Sodium in PDB 3pfv: Crystal Structure of Cbl-B Tkb Domain in Complex with Egfr PY1069 Peptide

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

Resolution Low / High (Å)	49.47 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.063, 98.934, 61.978, 90.00, 110.63, 90.00
R / Rfree (%)	21.6 / 26.2

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

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Cbl-B Tkb Domain in Complex with Egfr PY1069 Peptide (pdb code 3pfv). 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-B Tkb Domain in Complex with Egfr PY1069 Peptide, PDB code: 3pfv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cbl-B 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-B Tkb Domain in Complex with Egfr PY1069 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:35.4 occ:1.00 O A:TYR227 2.3 29.4 1.0 OE1 A:GLU232 2.4 33.1 1.0 OE2 A:GLU232 2.4 25.9 1.0 OD1 A:ASN225 2.5 39.6 1.0 OD1 A:ASP221 2.5 35.7 1.0 OG1 A:THR223 2.6 28.2 1.0 CD A:GLU232 2.8 28.7 1.0 O A:HOH432 2.9 52.4 1.0 CG A:ASN225 3.3 40.4 1.0 C A:TYR227 3.5 32.1 1.0 CG A:ASP221 3.5 25.4 1.0 ND2 A:ASN225 3.7 49.4 1.0 CB A:THR223 3.9 26.7 1.0 N A:THR223 4.0 25.6 1.0 CA A:ASP221 4.1 24.5 1.0 N A:ASN225 4.1 35.3 1.0 N A:TYR227 4.1 33.1 1.0 N A:CYS224 4.2 34.5 1.0 CA A:THR223 4.2 27.2 1.0 OD2 A:ASP221 4.3 31.8 1.0 CG A:GLU232 4.3 25.3 1.0 C A:ASP221 4.3 24.6 1.0 CB A:ASP221 4.3 24.7 1.0 CA A:TYR227 4.4 32.9 1.0 N A:ILE228 4.4 27.6 1.0 C A:THR223 4.4 33.9 1.0 CA A:ILE228 4.4 26.3 1.0 CB A:ASN225 4.5 40.4 1.0 N A:LEU222 4.6 24.9 1.0 CD1 A:ILE228 4.6 25.1 1.0 CG2 A:THR223 4.6 26.5 1.0 CB A:TYR227 4.6 38.9 1.0 CA A:ASN225 4.7 41.2 1.0 O A:ASP221 4.8 24.9 1.0 N A:ASP226 4.8 30.6 1.0 N A:SER229 4.8 28.2 1.0 C A:ASN225 4.9 40.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cbl-B 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-B Tkb Domain in Complex with Egfr PY1069 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:42.0 occ:1.00 O B:TYR227 2.2 33.1 1.0 OE2 B:GLU232 2.4 29.6 1.0 OD1 B:ASN225 2.4 42.7 1.0 OD1 B:ASP221 2.4 38.1 1.0 OG1 B:THR223 2.7 31.3 1.0 OE1 B:GLU232 2.7 34.2 1.0 O B:HOH388 2.9 44.8 1.0 CD B:GLU232 3.0 30.5 1.0 CG B:ASN225 3.3 43.5 1.0 C B:TYR227 3.3 34.6 1.0 CG B:ASP221 3.4 27.2 1.0 ND2 B:ASN225 3.8 53.4 1.0 N B:TYR227 4.0 35.5 1.0 CB B:THR223 4.1 29.6 1.0 N B:ASN225 4.1 37.0 1.0 CA B:ASP221 4.1 26.0 1.0 N B:THR223 4.2 27.8 1.0 OD2 B:ASP221 4.2 33.1 1.0 CA B:TYR227 4.2 35.4 1.0 CB B:ASP221 4.3 26.5 1.0 N B:ILE228 4.3 30.1 1.0 N B:CYS224 4.3 36.0 1.0 CA B:ILE228 4.3 28.7 1.0 C B:ASP221 4.4 26.0 1.0 CB B:ASN225 4.4 43.8 1.0 CG B:GLU232 4.4 28.0 1.0 CA B:THR223 4.5 28.9 1.0 CB B:TYR227 4.5 42.3 1.0 C B:THR223 4.6 36.5 1.0 CA B:ASN225 4.6 44.0 1.0 N B:ASP226 4.7 33.3 1.0 CD1 B:ILE228 4.7 26.9 1.0 N B:LEU222 4.7 25.9 1.0 C B:ASN225 4.8 43.1 1.0 N B:SER229 4.8 30.7 1.0 CG2 B:THR223 4.8 29.6 1.0 O B:ASP221 4.9 26.2 1.0

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