Calcium in PDB 2y1m: Structure of Native C-Cbl

The structure of Structure of Native C-Cbl, PDB code: 2y1m was solved by H.Dou, G.J.Sibbet, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.615 / 2.67
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	146.800, 148.560, 348.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.84 / 26.29

The structure of Structure of Native C-Cbl also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

The binding sites of Calcium atom in the Structure of Native C-Cbl (pdb code 2y1m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Native C-Cbl, PDB code: 2y1m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1438 b:57.1 occ:1.00 OD1 A:ASN233 2.5 38.4 1.0 O A:TYR235 2.6 36.0 1.0 OE2 A:GLU240 2.7 41.4 1.0 OG1 A:THR231 2.8 40.0 1.0 OD1 A:ASP229 2.8 40.1 1.0 OE1 A:GLU240 3.0 35.6 1.0 CD A:GLU240 3.2 40.5 1.0 CG A:ASN233 3.5 41.7 1.0 CG A:ASP229 3.5 40.3 1.0 C A:TYR235 3.7 39.5 1.0 N A:THR231 3.9 35.3 1.0 N A:ASN233 3.9 39.7 1.0 CB A:THR231 3.9 39.9 1.0 OD2 A:ASP229 4.0 44.5 1.0 N A:CYS232 4.1 36.6 1.0 ND2 A:ASN233 4.1 48.2 1.0 CA A:ASP229 4.2 33.6 1.0 N A:TYR235 4.2 43.3 1.0 CA A:THR231 4.2 39.7 1.0 C A:THR231 4.3 38.4 1.0 C A:ASP229 4.3 36.6 1.0 CB A:ASP229 4.3 29.9 1.0 N A:LEU230 4.4 41.1 1.0 CA A:TYR235 4.5 42.9 1.0 CG2 A:THR231 4.5 38.3 1.0 CB A:ASN233 4.5 41.2 1.0 CA A:ASN233 4.6 40.1 1.0 N A:ASP234 4.6 40.2 1.0 N A:ILE236 4.7 40.0 1.0 CG A:GLU240 4.7 35.0 1.0 CA A:ILE236 4.7 37.3 1.0 O A:ASP229 4.7 38.7 1.0 CB A:TYR235 4.8 42.0 1.0 CA A:CYS232 4.8 37.1 1.0 C A:CYS232 4.8 41.9 1.0 C A:ASN233 4.9 39.4 1.0 O A:THR231 5.0 38.1 1.0 C A:LEU230 5.0 38.0 1.0

Calcium binding site 2 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1438 b:56.6 occ:1.00 ND2 B:ASN233 2.5 42.8 1.0 O B:TYR235 2.6 44.0 1.0 OD1 B:ASP229 2.7 45.2 1.0 CG B:ASN233 3.0 44.2 1.0 OG1 B:THR231 3.0 44.4 1.0 O B:HOH2008 3.0 42.0 1.0 OE2 B:GLU240 3.2 44.5 1.0 N B:TYR235 3.3 42.8 1.0 OD1 B:ASN233 3.3 46.7 1.0 C B:TYR235 3.4 42.8 1.0 N B:ASN233 3.5 41.6 1.0 CG B:ASP229 3.5 40.4 1.0 OE1 B:GLU240 3.6 36.9 1.0 CA B:TYR235 3.7 37.7 1.0 N B:ASP234 3.7 42.9 1.0 OD2 B:ASP229 3.8 36.9 1.0 CD B:GLU240 3.8 40.8 1.0 CB B:TYR235 3.9 41.3 1.0 CA B:ASN233 3.9 45.6 1.0 C B:ASN233 4.0 45.1 1.0 CB B:ASN233 4.0 48.8 1.0 CB B:THR231 4.2 44.2 1.0 N B:CYS232 4.3 40.5 1.0 C B:ASP234 4.3 45.0 1.0 N B:ILE236 4.5 42.0 1.0 C B:THR231 4.5 39.4 1.0 C B:CYS232 4.5 42.5 1.0 CA B:ASP234 4.5 43.1 1.0 N B:THR231 4.6 38.5 1.0 CA B:THR231 4.7 41.0 1.0 O B:ASN233 4.7 41.0 1.0 CB B:ASP229 4.7 35.8 1.0 CA B:CYS232 4.8 43.8 1.0 CA B:ASP229 4.9 37.7 1.0 CA B:ILE236 4.9 38.7 1.0 C B:ASP229 4.9 42.8 1.0

Calcium binding site 3 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1438 b:66.1 occ:1.00 O C:TYR235 2.4 44.4 1.0 OD1 C:ASN233 2.8 57.4 1.0 OD1 C:ASP229 2.9 47.7 1.0 OG1 C:THR231 3.0 45.8 1.0 OE2 C:GLU240 3.1 46.5 1.0 CG C:ASN233 3.1 54.7 1.0 ND2 C:ASN233 3.1 47.9 1.0 C C:TYR235 3.3 48.0 1.0 O C:HOH2008 3.4 49.8 1.0 CG C:ASP229 3.4 46.2 1.0 N C:TYR235 3.5 51.3 1.0 OE1 C:GLU240 3.6 43.5 1.0 OD2 C:ASP229 3.7 48.4 1.0 CD C:GLU240 3.7 44.7 1.0 N C:ASN233 3.7 44.3 1.0 CA C:TYR235 3.9 49.3 1.0 CB C:TYR235 4.2 48.8 1.0 N C:ASP234 4.2 41.3 1.0 CB C:ASN233 4.2 50.0 1.0 CA C:ASN233 4.2 42.5 1.0 CB C:THR231 4.3 47.6 1.0 C C:ASN233 4.3 45.4 1.0 N C:THR231 4.3 47.9 1.0 N C:CYS232 4.4 47.2 1.0 CA C:ASP229 4.4 43.7 1.0 N C:ILE236 4.4 49.0 1.0 CB C:ASP229 4.4 41.4 1.0 C C:THR231 4.5 53.4 1.0 CA C:THR231 4.6 52.1 1.0 C C:ASP234 4.7 51.1 1.0 C C:ASP229 4.7 46.0 1.0 CA C:ILE236 4.8 47.6 1.0 C C:CYS232 4.8 49.7 1.0 N C:LEU230 4.9 47.8 1.0 CA C:ASP234 4.9 45.2 1.0 CA C:CYS232 5.0 52.1 1.0 O C:ASN233 5.0 50.7 1.0 O C:THR231 5.0 54.2 1.0

Calcium binding site 4 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1438 b:63.6 occ:1.00 O D:TYR235 2.5 42.6 1.0 OD1 D:ASN233 2.5 41.0 1.0 OD1 D:ASP229 2.7 43.1 1.0 OG1 D:THR231 2.7 43.9 1.0 OE2 D:GLU240 2.8 40.6 1.0 CG D:ASN233 3.2 47.5 1.0 OE1 D:GLU240 3.3 39.9 1.0 O D:HOH2003 3.3 52.0 1.0 CG D:ASP229 3.3 45.7 1.0 CD D:GLU240 3.4 40.1 1.0 C D:TYR235 3.6 45.2 1.0 ND2 D:ASN233 3.7 52.0 1.0 OD2 D:ASP229 3.7 41.6 1.0 N D:ASN233 3.7 42.3 1.0 N D:THR231 3.9 45.6 1.0 N D:TYR235 3.9 46.3 1.0 CB D:THR231 4.0 40.0 1.0 N D:CYS232 4.1 41.3 1.0 CA D:THR231 4.2 43.6 1.0 C D:THR231 4.2 43.9 1.0 N D:ASP234 4.2 34.0 1.0 CA D:TYR235 4.2 46.1 1.0 CA D:ASP229 4.3 43.2 1.0 CB D:ASN233 4.3 43.7 1.0 CB D:ASP229 4.3 39.6 1.0 CA D:ASN233 4.3 37.6 1.0 C D:ASP229 4.4 46.4 1.0 N D:LEU230 4.5 44.7 1.0 C D:ASN233 4.5 37.7 1.0 N D:ILE236 4.6 43.4 1.0 CB D:TYR235 4.6 43.4 1.0 C D:CYS232 4.7 44.9 1.0 CA D:ILE236 4.8 41.9 1.0 CA D:CYS232 4.8 43.2 1.0 O D:THR231 4.9 42.5 1.0 CD1 D:ILE236 4.9 43.7 1.0 C D:ASP234 4.9 43.5 1.0 O D:ASP229 4.9 53.4 1.0 CG D:GLU240 5.0 41.5 1.0

Calcium binding site 5 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1438 b:72.8 occ:1.00 OD1 E:ASN233 2.6 57.7 1.0 OG1 E:THR231 2.7 56.4 1.0 O E:TYR235 2.7 52.4 1.0 OD1 E:ASP229 2.9 58.5 1.0 CG E:ASN233 3.1 63.9 1.0 OE2 E:GLU240 3.2 57.7 1.0 ND2 E:ASN233 3.4 67.7 1.0 O E:HOH2002 3.4 59.1 1.0 C E:TYR235 3.5 55.9 1.0 CG E:ASP229 3.6 51.5 1.0 N E:ASN233 3.6 52.5 1.0 OE1 E:GLU240 3.7 57.5 1.0 N E:TYR235 3.7 61.1 1.0 CD E:GLU240 3.9 58.0 1.0 OD2 E:ASP229 3.9 55.9 1.0 CB E:THR231 3.9 55.2 1.0 CA E:TYR235 3.9 60.4 1.0 N E:CYS232 4.0 56.1 1.0 CB E:TYR235 4.1 56.9 1.0 CA E:ASN233 4.2 50.8 1.0 N E:ASP234 4.2 56.9 1.0 CB E:ASN233 4.2 54.5 1.0 N E:THR231 4.3 52.1 1.0 C E:THR231 4.3 57.7 1.0 CA E:THR231 4.4 58.3 1.0 C E:ASN233 4.4 53.5 1.0 C E:CYS232 4.5 64.5 1.0 N E:ILE236 4.6 54.6 1.0 CA E:CYS232 4.7 60.6 1.0 CB E:ASP229 4.7 43.3 1.0 CA E:ASP229 4.8 50.4 1.0 C E:ASP234 4.8 63.3 1.0 O E:HOH2001 4.9 57.3 1.0 C E:ASP229 4.9 56.5 1.0

Calcium binding site 6 out of 6 in the Structure of Native C-Cbl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1438 b:77.2 occ:1.00 O F:TYR235 2.5 56.5 1.0 OD1 F:ASN233 2.7 55.4 1.0 OE2 F:GLU240 2.8 55.7 1.0 OG1 F:THR231 2.9 62.6 1.0 OD1 F:ASP229 3.0 53.6 1.0 CG F:ASP229 3.3 51.6 1.0 CG F:ASN233 3.3 58.7 1.0 OE1 F:GLU240 3.4 51.3 1.0 CD F:GLU240 3.4 51.5 1.0 OD2 F:ASP229 3.6 52.4 1.0 C F:TYR235 3.7 58.8 1.0 N F:THR231 3.8 49.4 1.0 N F:ASN233 3.8 51.4 1.0 ND2 F:ASN233 3.9 65.7 1.0 CB F:THR231 3.9 58.7 1.0 CA F:ASP229 3.9 51.6 1.0 CB F:ASP229 4.0 48.2 1.0 C F:ASP229 4.1 52.0 1.0 CA F:THR231 4.1 55.6 1.0 N F:CYS232 4.2 52.1 1.0 C F:THR231 4.2 58.0 1.0 N F:LEU230 4.2 52.5 1.0 CG2 F:THR231 4.2 56.8 1.0 N F:TYR235 4.2 57.8 1.0 CB F:ASN233 4.3 59.5 1.0 CA F:ASN233 4.4 55.1 1.0 CA F:TYR235 4.5 58.1 1.0 N F:ASP234 4.6 48.5 1.0 O F:ASP229 4.6 46.9 1.0 N F:ILE236 4.7 53.0 1.0 C F:ASN233 4.7 54.6 1.0 CA F:ILE236 4.7 47.5 1.0 CG F:GLU240 4.8 43.6 1.0 O F:THR231 4.8 56.6 1.0 C F:CYS232 4.8 53.1 1.0 CB F:TYR235 4.9 54.3 1.0 CA F:CYS232 4.9 51.7 1.0 C F:LEU230 4.9 50.1 1.0 CD1 F:ILE236 5.0 48.0 1.0

H.Dou, L.Buetow, A.Hock, G.J.Sibbet, K.H.Vousden, D.T.Huang. Structural Basis For Autoinhibition and Phosphorylation- Dependent Activation of C-Cbl. Nat.Struct.Mol.Biol. V. 19 184 2012.
ISSN: ISSN 1545-9993
PubMed: 22266821
DOI: 10.1038/NSMB.2231