Sodium in PDB 6wo2: Crystal Structure of the GRB2 SH2 Domain in Complex with A Tripeptide: Ac-Py-AC6C-N-Isohexyl

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Tripeptide: Ac-Py-AC6C-N-Isohexyl, PDB code: 6wo2 was solved by S.F.Martin, J.H.Clements, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.48 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.225, 62.720, 90.137, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 27.5

The structure of Crystal Structure of the GRB2 SH2 Domain in Complex with A Tripeptide: Ac-Py-AC6C-N-Isohexyl also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Tripeptide: Ac-Py-AC6C-N-Isohexyl (pdb code 6wo2). 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 Tripeptide: Ac-Py-AC6C-N-Isohexyl, PDB code: 6wo2:

Sodium binding site 1 out of 1 in the Crystal Structure of the GRB2 SH2 Domain in Complex with A Tripeptide: Ac-Py-AC6C-N-Isohexyl


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 Tripeptide: Ac-Py-AC6C-N-Isohexyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:19.3 occ:1.00 O B:HOH301 2.0 30.2 1.0 O B:HOH305 2.3 42.7 1.0 O B:HOH330 2.4 35.2 1.0 NE2 B:HIS58 2.5 41.0 1.0 OE1 B:GLU54 2.5 57.8 1.0 CE1 B:HIS58 2.5 39.9 1.0 OE2 B:GLU54 2.8 60.8 1.0 CD B:GLU54 2.9 59.3 1.0 O B:MET55 3.3 50.7 1.0 ND1 B:HIS58 3.7 37.6 1.0 O A:PHE62 3.7 19.8 1.0 CD2 B:HIS58 3.7 38.4 1.0 O B:LYS56 4.0 40.1 1.0 O B:HOH321 4.2 25.7 0.5 OD1 B:ASN129 4.2 17.8 1.0 CG B:HIS58 4.3 33.9 1.0 CG B:GLU54 4.3 57.5 1.0 C B:MET55 4.4 50.0 1.0 CG2 A:ILE65 4.5 26.4 1.0 C A:PHE62 4.8 18.0 1.0 N B:MET55 4.9 53.1 1.0 N B:GLU54 4.9 55.3 1.0 CA B:MET55 4.9 51.8 1.0

D.L.Cramer, B.Cheng, J.Tian, J.H.Clements, R.M.Wypych, S.F.Martin. Some Thermodynamic Effects of Varying Nonpolar Surfaces in Protein-Ligand Interactions. Eur.J.Med.Chem. V. 208 12771 2020.
ISSN: ISSN 0223-5234
PubMed: 32916312
DOI: 10.1016/J.EJMECH.2020.112771