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Sodium 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:

Chlorine (Cl) 3 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 Glycine (pdb code 5x2q). 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 Glycine, PDB code: 5x2q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5x2q

Go back to Sodium Binding Sites List in 5x2q
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 Glycine


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

b:35.2
occ:1.00
 O A:ILE81 2.4 23.6 1.0
O A:LEU87 2.5 41.2 1.0
O A:SER84 2.5 35.2 1.0
O A:HOH1018 2.6 27.8 1.0
O A:HOH1056 2.6 29.5 1.0
O A:LEU88 2.8 30.4 1.0
C A:ILE81 3.5 23.4 1.0
C A:SER84 3.5 25.3 1.0
C A:LEU88 3.6 30.9 1.0
C A:LEU87 3.7 32.2 1.0
O A:ASN82 3.7 41.1 1.0
CA A:ASN82 3.8 21.3 1.0
C A:ASN82 3.8 31.2 1.0
N A:SER84 3.9 22.7 1.0
CA A:SER84 4.0 23.2 1.0
CB A:SER84 4.0 22.6 1.0
N A:ASN82 4.1 20.7 1.0
CB A:LEU88 4.1 26.1 1.0
CA A:LEU88 4.2 26.3 1.0
CG2 A:ILE81 4.3 20.7 1.0
N A:LEU88 4.4 31.6 1.0
O A:VAL91 4.5 26.9 1.0
N A:PRO89 4.5 29.6 1.0
OG A:SER84 4.5 32.8 1.0
CA A:ILE81 4.7 20.6 1.0
N A:ASN83 4.7 22.0 1.0
CA A:PRO89 4.7 28.2 1.0
N A:SER85 4.7 24.7 1.0
CA A:LEU87 4.8 26.9 1.0
C A:ASN83 4.9 25.4 1.0
OD1 A:ASN82 4.9 31.1 1.0
N A:LEU87 4.9 25.8 1.0

Sodium binding site 2 out of 5 in 5x2q

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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 Glycine


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

b:54.2
occ:1.00
 O A:ASN423 2.7 43.1 1.0
O A:PHE178 2.7 38.7 1.0
O A:TYR175 2.7 25.2 1.0
O A:PHE169 3.2 43.0 1.0
CD A:GLU172 3.4 74.0 1.0
OE1 A:GLU172 3.4 79.6 1.0
OE2 A:GLU172 3.4 78.8 1.0
C A:ASN423 3.8 29.8 1.0
C A:PHE178 3.8 31.3 1.0
C A:TYR175 3.9 32.4 1.0
CB A:PHE178 4.2 21.8 1.0
CG A:GLU172 4.2 61.1 1.0
CA A:GLU172 4.3 44.3 1.0
CB A:TYR175 4.3 22.7 1.0
CA A:PHE178 4.4 26.3 1.0
C A:PHE169 4.4 34.4 1.0
N A:PHE178 4.4 30.2 1.0
N A:GLU172 4.5 47.8 1.0
O A:LYS171 4.6 48.8 1.0
CA A:GLY424 4.6 37.0 1.0
N A:GLY424 4.6 30.4 1.0
C A:LYS171 4.6 47.3 1.0
CA A:TYR175 4.7 28.1 1.0
CA A:ASN423 4.7 31.6 1.0
CD1 A:PHE178 4.8 26.3 1.0
CB A:GLU172 4.8 47.5 1.0
C A:SER170 4.8 30.6 1.0
N A:PRO176 4.9 36.5 1.0
N A:LEU179 4.9 23.7 1.0
N A:LYS171 5.0 28.2 1.0

Sodium binding site 3 out of 5 in 5x2q

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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 Glycine


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

b:37.4
occ:1.00
 O C:ILE81 2.5 20.2 1.0
O C:HOH1055 2.6 19.0 1.0
O C:HOH1023 2.6 29.7 1.0
O C:LEU87 2.6 23.6 1.0
O C:LEU88 2.6 44.0 1.0
O C:SER84 2.6 44.0 1.0
C C:LEU88 3.4 38.4 1.0
C C:ILE81 3.5 19.3 1.0
C C:SER84 3.7 22.6 1.0
O C:HOH1058 3.7 37.8 1.0
C C:LEU87 3.8 23.9 1.0
CA C:ASN82 3.8 19.8 1.0
O C:ASN82 3.8 25.9 1.0
C C:ASN82 3.9 20.6 1.0
CB C:LEU88 3.9 26.7 1.0
N C:ASN82 4.0 19.2 1.0
N C:SER84 4.1 28.4 1.0
CA C:LEU88 4.1 34.7 1.0
CA C:SER84 4.2 21.9 1.0
N C:PRO89 4.3 33.8 1.0
O C:VAL91 4.3 26.4 1.0
CB C:SER84 4.3 21.2 1.0
CG2 C:ILE81 4.3 18.5 1.0
N C:LEU88 4.4 25.5 1.0
CA C:PRO89 4.6 31.9 1.0
CA C:ILE81 4.7 18.7 1.0
N C:ASN83 4.7 20.5 1.0
N C:SER85 4.8 23.5 1.0
OD1 C:ASN82 4.8 28.4 1.0
OG C:SER84 4.8 21.9 1.0
CA C:LEU87 5.0 24.6 1.0
C C:ASN83 5.0 27.5 1.0

Sodium binding site 4 out of 5 in 5x2q

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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 Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na962

b:35.4
occ:1.00
 O C:HOH1002 2.5 30.1 1.0
OE1 C:GLU172 2.6 73.7 1.0
O C:PHE169 2.6 22.5 1.0
O C:ASN423 2.8 28.1 1.0
O C:TYR175 3.0 36.0 1.0
O C:PHE178 3.1 26.7 1.0
CD C:GLU172 3.5 74.4 1.0
C C:ASN423 3.8 27.6 1.0
C C:PHE169 3.8 25.5 1.0
OE2 C:GLU172 4.1 68.6 1.0
C C:TYR175 4.1 30.7 1.0
CA C:GLU172 4.2 30.8 1.0
N C:GLU172 4.2 28.0 1.0
C C:SER170 4.2 31.4 1.0
CB C:TYR175 4.2 25.8 1.0
C C:PHE178 4.2 19.4 1.0
C C:LYS171 4.2 36.3 1.0
O C:LYS171 4.3 37.6 1.0
CA C:SER170 4.3 21.8 1.0
N C:LYS171 4.4 34.3 1.0
CA C:ASN423 4.5 23.9 1.0
O C:SER170 4.5 34.6 1.0
N C:SER170 4.6 21.8 1.0
CG C:GLU172 4.6 63.8 1.0
CB C:PHE178 4.6 18.7 1.0
N C:GLY424 4.7 25.6 1.0
CB C:GLU172 4.7 31.7 1.0
CA C:TYR175 4.7 27.8 1.0
CA C:PHE178 4.8 17.4 1.0
N C:PHE178 4.8 20.8 1.0
CA C:PHE169 4.9 28.9 1.0
CA C:GLY424 4.9 23.8 1.0
CB C:ASN423 4.9 23.1 1.0
CD1 C:PHE178 4.9 25.8 1.0
CA C:LYS171 4.9 36.8 1.0

Sodium binding site 5 out of 5 in 5x2q

Go back to Sodium Binding Sites List in 5x2q
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 Glycine


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 Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na961

b:34.9
occ:1.00
 O D:HOH635 2.4 35.9 1.0
O D:ASN89 2.4 44.3 1.0
O D:LEU92 2.5 28.8 1.0
O D:HOH640 2.5 35.8 1.0
O D:ILE86 2.7 36.8 1.0
C D:ASN89 3.4 38.1 1.0
O D:LEU93 3.6 40.3 1.0
O D:ASN87 3.6 38.6 1.0
C D:LEU92 3.7 35.3 1.0
CA D:ASN87 3.8 30.1 1.0
C D:ILE86 3.8 35.7 1.0
C D:ASN87 3.9 32.2 1.0
C D:LEU93 4.1 34.5 1.0
N D:SER90 4.1 38.4 1.0
CA D:SER90 4.2 40.5 1.0
N D:ASN89 4.2 34.6 1.0
CA D:ASN89 4.3 33.8 1.0
N D:ASN87 4.3 23.2 1.0
N D:LEU92 4.4 32.5 1.0
CA D:LEU92 4.5 34.9 1.0
C D:SER90 4.5 39.3 1.0
N D:LEU93 4.6 34.7 1.0
O D:VAL96 4.6 47.4 1.0
CB D:LEU93 4.6 27.0 1.0
CB D:ASN89 4.7 28.4 1.0
CA D:LEU93 4.7 27.8 1.0
N D:PRO94 4.7 40.0 1.0
N D:ALA88 4.8 35.0 1.0
CA D:PRO94 4.8 40.8 1.0
CG2 D:ILE86 4.8 27.1 1.0
OD1 D:ASN87 4.8 28.4 1.0
CB D:LEU92 4.9 29.5 1.0
C D:ALA88 4.9 33.8 1.0
O D:HOH650 4.9 45.9 1.0
O D:SER90 4.9 49.0 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 01:08:19 2024

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