Sodium in PDB 5ih2: Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl

The structure of Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl, PDB code: 5ih2 was solved by V.S.Bhatt, D.Zeng, I.Krieger, J.C.Sacchettini, J.-H.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.222, 29.479, 45.756, 90.00, 94.31, 90.00
R / Rfree (%)	17 / 24.3

The binding sites of Sodium atom in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl (pdb code 5ih2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl, PDB code: 5ih2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:28.5 occ:1.00 O A:HOH309 2.4 30.1 1.0 O A:ARG179 2.4 15.3 1.0 O B:HOH335 2.6 33.4 1.0 C A:ARG179 3.6 15.5 1.0 CA A:GLY180 4.1 16.8 1.0 N A:GLY180 4.3 15.7 1.0 OE2 B:GLU176 4.4 31.1 1.0 O A:GLU148 4.4 15.7 1.0 O A:GLU149 4.5 14.2 1.0 O A:ASP150 4.6 14.5 1.0 O A:HOH378 4.6 24.0 1.0 CA A:ARG179 4.7 15.3 1.0 N A:ARG179 4.8 17.1 1.0 C A:GLU149 4.9 14.7 1.0

Sodium binding site 2 out of 4 in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:29.3 occ:1.00 O A:HOH365 2.3 33.2 1.0 O A:ALA134 2.4 23.5 1.0 O A:HOH381 2.4 32.0 1.0 O A:HOH362 2.5 35.6 1.0 O A:HOH351 2.8 24.8 1.0 C A:ALA134 3.6 22.1 1.0 CA A:GLU135 4.2 20.8 1.0 O A:HOH379 4.3 39.5 1.0 N A:GLU135 4.3 21.3 1.0 N A:ALA134 4.6 26.3 1.0 CA A:ALA134 4.7 24.7 1.0 N A:TYR136 4.7 16.4 1.0 O A:HOH307 4.8 34.1 1.0 CD1 A:TYR136 4.9 22.7 1.0 C A:GLU135 5.0 17.7 1.0

Sodium binding site 3 out of 4 in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:15.9 occ:1.00 O M:HOH116 3.1 23.1 1.0 O A:HOH360 3.4 44.2 1.0 NZ A:LYS154 3.4 17.1 1.0 O A:HOH353 3.6 18.9 1.0 N A:ASN144 3.6 15.8 1.0 CA A:ASN144 3.7 16.8 1.0 C A:PHE143 3.8 15.9 1.0 CB A:ASP142 3.9 17.9 1.0 CB A:ASN144 3.9 17.3 1.0 O A:PHE143 4.1 16.5 1.0 N A:PHE143 4.2 15.2 1.0 O A:HOH316 4.3 25.6 1.0 OD1 A:ASN144 4.3 20.6 1.0 CA A:PHE143 4.5 15.4 1.0 O A:HOH361 4.5 26.3 1.0 C A:ASP142 4.6 16.1 1.0 CE A:LYS154 4.6 17.9 1.0 CG A:ASN144 4.6 20.1 1.0 OD2 A:ASP142 4.6 19.5 1.0 CG A:ASP142 4.7 19.8 1.0 CA A:ASP142 4.8 15.9 1.0 O A:HOH325 4.9 33.6 1.0 CD A:LYS154 4.9 18.2 1.0 O A:PHE153 5.0 15.4 1.0

Sodium binding site 4 out of 4 in the Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure, Thermodynamics, and the Role of Conformational Dynamics in the Interactions Between the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:18.7 occ:1.00 O B:HOH324 2.2 30.0 1.0 O B:HOH319 2.3 25.9 1.0 O B:GLY145 2.4 20.5 1.0 O B:ASP147 2.4 18.6 1.0 O B:ASP150 2.5 17.5 1.0 C B:ASP147 3.4 22.1 1.0 C B:GLY145 3.5 19.0 1.0 C B:ASP150 3.6 16.1 1.0 CA B:GLU148 3.7 23.7 0.5 O B:GLU148 3.7 24.7 0.5 O B:GLU148 3.8 23.9 0.5 C B:GLU148 3.8 23.6 0.5 C B:GLU148 3.9 23.2 0.5 CA B:GLU148 3.9 23.0 0.5 N B:ASP150 3.9 17.1 1.0 N B:GLU148 4.0 22.0 0.5 N B:GLU148 4.0 21.5 0.5 CD B:PRO152 4.1 15.4 1.0 C B:ASN146 4.1 22.7 1.0 CG B:PRO152 4.1 15.7 1.0 CA B:ASP150 4.1 16.4 1.0 O B:ASN146 4.2 22.2 1.0 N B:ASP147 4.2 20.9 1.0 O B:HOH317 4.3 36.1 1.0 CA B:GLY145 4.4 16.7 1.0 CA B:ASN146 4.4 21.9 1.0 N B:ASN146 4.4 20.0 1.0 CB B:ASP150 4.4 17.6 1.0 O B:HOH341 4.5 33.1 1.0 OE1 B:GLU148 4.5 22.2 0.5 CA B:ASP147 4.5 22.5 1.0 N B:GLU149 4.6 20.4 1.0 O B:HOH350 4.6 80.3 1.0 N B:LEU151 4.7 15.1 1.0 NZ B:LYS178 4.8 45.9 0.5 N B:PRO152 4.8 15.8 1.0 CD B:GLU148 4.9 25.6 0.5 C B:GLU149 4.9 17.6 1.0 CB B:GLU148 5.0 25.8 0.5 CA B:LEU151 5.0 14.2 1.0

V.S.Bhatt, D.Zeng, I.Krieger, J.C.Sacchettini, J.H.Cho. Binding Mechanism of the N-Terminal SH3 Domain of Crkii and Proline-Rich Motifs in Cabl. Biophys.J. V. 110 2630 2016.
ISSN: ESSN 1542-0086
PubMed: 27332121
DOI: 10.1016/J.BPJ.2016.05.008