Sodium in PDB 3ua6: Crystal Structure of the Human Fyn SH3 Domain

All present enzymatic activity of Crystal Structure of the Human Fyn SH3 Domain:
2.7.10.2;

The structure of Crystal Structure of the Human Fyn SH3 Domain, PDB code: 3ua6 was solved by A.Camara-Artigas, J.M.Martin-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.66 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.293, 47.074, 42.467, 90.00, 98.52, 90.00
R / Rfree (%)	17.7 / 24.6

The binding sites of Sodium atom in the Crystal Structure of the Human Fyn SH3 Domain (pdb code 3ua6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Human Fyn SH3 Domain, PDB code: 3ua6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Human Fyn SH3 Domain


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 Human Fyn SH3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na146 b:38.2 occ:1.00 O A:VAL138 2.1 16.9 1.0 O A:HOH14 2.3 34.8 1.0 O A:HOH17 2.4 29.1 1.0 O B:HOH41 2.4 25.2 1.0 O A:SER135 2.8 17.2 1.0 C A:VAL138 3.4 15.2 1.0 C A:SER135 3.9 15.3 1.0 CA A:ASN136 4.0 16.9 1.0 N A:VAL138 4.1 14.3 1.0 O A:HOH33 4.1 27.6 1.0 C A:ASN136 4.2 15.9 1.0 N A:ALA139 4.3 13.3 1.0 CA A:ALA139 4.3 16.2 1.0 O A:ASN136 4.3 17.6 1.0 CA A:VAL138 4.3 13.1 1.0 CE B:LYS108 4.3 38.4 1.0 N A:ASN136 4.4 15.6 1.0 NZ B:LYS108 4.4 39.5 1.0 O B:HOH29 4.5 23.5 1.0 O B:HOH10 4.5 14.9 1.0 CG2 A:VAL138 4.6 15.6 1.0 N A:TYR137 4.8 12.8 1.0 CD1 A:LEU90 5.0 16.2 1.0 CD B:LYS108 5.0 27.9 1.0 CB A:ALA139 5.0 16.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Human Fyn SH3 Domain


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 Human Fyn SH3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na147 b:33.7 occ:1.00 O A:ASP100 2.2 20.3 1.0 O A:HOH40 2.3 37.2 1.0 O A:THR97 2.6 21.4 1.0 O A:HOH21 2.7 23.2 1.0 C A:ASP100 3.4 19.7 1.0 CB A:ALA95 3.4 20.6 1.0 CA A:GLU98 3.7 27.6 1.0 C A:THR97 3.7 24.1 1.0 C A:GLU98 3.8 25.2 1.0 O A:GLU98 3.9 25.4 1.0 CA A:LEU101 4.1 16.9 1.0 N A:GLU98 4.2 26.0 1.0 N A:LEU101 4.2 18.8 1.0 N A:ASP100 4.3 19.1 1.0 CA A:ASP100 4.4 17.4 1.0 N A:ASP99 4.4 23.2 1.0 N A:SER102 4.5 15.2 1.0 OD1 A:ASP100 4.6 19.9 1.0 C A:LEU101 4.7 17.6 1.0 C A:ASP99 4.8 20.4 1.0 O A:HOH47 4.8 41.8 1.0 CA A:ALA95 4.8 18.2 1.0 N A:THR97 4.9 23.3 1.0 CA A:THR97 5.0 22.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Human Fyn SH3 Domain


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 Human Fyn SH3 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:33.7 occ:1.00 O B:HOH44 2.2 27.0 1.0 O B:SER135 2.3 18.8 1.0 O B:HOH5 2.5 21.7 1.0 O B:VAL138 2.5 22.8 1.0 C B:SER135 3.4 18.1 1.0 C B:VAL138 3.7 18.5 1.0 CA B:ASN136 3.9 19.2 1.0 N B:ASN136 4.1 18.1 1.0 CG2 B:VAL138 4.2 18.4 1.0 N B:VAL138 4.3 15.6 1.0 C B:ASN136 4.3 19.3 1.0 CH2 B:TRP120 4.5 25.6 1.0 CA B:SER135 4.5 17.3 1.0 CA B:VAL138 4.5 16.2 1.0 CZ3 B:TRP120 4.6 28.5 1.0 CB B:SER135 4.6 21.1 1.0 O B:ASN136 4.6 18.9 1.0 N B:ALA139 4.6 21.0 1.0 CA B:ALA139 4.7 19.9 1.0 N B:TYR137 4.9 15.9 1.0 OG B:SER135 5.0 22.4 1.0 CB B:VAL138 5.0 14.7 1.0

J.M.Martin-Garcia, I.Luque, J.Ruiz-Sanz, A.Camara-Artigas. The Promiscuous Binding of the Fyn SH3 Domain to A Peptide From the NS5A Protein. Acta Crystallogr.,Sect.D V. 68 1030 2012.
ISSN: ISSN 0907-4449
PubMed: 22868769
DOI: 10.1107/S0907444912019798