Chlorine 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:

Calcium

(Ca)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin, PDB code: 5axi:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl402 b:25.4 occ:1.00 O B:HOH536 3.1 26.9 1.0 O A:HOH573 3.1 28.4 1.0 NH1 A:ARG183 3.2 26.5 1.0 O A:HOH541 3.2 18.6 1.0 NH1 B:ARG183 3.2 29.6 1.0 CD B:ARG183 3.7 28.3 1.0 CD A:ARG183 3.8 28.8 1.0 CB B:ALA179 4.1 27.2 1.0 CB A:ALA179 4.2 27.5 1.0 CZ A:ARG183 4.3 27.6 1.0 CZ B:ARG183 4.3 28.8 1.0 CG B:ARG172 4.4 25.4 1.0 NE B:ARG183 4.5 28.6 1.0 NE A:ARG183 4.5 28.4 1.0 CG A:ARG172 4.5 26.6 1.0 O B:HOH540 4.8 28.4 1.0 CG B:ARG183 4.9 28.6 1.0 O A:HOH531 4.9 31.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl403 b:36.4 occ:1.00 N A:TRP243 3.1 28.7 1.0 O A:HOH544 3.2 25.2 1.0 O A:HOH552 3.3 34.0 1.0 CE A:LYS175 3.6 25.6 1.0 CA A:PRO242 3.6 28.2 1.0 CB A:LYS175 3.7 25.8 1.0 CB A:TRP243 3.8 28.0 1.0 C A:PRO242 3.9 28.0 1.0 CB A:GLN241 3.9 28.1 1.0 CA A:TRP243 4.0 28.3 1.0 CG A:LYS175 4.1 26.0 1.0 CB A:PRO242 4.2 29.1 1.0 CB A:ASP177 4.4 28.7 1.0 CD A:LYS175 4.5 25.7 1.0 CA A:GLN241 4.5 28.7 1.0 NZ A:LYS175 4.7 26.2 1.0 CA A:LYS175 4.8 24.8 1.0 N A:PRO242 4.8 29.4 1.0 OD2 A:ASP177 4.9 34.8 1.0 N A:ASP177 4.9 27.0 1.0 OE1 A:GLN241 4.9 29.3 1.0 N A:ALA178 5.0 26.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl404 b:41.0 occ:1.00 NZ A:LYS189 3.0 38.2 1.0 O A:HOH564 3.0 30.3 1.0 CE A:LYS189 3.2 36.5 1.0 N A:THR190 3.4 32.8 1.0 N A:ILE191 3.6 31.0 1.0 O A:ILE191 3.7 30.4 1.0 O A:HOH524 3.8 29.8 1.0 CG2 A:ILE191 3.9 32.0 1.0 OE1 A:GLU105 4.0 43.2 1.0 CA A:LYS189 4.1 30.0 1.0 OG1 A:THR190 4.2 37.1 1.0 CB A:LYS189 4.2 32.1 1.0 C A:LYS189 4.2 31.5 1.0 CD A:LYS189 4.3 35.3 1.0 CA A:THR190 4.3 33.6 1.0 C A:THR190 4.5 31.6 1.0 CA A:ILE191 4.5 31.5 1.0 C A:ILE191 4.5 30.9 1.0 CG2 A:THR190 4.6 34.7 1.0 CB A:THR190 4.6 33.4 1.0 CB A:GLU105 4.6 39.4 1.0 CG A:LYS189 4.7 33.4 1.0 CD A:GLU105 4.7 45.2 1.0 CB A:ILE191 4.7 31.9 1.0 N A:TYR106 5.0 35.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Cbl-B Tkb Domain in Complex with Cblin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:31.0 occ:1.00 N B:TRP243 3.1 30.1 1.0 CD B:LYS175 3.6 30.1 1.0 CA B:PRO242 3.7 31.1 1.0 CB B:TRP243 3.8 29.1 1.0 C B:PRO242 3.9 30.1 1.0 CB B:LYS175 3.9 29.4 1.0 CG B:LYS175 4.0 29.5 1.0 CB B:GLN241 4.0 28.6 1.0 CA B:TRP243 4.0 30.1 1.0 CB B:PRO242 4.2 30.5 1.0 CA B:GLN241 4.5 28.6 1.0 CB B:ASP177 4.6 30.2 1.0 O B:HOH502 4.8 27.8 1.0 CE B:LYS175 4.8 32.4 1.0 N B:PRO242 4.9 30.9 1.0 CA B:LYS175 5.0 28.6 1.0 OE1 B:GLN241 5.0 31.0 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