 42.1 1.0 O A:SER84 2.5 35.4 1.0 O A:HOH1077 2.5 29.4 1.0 O A:ILE81 2.6 34.7 1.0 C A:LEU88 3.3 41.5 1.0 C A:ILE81 3.6 32.2 1.0 C A:LEU87 3.7 41.0 1.0 C A:SER84 3.7 32.6 1.0 CB A:LEU88 3.7 30.0 1.0 CA A:LEU88 3.9 38.1 1.0 CA A:ASN82 3.9 35.8 1.0 O A:ASN82 4.0 31.5 1.0 O A:VAL91 4.1 50.9 1.0 C A:ASN82 4.1 37.5 1.0 N A:SER84 4.2 32.3 1.0 N A:PRO89 4.2 41.6 1.0 N A:ASN82 4.2 38.7 1.0 CA A:SER84 4.3 37.5 1.0 N A:LEU88 4.3 39.2 1.0 CB A:SER84 4.3 37.5 1.0 O A:HOH1134 4.3 40.3 1.0 CG2 A:ILE81 4.4 32.5 1.0 CA A:PRO89 4.4 36.2 1.0 O A:HOH1164 4.6 54.5 1.0 OG A:SER84 4.7 37.3 1.0 N A:SER85 4.8 39.8 1.0 CA A:ILE81 4.8 35.4 1.0 N A:ASN90 4.9 47.3 1.0 CA A:LEU87 4.9 36.7 1.0 N A:ASN83 4.9 30.7 1.0 OD1 A:ASN82 4.9 36.9 1.0 C A:PRO89 5.0 38.4 1.0 N A:LEU87 5.0 33.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na961 b:39.9 occ:1.00 O C:HOH1023 2.4 35.4 1.0 O C:HOH1043 2.5 34.6 1.0 O C:LEU87 2.5 40.4 1.0 O C:ILE81 2.5 45.3 1.0 O C:SER84 2.6 43.6 1.0 O C:LEU88 2.8 37.3 1.0 C C:LEU88 3.5 41.0 1.0 C C:ILE81 3.6 41.2 1.0 C C:SER84 3.7 38.2 1.0 C C:LEU87 3.7 39.4 1.0 CA C:ASN82 3.8 37.4 1.0 O C:ASN82 3.8 42.2 1.0 CB C:LEU88 3.9 38.5 1.0 C C:ASN82 4.0 41.3 1.0 N C:SER84 4.1 37.0 1.0 CA C:LEU88 4.1 35.9 1.0 N C:ASN82 4.1 37.4 1.0 CB C:SER84 4.2 36.2 1.0 O C:HOH1094 4.2 54.3 1.0 CA C:SER84 4.2 38.3 1.0 O C:VAL91 4.2 46.8 1.0 N C:LEU88 4.4 40.0 1.0 N C:PRO89 4.4 43.7 1.0 CG2 C:ILE81 4.4 32.5 1.0 CA C:PRO89 4.6 45.5 1.0 OG C:SER84 4.7 44.6 1.0 N C:SER85 4.8 39.4 1.0 CA C:ILE81 4.8 33.2 1.0 N C:ASN83 4.8 38.2 1.0 CA C:LEU87 4.8 42.7 1.0 N C:LEU87 4.9 36.5 1.0 OD1 C:ASN82 4.9 38.1 1.0 N C:ASN90 5.0 56.0 1.0 C C:ASN83 5.0 39.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Glutamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na961 b:60.5 occ:1.00 O D:HOH1041 2.3 59.4 1.0 O D:ILE86 2.4 52.5 1.0 O D:LEU92 2.4 46.3 1.0 O D:ASN89 2.4 54.6 1.0 C D:ILE86 3.4 47.5 1.0 CA D:ASN87 3.5 53.0 1.0 C D:ASN89 3.6 51.5 1.0 O D:ASN87 3.6 58.5 1.0 O D:LEU93 3.6 64.8 1.0 C D:LEU92 3.7 48.1 1.0 C D:ASN87 3.7 59.0 1.0 N D:ASN87 3.9 44.6 1.0 C D:LEU93 4.1 58.5 1.0 N D:ASN89 4.2 50.5 1.0 CA D:ASN89 4.3 51.1 1.0 CG2 D:ILE86 4.4 37.2 1.0 N D:LEU92 4.5 46.7 1.0 N D:ALA88 4.5 53.4 1.0 CB D:ASN89 4.5 53.1 1.0 CA D:LEU92 4.5 46.8 1.0 N D:SER90 4.5 53.6 1.0 N D:LEU93 4.6 49.8 1.0 CB D:LEU93 4.6 53.3 1.0 CA D:SER90 4.6 63.9 1.0 CA D:LEU93 4.7 56.9 1.0 OD1 D:ASN87 4.7 53.7 1.0 CA D:ILE86 4.7 51.3 1.0 CB D:LEU92 4.7 43.1 1.0 N D:PRO94 4.7 64.5 1.0 O D:VAL96 4.7 55.5 1.0 C D:SER90 4.8 67.1 1.0 CB D:ASN87 4.8 50.8 1.0 C D:ALA88 4.9 52.5 1.0 CA D:PRO94 5.0 61.7 1.0

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