Calcium in PDB 5o76: Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant

All present enzymatic activity of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant:
2.3.2.27;

The structure of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant, PDB code: 5o76 was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.34 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.790, 101.281, 117.339, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24.8

The structure of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant (pdb code 5o76). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant, PDB code: 5o76:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:68.0 occ:1.00 OD1 A:ASP229 2.2 43.5 1.0 OD1 A:ASN233 2.4 44.8 1.0 O A:TYR235 2.4 41.6 1.0 OG1 A:THR231 2.5 42.1 1.0 OE2 A:GLU240 2.7 45.7 1.0 OE1 A:GLU240 2.8 49.5 1.0 O A:HOH613 3.0 41.3 1.0 CD A:GLU240 3.1 55.0 1.0 CG A:ASP229 3.2 44.2 1.0 CG A:ASN233 3.4 59.2 1.0 C A:TYR235 3.6 42.1 1.0 CB A:THR231 3.8 43.9 1.0 OD2 A:ASP229 3.9 50.8 1.0 HD22 A:ASN233 3.9 55.7 1.0 N A:THR231 3.9 37.3 1.0 ND2 A:ASN233 4.1 55.7 1.0 HD13 A:ILE236 4.1 43.8 1.0 N A:ASN233 4.1 38.9 1.0 CA A:ASP229 4.2 36.6 1.0 N A:CYS232 4.2 39.0 1.0 CB A:ASP229 4.2 38.0 1.0 CA A:THR231 4.2 37.4 1.0 N A:TYR235 4.2 40.0 1.0 C A:THR231 4.3 42.1 1.0 HG23 A:THR231 4.3 42.1 1.0 C A:ASP229 4.4 41.5 1.0 CA A:TYR235 4.4 39.5 1.0 N A:LEU230 4.5 37.3 1.0 N A:ILE236 4.5 37.9 1.0 CB A:ASN233 4.5 41.1 1.0 HD11 A:ILE199 4.6 63.1 1.0 CG A:GLU240 4.6 41.3 1.0 CG2 A:THR231 4.6 42.6 1.0 CA A:ILE236 4.6 36.8 1.0 CB A:TYR235 4.6 40.9 1.0 CA A:ASN233 4.7 39.6 1.0 N A:ASP234 4.8 42.0 1.0 HD12 A:ILE236 4.8 43.2 1.0 HG21 A:THR231 4.9 43.0 1.0 OE2 A:GLU164 4.9 44.0 1.0 CD1 A:ILE236 4.9 43.6 1.0 CA A:CYS232 5.0 39.5 1.0 C A:ASN233 5.0 44.7 1.0

Calcium binding site 2 out of 2 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:67.7 occ:1.00 O C:TYR235 2.2 49.1 1.0 OD1 C:ASP229 2.3 49.6 1.0 OD1 C:ASN233 2.4 49.0 1.0 OE2 C:GLU240 2.6 72.1 1.0 O C:HOH602 2.7 46.4 1.0 OG1 C:THR231 2.7 53.4 1.0 OE1 C:GLU240 2.8 60.6 1.0 CD C:GLU240 3.1 74.6 1.0 C C:TYR235 3.3 51.0 1.0 CG C:ASP229 3.4 50.4 1.0 CG C:ASN233 3.5 64.2 1.0 HD13 C:ILE236 3.9 55.6 1.0 HD21 C:ASN233 3.9 61.4 1.0 N C:TYR235 4.0 48.1 1.0 CB C:THR231 4.0 51.4 1.0 CA C:ASP229 4.1 43.4 1.0 CB C:ASP229 4.1 45.0 1.0 N C:THR231 4.1 44.7 1.0 ND2 C:ASN233 4.1 61.4 1.0 CA C:TYR235 4.2 48.6 1.0 N C:ASN233 4.2 48.4 1.0 OD2 C:ASP229 4.2 55.1 1.0 N C:ILE236 4.3 48.2 1.0 N C:CYS232 4.4 47.8 1.0 CA C:THR231 4.4 45.1 1.0 C C:ASP229 4.4 46.4 1.0 HG23 C:THR231 4.5 46.6 1.0 CA C:ILE236 4.5 47.6 1.0 CB C:TYR235 4.5 50.6 1.0 N C:LEU230 4.6 43.1 1.0 CG C:GLU240 4.6 55.5 1.0 C C:THR231 4.6 50.2 1.0 CB C:ASN233 4.6 50.3 1.0 HD11 C:ILE199 4.7 70.6 1.0 HD12 C:ILE236 4.7 55.0 1.0 N C:ASP234 4.7 49.4 1.0 CD1 C:ILE236 4.8 55.5 1.0 CA C:ASN233 4.8 49.0 1.0 CG2 C:THR231 4.8 47.0 1.0 N C:SER237 4.9 46.4 1.0 C C:ASN233 5.0 53.3 1.0

M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, G.J.Sibbet, B.O.Smith, W.Zhang, S.S.Sidhu, D.T.Huang. A General Strategy For Discovery of Inhibitors and Activators of Ring and U-Box E3 Ligases with Ubiquitin Variants. Mol. Cell V. 68 456 2017.
ISSN: ISSN 1097-4164
PubMed: 29053960
DOI: 10.1016/J.MOLCEL.2017.09.027