Calcium in PDB 5axi: Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin

The structure of Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin, PDB code: 5axi was solved by A.Ohno, N.Maita, A.Ochi, R.Nakao, T.Nikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.05 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.144, 94.091, 133.949, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 26.4

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

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin (pdb code 5axi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin, PDB code: 5axi:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


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 Cbl-B Tkb Domain in Complex with Cblin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:46.3 occ:1.00 OD1 A:ASP221 2.2 24.1 1.0 OE2 A:GLU232 2.4 24.9 1.0 OD1 A:ASN225 2.5 30.7 1.0 O A:TYR227 2.5 30.6 1.0 OE1 A:GLU232 2.5 24.4 1.0 OG1 A:THR223 2.6 25.9 1.0 CD A:GLU232 2.8 24.2 1.0 CG A:ASP221 3.4 23.9 1.0 CG A:ASN225 3.4 30.7 1.0 C A:TYR227 3.7 29.2 1.0 N A:THR223 3.8 29.7 1.0 ND2 A:ASN225 3.9 30.9 1.0 CB A:THR223 3.9 26.8 1.0 CA A:ASP221 3.9 25.4 1.0 C A:ASP221 4.0 26.2 1.0 N A:CYS224 4.1 32.8 1.0 N A:ASN225 4.1 31.9 1.0 CB A:ASP221 4.2 24.4 1.0 N A:LEU222 4.2 27.3 1.0 OD2 A:ASP221 4.2 24.5 1.0 CA A:THR223 4.3 28.3 1.0 N A:TYR227 4.3 29.9 1.0 CG A:GLU232 4.3 23.7 1.0 C A:THR223 4.4 29.9 1.0 CA A:ILE228 4.5 28.4 1.0 CG2 A:THR223 4.5 26.1 1.0 O A:ASP221 4.5 27.4 1.0 CA A:TYR227 4.5 30.3 1.0 N A:ILE228 4.5 28.6 1.0 CB A:ASN225 4.5 29.6 1.0 CD1 A:ILE228 4.6 28.5 1.0 CA A:ASN225 4.8 30.1 1.0 N A:ASP226 4.8 30.6 1.0 C A:LEU222 4.9 28.8 1.0 N A:SER229 4.9 28.0 1.0 CB A:TYR227 4.9 31.3 1.0 CA A:CYS224 4.9 33.6 1.0 C A:ASN225 5.0 29.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


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 Cbl-B Tkb Domain in Complex with Cblin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:55.2 occ:1.00 OD1 B:ASP221 2.0 34.3 1.0 O B:TYR227 2.3 37.4 1.0 OD1 B:ASN225 2.4 38.0 1.0 OE2 B:GLU232 2.4 30.4 1.0 OE1 B:GLU232 2.5 30.4 1.0 OG1 B:THR223 2.6 32.7 1.0 CD B:GLU232 2.8 30.4 1.0 CG B:ASP221 3.2 34.5 1.0 C B:TYR227 3.3 35.1 1.0 CG B:ASN225 3.4 36.4 1.0 O B:HOH535 3.4 37.1 1.0 CB B:THR223 3.9 32.9 1.0 ND2 B:ASN225 3.9 37.4 1.0 CA B:ASP221 3.9 35.5 1.0 N B:THR223 4.0 34.2 1.0 OD2 B:ASP221 4.0 35.7 1.0 N B:TYR227 4.1 34.0 1.0 CB B:ASP221 4.1 34.7 1.0 N B:ASN225 4.1 35.1 1.0 N B:ILE228 4.2 31.1 1.0 CA B:ILE228 4.2 29.2 1.0 CA B:TYR227 4.2 36.6 1.0 C B:ASP221 4.3 36.2 1.0 CG B:GLU232 4.3 29.6 1.0 CA B:THR223 4.3 34.6 1.0 N B:CYS224 4.4 38.4 1.0 C B:THR223 4.5 36.3 1.0 CD1 B:ILE228 4.5 28.7 1.0 N B:LEU222 4.5 36.3 1.0 CB B:ASN225 4.6 35.9 1.0 CG2 B:THR223 4.6 32.7 1.0 CB B:TYR227 4.7 37.9 1.0 N B:SER229 4.7 25.9 1.0 N B:ASP226 4.7 35.6 1.0 CA B:ASN225 4.7 35.8 1.0 O B:ASP221 4.8 34.3 1.0 C B:ASN225 4.9 35.7 1.0 C B:ILE228 5.0 27.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:59.6 occ:1.00 O C:TYR227 2.0 47.7 1.0 OD1 C:ASP221 2.4 47.3 1.0 OE1 C:GLU232 2.5 52.7 1.0 OE2 C:GLU232 2.6 48.9 1.0 OD1 C:ASN225 2.6 41.0 1.0 OG1 C:THR223 2.7 45.9 1.0 CD C:GLU232 2.9 52.0 1.0 C C:TYR227 3.2 48.5 1.0 CG C:ASP221 3.3 46.1 1.0 CG C:ASN225 3.5 42.3 1.0 N C:TYR227 3.8 50.7 1.0 CA C:TYR227 4.0 52.0 1.0 ND2 C:ASN225 4.0 45.0 1.0 CA C:ASP221 4.0 43.6 1.0 CB C:THR223 4.1 44.7 1.0 OD2 C:ASP221 4.1 49.3 1.0 N C:ILE228 4.1 46.0 1.0 N C:THR223 4.2 43.4 1.0 CB C:ASP221 4.2 43.9 1.0 N C:ASN225 4.2 40.9 1.0 CA C:ILE228 4.3 46.3 1.0 N C:CYS224 4.3 43.9 1.0 C C:ASP221 4.4 41.4 1.0 CG C:GLU232 4.4 47.6 1.0 CB C:TYR227 4.4 54.5 1.0 CA C:THR223 4.5 44.4 1.0 C C:THR223 4.6 43.7 1.0 N C:LEU222 4.6 42.3 1.0 N C:SER229 4.6 48.2 1.0 CB C:ASN225 4.6 43.0 1.0 CG2 C:THR223 4.7 45.5 1.0 N C:ASP226 4.7 47.4 1.0 CA C:ASN225 4.8 42.7 1.0 C C:ASN225 4.9 43.5 1.0 O C:ASP221 4.9 40.0 1.0 CD1 C:ILE228 4.9 46.1 1.0 C C:ILE228 5.0 48.8 1.0

A.Ohno, A.Ochi, N.Maita, T.Ueji, A.Bando, R.Nakao, K.Hirasaka, T.Abe, S.Teshima-Kondo, H.Nemoto, Y.Okumura, A.Higashibata, S.Yano, H.Tochio, T.Nikawa. Structural Analysis of the Tkb Domain of Ubiquitin Ligase Cbl-B Complexed with Its Small Inhibitory Peptide, Cblin Arch.Biochem.Biophys. V. 594 1 2016.
ISSN: ESSN 1096-0384
PubMed: 26874193
DOI: 10.1016/J.ABB.2016.02.014