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Sodium in PDB 5x2o: Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine

Protein crystallography data

The structure of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine, PDB code: 5x2o 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) 49.42 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.905, 113.677, 128.636, 90.00, 92.23, 90.00
R / Rfree (%) 18.5 / 27.2

Other elements in 5x2o:

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

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

Sodium Binding Sites:

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-Arginine (pdb code 5x2o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 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-Arginine, PDB code: 5x2o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5x2o

Go back to Sodium Binding Sites List in 5x2o
Sodium binding site 1 out of 5 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine


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-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na961

b:34.8
occ:1.00
 O A:HOH1017 2.4 36.6 1.0
O A:ILE81 2.6 28.3 1.0
O A:SER84 2.6 52.8 1.0
O A:LEU88 2.6 44.5 1.0
O A:LEU87 2.8 37.7 1.0
O A:ASN82 3.6 30.1 1.0
C A:LEU88 3.6 45.6 1.0
C A:ILE81 3.6 37.0 1.0
C A:SER84 3.7 48.9 1.0
CA A:ASN82 3.8 28.2 1.0
C A:ASN82 3.9 29.4 1.0
O A:HOH1028 4.0 47.0 1.0
C A:LEU87 4.0 38.9 1.0
N A:SER84 4.0 42.9 1.0
O A:VAL91 4.1 39.7 1.0
N A:ASN82 4.1 36.1 1.0
CB A:LEU88 4.2 37.8 1.0
CA A:SER84 4.3 44.8 1.0
CA A:LEU88 4.4 39.4 1.0
CG2 A:ILE81 4.4 26.4 1.0
N A:PRO89 4.5 46.6 1.0
CB A:SER84 4.6 34.1 1.0
CA A:PRO89 4.7 37.0 1.0
N A:LEU88 4.7 41.1 1.0
OD1 A:ASN82 4.8 28.7 1.0
N A:ASN83 4.8 29.6 1.0
N A:ASN90 4.8 53.3 1.0
CA A:ILE81 4.9 30.9 1.0
N A:SER85 4.9 44.0 1.0
OG A:SER84 4.9 34.0 1.0
C A:VAL91 5.0 35.8 1.0

Sodium binding site 2 out of 5 in 5x2o

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Sodium binding site 2 out of 5 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine


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-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na962

b:60.0
occ:1.00
 O A:HOH1001 2.4 48.4 1.0
O A:TYR175 2.5 33.1 1.0
O A:ASN423 2.6 62.9 1.0
O A:PHE178 2.8 37.4 1.0
C A:ASN423 3.7 48.5 1.0
C A:TYR175 3.7 31.3 1.0
CA A:GLU172 3.8 59.0 1.0
C A:PHE178 3.9 36.5 1.0
O A:PHE169 3.9 41.7 1.0
CB A:GLU172 4.0 61.8 1.0
CG A:GLU172 4.0 63.5 1.0
N A:PHE178 4.3 27.3 1.0
CB A:PHE178 4.3 37.0 1.0
CA A:PHE178 4.4 37.7 1.0
O A:PRO176 4.5 45.6 1.0
CB A:TYR175 4.5 23.3 1.0
N A:GLY424 4.5 41.9 1.0
CA A:GLY424 4.6 40.6 1.0
CA A:ASN423 4.6 35.0 1.0
N A:PRO176 4.6 41.4 1.0
C A:PRO176 4.6 36.7 1.0
CA A:PRO176 4.6 41.1 1.0
O A:GLU172 4.6 59.2 1.0
N A:GLU172 4.6 59.0 1.0
CA A:TYR175 4.7 40.2 1.0
C A:GLU172 4.8 50.2 1.0
N A:LEU179 5.0 31.3 1.0

Sodium binding site 3 out of 5 in 5x2o

Go back to Sodium Binding Sites List in 5x2o
Sodium binding site 3 out of 5 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine


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-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na961

b:37.4
occ:1.00
 O C:ILE81 2.5 27.8 1.0
O C:LEU88 2.5 41.2 1.0
O C:SER84 2.6 39.6 1.0
O C:LEU87 2.8 35.8 1.0
O C:ASN82 3.5 29.6 1.0
C C:ILE81 3.6 29.7 1.0
C C:LEU88 3.6 36.2 1.0
CA C:ASN82 3.6 33.2 1.0
C C:ASN82 3.7 28.8 1.0
C C:SER84 3.7 36.7 1.0
N C:ASN82 4.0 34.7 1.0
C C:LEU87 4.0 32.9 1.0
N C:SER84 4.0 33.6 1.0
O C:VAL91 4.1 33.5 1.0
CB C:LEU88 4.2 28.8 1.0
CA C:SER84 4.3 30.4 1.0
CA C:LEU88 4.4 28.6 1.0
CB C:SER84 4.4 31.1 1.0
N C:PRO89 4.5 43.4 1.0
CG2 C:ILE81 4.6 26.8 1.0
CA C:PRO89 4.6 36.0 1.0
N C:ASN83 4.6 28.1 1.0
N C:LEU88 4.7 28.5 1.0
N C:ASN90 4.8 46.0 1.0
OD1 C:ASN82 4.8 31.4 1.0
CA C:ILE81 4.8 28.4 1.0
N C:SER85 4.8 36.2 1.0
C C:ASN83 4.9 41.0 1.0
CB C:ASN82 5.0 45.2 1.0
C C:VAL91 5.0 29.0 1.0

Sodium binding site 4 out of 5 in 5x2o

Go back to Sodium Binding Sites List in 5x2o
Sodium binding site 4 out of 5 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na962

b:54.4
occ:1.00
 O C:ASN423 2.4 38.9 1.0
O C:PHE169 2.4 29.5 1.0
O C:PHE178 2.6 27.1 1.0
C C:ASN423 3.5 38.4 1.0
C C:PHE169 3.6 33.5 1.0
O C:TYR175 3.7 35.9 1.0
C C:PHE178 3.7 29.0 1.0
CB C:PHE178 4.2 28.0 1.0
CD1 C:PHE178 4.3 18.9 1.0
CA C:GLY424 4.3 30.0 1.0
N C:GLY424 4.3 39.2 1.0
CA C:SER170 4.3 23.4 1.0
CA C:ASN423 4.4 34.8 1.0
N C:SER170 4.4 29.5 1.0
CA C:PHE178 4.4 26.9 1.0
CB C:TYR175 4.6 24.1 1.0
C C:SER170 4.6 28.5 1.0
C C:GLY424 4.7 30.3 1.0
CA C:PHE169 4.7 34.9 1.0
N C:PHE178 4.7 26.8 1.0
N C:LEU179 4.7 19.5 1.0
CB C:ASN423 4.7 42.0 1.0
CG C:PHE178 4.7 19.2 1.0
C C:TYR175 4.8 30.9 1.0
CA C:LEU179 4.9 22.7 1.0
N C:LYS171 4.9 28.5 1.0
O C:GLY424 4.9 20.3 1.0
CB C:PHE169 4.9 33.3 1.0
OE1 C:GLU172 4.9 83.2 1.0

Sodium binding site 5 out of 5 in 5x2o

Go back to Sodium Binding Sites List in 5x2o
Sodium binding site 5 out of 5 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na961

b:37.6
occ:1.00
 O D:LEU92 2.3 40.6 1.0
O D:ASN89 2.4 52.9 1.0
O D:ILE86 2.6 35.5 1.0
O D:LEU93 3.3 42.4 1.0
C D:LEU92 3.5 48.5 1.0
C D:ASN89 3.5 42.8 1.0
O D:ASN87 3.5 35.5 1.0
CA D:ASN87 3.7 42.3 1.0
C D:ILE86 3.7 30.6 1.0
C D:LEU93 3.8 39.3 1.0
C D:ASN87 3.8 46.6 1.0
N D:ASN87 4.2 32.0 1.0
CB D:LEU93 4.3 45.4 1.0
N D:LEU93 4.3 54.4 1.0
CA D:LEU93 4.4 33.5 1.0
N D:LEU92 4.4 48.6 1.0
CA D:SER90 4.4 40.9 1.0
N D:SER90 4.4 43.0 1.0
CA D:LEU92 4.4 43.7 1.0
CA D:ASN89 4.5 45.1 1.0
N D:PRO94 4.5 44.5 1.0
OD1 D:ASN87 4.6 34.8 1.0
N D:ASN89 4.6 49.5 1.0
O D:VAL96 4.6 35.3 1.0
C D:SER90 4.6 61.9 1.0
CB D:ASN89 4.7 42.8 1.0
CG2 D:ILE86 4.7 32.6 1.0
CA D:PRO94 4.7 51.1 1.0
N D:ALA88 4.8 46.8 1.0
CB D:LEU92 4.9 42.1 1.0
O D:SER90 4.9 65.3 1.0
CB D:ASN87 5.0 36.0 1.0
CA D:ILE86 5.0 29.9 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: Tue Oct 8 01:08:10 2024

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