Atomistry » Sodium » PDB 5wke-5x2q » 5x2q
Atomistry »
  Sodium »
    PDB 5wke-5x2q »
      5x2q »

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

Go back to Sodium Binding Sites List in 5x2q
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

Go back to Sodium Binding Sites List in 5x2q
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

Go back to Sodium Binding Sites List in 5x2q
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy