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Sodium in PDB 5x2n: Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Alanine

Protein crystallography data

The structure of Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Alanine, PDB code: 5x2n 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) 49.66 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.372, 117.472, 130.055, 90.00, 91.93, 90.00
R / Rfree (%) 19.5 / 24.4

Other elements in 5x2n:

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

Chlorine (Cl) 2 atoms

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-Alanine (pdb code 5x2n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 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-Alanine, PDB code: 5x2n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5x2n

Go back to Sodium Binding Sites List in 5x2n
Sodium binding site 1 out of 2 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Alanine


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

b:35.1
occ:1.00
O A:LEU87 2.4 38.6 1.0
O A:ILE81 2.5 31.0 1.0
O A:HOH1068 2.5 30.8 1.0
O A:HOH1048 2.5 37.4 1.0
O A:SER84 2.6 33.6 1.0
O A:LEU88 2.8 33.0 1.0
C A:LEU88 3.5 33.0 1.0
C A:LEU87 3.5 38.5 1.0
C A:ILE81 3.6 30.9 1.0
C A:SER84 3.7 33.6 1.0
CB A:LEU88 3.7 33.1 1.0
CA A:ASN82 4.0 33.1 1.0
CA A:LEU88 4.0 33.1 1.0
CB A:SER84 4.1 33.7 1.0
O A:ASN82 4.2 33.0 1.0
N A:SER84 4.2 33.8 1.0
C A:ASN82 4.2 33.1 1.0
CA A:SER84 4.2 33.7 1.0
N A:LEU88 4.2 33.1 1.0
N A:ASN82 4.2 33.2 1.0
O A:HOH1092 4.2 37.3 1.0
CG2 A:ILE81 4.2 30.9 1.0
N A:PRO89 4.4 40.5 1.0
O A:VAL91 4.4 40.6 1.0
OG A:SER84 4.4 33.6 1.0
CA A:ILE81 4.7 31.0 1.0
CA A:PRO89 4.7 40.5 1.0
CA A:LEU87 4.7 38.5 1.0
N A:SER85 4.8 38.6 1.0
N A:LEU87 4.9 38.5 1.0
OD1 A:ASN82 4.9 33.0 1.0
N A:ASN83 5.0 32.8 1.0
CG A:LEU88 5.0 33.2 1.0

Sodium binding site 2 out of 2 in 5x2n

Go back to Sodium Binding Sites List in 5x2n
Sodium binding site 2 out of 2 in the Crystal Structure of the Medaka Fish Taste Receptor T1R2A-T1R3 Ligand Binding Domains in Complex with L-Alanine


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

b:39.1
occ:1.00
O C:HOH1050 2.3 33.8 1.0
O C:LEU87 2.4 33.4 1.0
O C:ILE81 2.5 29.6 1.0
O C:HOH1029 2.6 33.9 1.0
O C:SER84 2.7 32.6 1.0
O C:LEU88 2.8 31.9 1.0
C C:LEU88 3.4 31.8 1.0
C C:LEU87 3.6 33.2 1.0
C C:ILE81 3.6 29.8 1.0
C C:SER84 3.7 32.6 1.0
CB C:LEU88 3.8 31.8 1.0
CA C:ASN82 4.0 29.7 1.0
CA C:LEU88 4.0 31.7 1.0
O C:ASN82 4.0 29.6 1.0
O C:HOH1107 4.1 38.4 1.0
CB C:SER84 4.1 32.6 1.0
C C:ASN82 4.2 29.7 1.0
N C:SER84 4.2 32.8 1.0
CG2 C:ILE81 4.2 29.6 1.0
CA C:SER84 4.2 32.7 1.0
N C:LEU88 4.2 31.7 1.0
N C:ASN82 4.2 29.7 1.0
N C:PRO89 4.3 41.7 1.0
O C:VAL91 4.4 39.8 1.0
CA C:PRO89 4.6 41.8 1.0
OG C:SER84 4.6 32.5 1.0
CA C:ILE81 4.7 29.8 1.0
CA C:LEU87 4.7 33.2 1.0
N C:SER85 4.8 35.6 1.0
OD1 C:ASN82 4.9 29.6 1.0
N C:LEU87 4.9 33.2 1.0
N C:ASN83 5.0 32.4 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 Dec 15 11:48:39 2020

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