Sodium in PDB 5f71: Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3)

The structure of Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3), PDB code: 5f71 was solved by G.F.Gao, G.Lu, H.Wang, J.Qi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.81 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.997, 61.957, 67.152, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.7

The binding sites of Sodium atom in the Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3) (pdb code 5f71). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3), PDB code: 5f71:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na200 b:30.0 occ:1.00 O A:TYR56 2.8 33.6 1.0 O A:TYR61 2.8 25.1 1.0 O A:SER59 3.0 24.0 1.0 OG A:SER59 3.1 20.4 1.0 CD2 A:TRP62 3.3 28.4 1.0 CE2 A:TRP62 3.3 25.9 1.0 CE3 A:TRP62 3.3 21.5 1.0 CZ3 A:TRP62 3.4 26.9 1.0 CZ2 A:TRP62 3.4 24.8 1.0 CH2 A:TRP62 3.4 23.8 1.0 C A:SER59 3.5 25.1 1.0 CE1 A:TYR56 3.6 21.9 1.0 C A:TYR61 3.6 21.7 1.0 CD1 A:TYR56 3.7 25.3 1.0 N A:TYR61 3.8 23.4 1.0 C A:TYR56 3.8 30.7 1.0 N A:SER59 3.9 28.4 1.0 CA A:SER59 3.9 27.1 1.0 CB A:SER59 4.0 23.2 1.0 NE1 A:TRP62 4.0 27.5 1.0 CG A:TRP62 4.0 24.4 1.0 CZ A:TYR56 4.1 22.5 1.0 CG A:TYR56 4.3 24.9 1.0 CA A:TYR61 4.3 22.2 1.0 N A:ARG60 4.3 26.9 1.0 CD1 A:TRP62 4.4 25.4 1.0 C A:ARG60 4.5 29.7 1.0 N A:TRP62 4.5 22.6 1.0 CA A:TYR56 4.5 28.4 1.0 CA A:TRP62 4.7 21.8 1.0 O A:HOH306 4.7 30.7 1.0 CE2 A:TYR56 4.7 25.1 1.0 OH A:TYR56 4.7 20.7 1.0 CD2 A:TYR56 4.7 25.2 1.0 CA A:ARG60 4.8 26.0 1.0 N A:TRP57 4.8 30.9 1.0 C A:TRP57 4.8 27.6 1.0 CA A:TRP57 4.9 29.4 1.0 C A:THR58 4.9 29.0 1.0 CB A:TRP62 4.9 20.0 1.0 N A:THR58 4.9 21.5 1.0

Sodium binding site 2 out of 2 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human T-Cell Immunoglobulin and Mucin Domain Protein 3 (Htim-3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na200 b:30.0 occ:1.00 O B:TYR56 2.8 24.7 1.0 O B:TYR61 2.9 25.6 1.0 OG B:SER59 3.0 24.1 1.0 O B:SER59 3.1 31.4 1.0 CD2 B:TRP62 3.2 38.8 1.0 CE2 B:TRP62 3.2 41.8 1.0 CE3 B:TRP62 3.3 35.6 1.0 CZ2 B:TRP62 3.4 44.9 1.0 C B:TYR61 3.5 28.3 1.0 CZ3 B:TRP62 3.5 41.2 1.0 CH2 B:TRP62 3.5 45.0 1.0 C B:SER59 3.6 27.4 1.0 CE1 B:TYR56 3.8 20.8 1.0 N B:TYR61 3.8 23.2 1.0 CD1 B:TYR56 3.8 25.2 1.0 NE1 B:TRP62 3.8 37.4 1.0 CG B:TRP62 3.8 37.7 1.0 C B:TYR56 3.9 27.0 1.0 CA B:SER59 4.1 29.3 1.0 CB B:SER59 4.1 27.6 1.0 N B:SER59 4.1 26.6 1.0 CD1 B:TRP62 4.2 37.4 1.0 CA B:TYR61 4.2 24.2 1.0 N B:TRP62 4.2 27.9 1.0 CZ B:TYR56 4.3 24.6 1.0 CA B:TRP62 4.3 29.7 1.0 CG B:TYR56 4.4 24.6 1.0 C B:ARG60 4.5 27.3 1.0 N B:ARG60 4.5 23.4 1.0 CA B:TYR56 4.6 30.2 1.0 CB B:TRP62 4.7 30.7 1.0 CE2 B:TYR56 4.8 23.6 1.0 CD2 B:TYR56 4.8 23.5 1.0 OH B:TYR56 4.9 21.0 1.0 CA B:ARG60 4.9 27.7 1.0 N B:TRP57 4.9 33.2 1.0 C B:TRP57 5.0 32.3 1.0 CA B:TRP57 5.0 31.0 1.0

H.Wang, J.X.Qi, N.N.Liu. Crystal Structures of Human Tim Members: Ebolavirus Entry-Enhancing Receptors Chin.Sci.Bull. V. 60 3438 2015.
ISSN: ISSN 1001-6538
DOI: 10.1360/N972015-01255