Sodium in PDB 3op0: Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide

The structure of Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide, PDB code: 3op0 was solved by A.Chaikuad, K.Guo, C.D.O.Cooper, V.Ayinampudi, T.Krojer, E.Ugochukwu, J.R.C.Muniz, M.Vollmar, P.Canning, F.Von Delft, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, C.Bountra, A.Bullock, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 2.52
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	90.250, 90.250, 191.581, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 26.6

The structure of Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide (pdb code 3op0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide, PDB code: 3op0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide


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 Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:18.2 occ:1.00 OE2 A:GLU210 2.3 22.7 1.0 OD1 A:ASP199 2.3 21.2 1.0 OG1 A:THR201 2.3 24.1 1.0 O A:HIS205 2.3 23.0 1.0 OG A:SER203 2.3 25.0 1.0 O A:HOH331 2.6 23.8 1.0 OE1 A:GLU210 2.9 21.9 1.0 CD A:GLU210 2.9 21.1 1.0 CG A:ASP199 3.4 22.0 1.0 CB A:SER203 3.5 24.6 1.0 C A:HIS205 3.5 22.9 1.0 CB A:THR201 3.6 23.3 1.0 O A:HOH406 3.6 25.6 1.0 N A:THR201 3.9 23.4 1.0 N A:SER203 3.9 24.6 1.0 O A:HOH333 4.1 16.2 1.0 CA A:THR201 4.2 23.5 1.0 OD2 A:ASP199 4.2 22.6 1.0 N A:HIS205 4.2 24.1 1.0 CA A:ASP199 4.2 22.3 1.0 CA A:SER203 4.2 24.9 1.0 N A:CSO202 4.3 24.0 1.0 CG2 A:THR201 4.3 23.0 1.0 CB A:ASP199 4.3 22.1 1.0 C A:ASP199 4.4 22.6 1.0 C A:THR201 4.4 23.7 1.0 CA A:HIS205 4.4 23.4 1.0 CG A:GLU210 4.4 22.3 1.0 N A:VAL206 4.5 23.1 1.0 N A:LEU200 4.5 22.7 1.0 N A:GLY204 4.6 24.6 1.0 CA A:VAL206 4.6 22.6 1.0 OE2 A:GLU134 4.7 24.9 1.0 C A:SER203 4.7 25.1 1.0 O A:ASP199 4.8 23.1 1.0 CB A:HIS205 5.0 23.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide


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 Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:17.3 occ:1.00 OD1 B:ASP199 2.2 21.6 1.0 OE2 B:GLU210 2.3 22.3 1.0 OG1 B:THR201 2.3 24.2 1.0 OG B:SER203 2.3 25.5 1.0 O B:HIS205 2.3 22.9 1.0 O B:HOH471 2.6 32.4 1.0 OE1 B:GLU210 2.9 21.8 1.0 CD B:GLU210 3.0 21.0 1.0 CG B:ASP199 3.4 22.0 1.0 CB B:SER203 3.5 25.1 1.0 C B:HIS205 3.5 23.2 1.0 CB B:THR201 3.6 23.2 1.0 O B:HOH424 3.9 24.2 1.0 N B:THR201 3.9 23.4 1.0 N B:SER203 3.9 24.9 1.0 CA B:THR201 4.2 23.7 1.0 OD2 B:ASP199 4.2 22.9 1.0 N B:HIS205 4.2 24.4 1.0 N B:CSO202 4.2 23.9 1.0 CA B:ASP199 4.2 22.3 1.0 CA B:SER203 4.2 25.4 1.0 O B:HOH340 4.2 16.3 1.0 CG2 B:THR201 4.3 22.9 1.0 CB B:ASP199 4.3 22.2 1.0 C B:ASP199 4.3 22.5 1.0 C B:THR201 4.4 23.8 1.0 CA B:HIS205 4.4 23.8 1.0 CG B:GLU210 4.5 22.3 1.0 N B:VAL206 4.5 23.3 1.0 N B:GLY204 4.5 24.8 1.0 N B:LEU200 4.5 22.6 1.0 CA B:VAL206 4.6 22.6 1.0 C B:SER203 4.7 25.4 1.0 OE2 B:GLU134 4.7 25.4 1.0 O B:ASP199 4.8 23.2 1.0 CB B:HIS205 5.0 23.7 1.0 C B:CSO202 5.0 25.2 1.0

A.Chaikuad, K.Guo, C.D.O.Cooper, V.Ayinampudi, T.Krojer, E.Ugochukwu, J.R.C.Muniz, M.Vollmar, P.Canning, F.Von Delft, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, C.Bountra, A.Bullock. Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex with Egfr PY1069 Peptide To Be Published.