Calcium in PDB 3vrq: Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant)

The structure of Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant), PDB code: 3vrq was solved by K.Takeshita, T.Tezuka, Y.Isozaki, E.Yamashita, M.Suzuki, Y.Yamanashi, T.Yamamoto, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.98 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.600, 66.211, 81.558, 90.00, 106.02, 90.00
R / Rfree (%)	21.5 / 26.4

The binding sites of Calcium atom in the Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant) (pdb code 3vrq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant), PDB code: 3vrq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:53.1 occ:1.00 OD1 A:ASP199 2.1 25.4 1.0 O A:HIS205 2.3 23.6 1.0 OG A:SER203 2.7 26.6 1.0 OG1 A:THR201 2.7 24.2 1.0 OE2 A:GLU210 2.8 30.2 1.0 CG A:ASP199 3.1 24.4 1.0 OE1 A:GLU210 3.2 31.9 1.0 CD A:GLU210 3.4 28.9 1.0 C A:HIS205 3.4 23.7 1.0 CB A:SER203 3.7 28.1 1.0 N A:SER203 3.8 28.7 1.0 OD2 A:ASP199 3.8 28.5 1.0 N A:HIS205 4.0 24.9 1.0 CB A:THR201 4.0 26.1 1.0 CA A:ASP199 4.1 23.5 1.0 CB A:ASP199 4.1 23.0 1.0 N A:THR201 4.2 24.9 1.0 N A:CYS202 4.2 26.8 1.0 CA A:HIS205 4.2 24.6 1.0 CA A:SER203 4.2 27.6 1.0 O A:HOH513 4.3 19.9 1.0 C A:ASP199 4.4 23.3 1.0 CA A:THR201 4.4 25.3 1.0 C A:THR201 4.4 26.7 1.0 N A:VAL206 4.5 22.5 1.0 N A:GLY204 4.6 26.5 1.0 CA A:VAL206 4.6 19.8 1.0 OE2 A:GLU134 4.7 32.1 1.0 C A:SER203 4.7 27.5 1.0 N A:LEU200 4.7 23.2 1.0 CB A:HIS205 4.7 24.2 1.0 CG2 A:THR201 4.7 24.6 1.0 C A:CYS202 4.8 28.7 1.0 O A:ASP199 4.8 23.4 1.0 CG A:GLU210 4.9 24.0 1.0 CA A:CYS202 4.9 28.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Tyrosine Kinase Binding Domain of Cbl-C (Pl Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:56.5 occ:1.00 OD1 B:ASP199 2.3 26.1 1.0 O B:HIS205 2.4 24.3 1.0 O B:HOH507 2.5 29.4 1.0 OG1 B:THR201 2.6 24.5 1.0 OE2 B:GLU210 2.6 31.1 1.0 OG B:SER203 2.8 26.7 1.0 OE1 B:GLU210 2.9 32.2 1.0 CD B:GLU210 3.1 29.2 1.0 CG B:ASP199 3.4 24.4 1.0 C B:HIS205 3.5 23.9 1.0 CB B:THR201 3.9 26.0 1.0 CB B:SER203 4.0 27.9 1.0 N B:SER203 4.1 28.6 1.0 N B:THR201 4.1 24.9 1.0 OD2 B:ASP199 4.1 28.8 1.0 CA B:ASP199 4.2 23.8 1.0 O B:HOH516 4.2 33.5 1.0 OE2 B:GLU134 4.3 31.8 1.0 CB B:ASP199 4.3 22.8 1.0 N B:HIS205 4.3 25.1 1.0 CA B:THR201 4.3 25.7 1.0 N B:CYS202 4.4 26.8 1.0 C B:ASP199 4.4 23.5 1.0 CA B:HIS205 4.4 25.0 1.0 N B:VAL206 4.4 22.9 1.0 CA B:VAL206 4.5 20.5 1.0 C B:THR201 4.5 26.7 1.0 CG2 B:THR201 4.6 24.7 1.0 N B:LEU200 4.6 23.3 1.0 CA B:SER203 4.6 28.0 1.0 CG B:GLU210 4.6 23.9 1.0 N B:SER207 4.8 18.5 1.0 CB B:HIS205 4.9 24.3 1.0 OE1 B:GLU134 4.9 32.3 1.0 O B:ASP199 5.0 23.6 1.0

K.Takeshita, T.Tezuka, Y.Isozaki, E.Yamashita, M.Suzuki, M.Kim, Y.Yamanashi, T.Yamamoto, A.Nakagawa. Structural Flexibility Regulates Phosphopeptide-Binding Activity of the Tyrosine Kinase Binding Domain of Cbl-C. J.Biochem. V. 152 487 2012.
ISSN: ISSN 0021-924X
PubMed: 22888118
DOI: 10.1093/JB/MVS085