Sodium in PDB 3s8o: Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide, PDB code: 3s8o was solved by J.H.Clements, F.M.Stephen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.154, 42.154, 109.513, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 20.1

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide (pdb code 3s8o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide, PDB code: 3s8o:

Sodium binding site 1 out of 1 in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide


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 GRB2 SH2 Domain in Complex with A Pyxn- Derived Tripeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:56.9 occ:1.00 O A:HOH207 2.2 22.1 1.0 O A:HOH191 2.3 22.3 0.5 O A:HOH202 2.4 16.0 0.5 O A:HOH192 2.8 48.2 1.0 NE2 A:HIS135 3.7 14.3 1.0 O A:HOH193 3.9 41.9 1.0 CG2 A:THR138 4.0 13.7 1.0 CE2 A:TYR134 4.1 15.4 1.0 O A:HOH52 4.2 34.6 1.0 CD1 A:TRP121 4.3 18.6 1.0 O A:SER139 4.4 15.9 1.0 OH A:TYR134 4.4 20.3 1.0 CB A:TRP121 4.5 14.9 1.0 O A:HOH29 4.5 21.0 1.0 CD2 A:HIS135 4.5 12.6 1.0 CE1 A:HIS135 4.6 12.6 1.0 CG A:TRP121 4.7 16.1 1.0 CZ A:TYR134 4.8 18.3 1.0 CG2 A:VAL123 4.8 15.2 1.0

J.M.Myslinski, J.E.Delorbe, J.H.Clements, S.F.Martin. Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing Nonpolar Surface Area. J.Am.Chem.Soc. V. 133 18518 2011.
ISSN: ISSN 0002-7863
PubMed: 22007755
DOI: 10.1021/JA2068752