Calcium in PDB 9erz: Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide

All present enzymatic activity of Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide:
2.3.2.27;

The structure of Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide, PDB code: 9erz was solved by S.F.Ahmed, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.20 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.783, 87.324, 84.353, 90, 99.39, 90
R / Rfree (%)	17.8 / 22.9

The binding sites of Calcium atom in the Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide (pdb code 9erz). 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 Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide, PDB code: 9erz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:80.2 occ:1.00 O A:TYR235 2.3 43.4 1.0 OD1 A:ASP229 2.3 42.5 1.0 OE2 A:GLU240 2.5 51.5 1.0 OD1 A:ASN233 2.5 50.5 1.0 OE1 A:GLU240 2.7 49.1 1.0 O A:HOH551 2.9 41.0 1.0 CD A:GLU240 2.9 48.3 1.0 OG1 A:THR231 3.0 45.5 1.0 C A:TYR235 3.3 46.2 1.0 CG A:ASN233 3.3 51.8 1.0 CG A:ASP229 3.4 48.7 1.0 ND2 A:ASN233 3.7 47.7 1.0 CA A:ASP229 4.0 39.0 1.0 N A:TYR235 4.1 44.0 1.0 CA A:TYR235 4.2 42.8 1.0 OD2 A:ASP229 4.2 47.5 1.0 N A:ASN233 4.2 41.9 1.0 CB A:ASP229 4.2 44.2 1.0 N A:ILE236 4.2 43.4 1.0 N A:THR231 4.2 36.9 1.0 CB A:THR231 4.2 41.9 1.0 CA A:ILE236 4.3 42.2 1.0 N A:CYS232 4.4 41.3 1.0 C A:ASP229 4.4 39.7 1.0 CG A:GLU240 4.4 44.5 1.0 CB A:TYR235 4.5 39.9 1.0 N A:LEU230 4.5 34.6 1.0 CA A:THR231 4.6 37.5 1.0 CB A:ASN233 4.6 51.8 1.0 C A:THR231 4.6 43.4 1.0 CD1 A:ILE236 4.7 40.3 1.0 N A:SER237 4.7 40.9 1.0 N A:ASP234 4.8 51.2 1.0 CA A:ASN233 4.8 53.0 1.0 CG2 A:THR231 4.8 34.9 1.0 OE1 A:GLU164 4.9 47.8 1.0 C A:ASN233 4.9 52.0 1.0 O A:ASP229 4.9 38.0 1.0 C A:ILE236 5.0 43.3 1.0

Calcium binding site 2 out of 2 in the Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cbl-Tkbd Bound to Ubiquitin-Fused Cblock Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:69.3 occ:1.00 O C:TYR235 2.3 35.3 1.0 OD1 C:ASP229 2.3 30.9 1.0 OD1 C:ASN233 2.4 34.6 1.0 OE2 C:GLU240 2.6 39.4 1.0 OE1 C:GLU240 2.6 35.5 1.0 O C:HOH514 2.9 34.5 1.0 CD C:GLU240 2.9 35.0 1.0 OG1 C:THR231 3.0 36.2 1.0 CG C:ASN233 3.3 36.4 1.0 C C:TYR235 3.4 33.6 1.0 CG C:ASP229 3.4 34.4 1.0 ND2 C:ASN233 3.7 34.9 1.0 N C:TYR235 4.0 33.7 1.0 CA C:ASP229 4.1 30.8 1.0 N C:THR231 4.1 27.6 1.0 N C:ASN233 4.2 34.8 1.0 OD2 C:ASP229 4.2 32.8 1.0 CA C:TYR235 4.2 35.3 1.0 CB C:THR231 4.3 35.5 1.0 CB C:ASP229 4.3 35.8 1.0 N C:ILE236 4.3 35.1 1.0 C C:ASP229 4.4 33.1 1.0 N C:CYS232 4.4 36.4 1.0 CA C:ILE236 4.4 30.0 1.0 CG C:GLU240 4.4 33.5 1.0 N C:LEU230 4.5 29.3 1.0 CB C:TYR235 4.5 30.3 1.0 CA C:THR231 4.5 30.9 1.0 CB C:ASN233 4.6 34.8 1.0 C C:THR231 4.6 31.0 1.0 CD1 C:ILE236 4.7 29.7 1.0 N C:ASP234 4.8 38.0 1.0 CA C:ASN233 4.8 38.5 1.0 N C:SER237 4.8 30.9 1.0 OE2 C:GLU164 4.9 39.5 1.0 O C:ASP229 4.9 31.9 1.0 C C:ASN233 4.9 36.8 1.0 CG2 C:THR231 5.0 33.7 1.0 O C:HOH528 5.0 51.6 1.0

S.F.Ahmed, J.Anand, W.Zhang, L.Buetow, L.Rishi, L.Mitchell, J.Bohlen, S.Lilla, G.J.Sibbet, C.Nixon, A.Patel, K.A.Majorek, S.Zanivan, J.C.Bustamante, S.S.Sidhu, K.Blyth, D.T.Huang. Locking Cbl Tkbd in Its Native Conformation Presents A Novel Therapeutic Opportunity in Mutant Cbl-Dependent Leukemia. Mol.Ther. 2025.
ISSN: ESSN 1525-0024
PubMed: 40329529
DOI: 10.1016/J.YMTHE.2025.04.042