Calcium in PDB 3plf: Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain

The structure of Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain, PDB code: 3plf was solved by Q.Sun, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.08 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.743, 104.483, 60.548, 90.00, 90.19, 90.00
R / Rfree (%)	15.9 / 18

The structure of Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain (pdb code 3plf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain, PDB code: 3plf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:31.0 occ:1.00 O B:TYR235 2.3 17.6 1.0 OD1 B:ASP229 2.4 15.1 1.0 OD1 B:ASN233 2.4 19.0 1.0 OE2 B:GLU240 2.5 14.0 1.0 OE1 B:GLU240 2.5 16.9 1.0 OG1 B:THR231 2.8 14.9 1.0 O B:HOH399 2.9 17.7 1.0 CD B:GLU240 2.9 15.7 1.0 CG B:ASP229 3.4 14.9 1.0 CG B:ASN233 3.4 19.1 1.0 C B:TYR235 3.5 16.3 1.0 ND2 B:ASN233 4.0 21.2 1.0 CB B:THR231 4.1 15.0 1.0 CA B:ASP229 4.1 14.0 1.0 N B:ASN233 4.1 18.7 1.0 N B:THR231 4.1 15.2 1.0 N B:TYR235 4.1 18.8 1.0 OD2 B:ASP229 4.2 18.1 1.0 N B:CYS232 4.2 14.1 1.0 CB B:ASP229 4.3 12.7 1.0 CA B:TYR235 4.3 18.2 1.0 N B:ILE236 4.3 15.4 1.0 C B:ASP229 4.4 14.3 1.0 CA B:THR231 4.4 14.4 1.0 CG B:GLU240 4.4 14.6 1.0 CA B:ILE236 4.4 13.7 1.0 CB B:ASN233 4.5 18.9 1.0 C B:THR231 4.5 15.5 1.0 CB B:TYR235 4.6 19.4 1.0 N B:LEU230 4.6 14.5 1.0 CA B:ASN233 4.7 18.8 1.0 CG2 B:THR231 4.7 12.5 1.0 N B:ASP234 4.7 18.9 1.0 C B:ASN233 4.8 20.1 1.0 O B:HOH4 4.8 26.3 1.0 OE2 B:GLU164 4.9 16.2 1.0 N B:SER237 4.9 13.2 1.0 O B:ASP229 4.9 15.3 1.0

Calcium binding site 2 out of 2 in the Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Reverse Binding Mode of Metrd Peptide Complexed with C-Cbl Tkb Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1 b:30.9 occ:1.00 OD1 D:ASN233 2.4 16.9 1.0 O D:TYR235 2.4 17.0 1.0 OD1 D:ASP229 2.4 15.7 1.0 OE2 D:GLU240 2.5 12.6 1.0 OE1 D:GLU240 2.6 16.7 1.0 OG1 D:THR231 2.7 14.3 1.0 O D:HOH403 2.8 16.0 1.0 CD D:GLU240 2.9 13.1 1.0 CG D:ASN233 3.4 18.9 1.0 CG D:ASP229 3.5 15.3 1.0 C D:TYR235 3.6 15.6 1.0 CB D:THR231 4.0 12.9 1.0 ND2 D:ASN233 4.0 20.6 1.0 N D:THR231 4.0 12.9 1.0 N D:ASN233 4.1 16.9 1.0 CA D:ASP229 4.2 13.3 1.0 N D:TYR235 4.2 17.5 1.0 N D:CYS232 4.3 13.9 1.0 OD2 D:ASP229 4.3 16.9 1.0 CA D:THR231 4.4 13.3 1.0 CG D:GLU240 4.4 10.4 1.0 CB D:ASP229 4.4 11.8 1.0 C D:ASP229 4.4 13.9 1.0 CA D:TYR235 4.4 16.5 1.0 N D:ILE236 4.4 14.6 1.0 CA D:ILE236 4.5 13.0 1.0 C D:THR231 4.5 13.7 1.0 CB D:ASN233 4.6 17.9 1.0 N D:LEU230 4.6 12.0 1.0 CG2 D:THR231 4.6 12.9 1.0 CB D:TYR235 4.7 14.6 1.0 OE2 D:GLU164 4.7 14.8 1.0 N D:ASP234 4.7 17.9 1.0 CA D:ASN233 4.8 17.6 1.0 N D:SER237 4.8 12.9 1.0 O D:HOH3 4.9 21.4 1.0 CD1 D:ILE236 4.9 13.2 1.0 O D:ASP229 4.9 13.5 1.0 C D:ASN233 4.9 17.8 1.0

Q.Sun, C.Ng, G.R.Guy, J.Sivaraman. An Adjacent Arginine, and the Phosphorylated Tyrosine in the C-Met Receptor Target Sequence, Dictates the Orientation of C-Cbl Binding Febs Lett. V. 585 281 2011.
ISSN: ISSN 0014-5793
PubMed: 21163258
DOI: 10.1016/J.FEBSLET.2010.11.060