Calcium in PDB 5j3x: Structure of C-Cbl Y371F

The structure of Structure of C-Cbl Y371F, PDB code: 5j3x was solved by D.T.Huang, L.Buetow, H.Dou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.37 / 2.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	147.842, 149.040, 344.118, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.4

The structure of Structure of C-Cbl Y371F also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

The binding sites of Calcium atom in the Structure of C-Cbl Y371F (pdb code 5j3x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of C-Cbl Y371F, PDB code: 5j3x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.2 occ:1.00 O A:TYR235 2.3 49.5 1.0 OD1 A:ASP229 2.3 83.8 1.0 OG1 A:THR231 2.4 71.6 1.0 OE2 A:GLU240 2.4 69.1 1.0 OD1 A:ASN233 2.4 58.9 1.0 OE1 A:GLU240 2.9 80.7 1.0 CD A:GLU240 3.0 80.9 1.0 O A:HOH602 3.2 86.7 1.0 C A:TYR235 3.4 69.9 1.0 CG A:ASN233 3.5 63.4 1.0 CG A:ASP229 3.5 78.0 1.0 CB A:THR231 3.7 75.9 1.0 N A:THR231 4.0 69.3 1.0 ND2 A:ASN233 4.0 62.1 1.0 N A:TYR235 4.1 64.8 1.0 N A:CYS232 4.1 62.9 1.0 N A:ASN233 4.1 66.4 1.0 CA A:TYR235 4.2 69.0 1.0 CA A:THR231 4.2 77.7 1.0 OD2 A:ASP229 4.2 80.0 1.0 CA A:ASP229 4.3 52.6 1.0 N A:ILE236 4.4 67.5 1.0 C A:THR231 4.4 66.9 1.0 CB A:ASP229 4.4 48.9 1.0 CG2 A:THR231 4.4 62.5 1.0 CG A:GLU240 4.5 88.2 1.0 C A:ASP229 4.5 58.9 1.0 CB A:TYR235 4.5 59.2 1.0 N A:LEU230 4.5 47.5 1.0 CA A:ILE236 4.5 60.8 1.0 CB A:ASN233 4.6 53.6 1.0 CA A:ASN233 4.8 48.2 1.0 CD1 A:ILE236 4.8 58.7 1.0 O A:HOH612 4.9 73.8 1.0 CA A:CYS232 4.9 69.6 1.0 N A:ASP234 4.9 60.6 1.0 C A:ASN233 5.0 54.2 1.0

Calcium binding site 2 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.6 occ:1.00 O B:TYR235 2.3 93.0 1.0 OD1 B:ASP229 2.3 0.2 1.0 OG1 B:THR231 2.4 80.7 1.0 OD1 B:ASN233 2.4 88.7 1.0 OE2 B:GLU240 2.4 99.7 1.0 OE1 B:GLU240 3.0 91.1 1.0 CD B:GLU240 3.1 0.7 1.0 O B:HOH608 3.1 84.9 1.0 CG B:ASP229 3.3 82.3 1.0 CG B:ASN233 3.4 90.5 1.0 C B:TYR235 3.5 91.1 1.0 CB B:THR231 3.8 73.9 1.0 ND2 B:ASN233 3.8 92.2 1.0 OD2 B:ASP229 3.9 76.3 1.0 N B:CYS232 4.0 76.0 1.0 N B:THR231 4.1 75.3 1.0 N B:ASN233 4.1 72.4 1.0 N B:TYR235 4.1 0.2 1.0 CA B:TYR235 4.2 90.5 1.0 CA B:THR231 4.3 76.9 1.0 CA B:ASP229 4.3 79.3 1.0 C B:THR231 4.4 77.6 1.0 CB B:ASP229 4.4 70.9 1.0 N B:ILE236 4.5 86.9 1.0 CB B:TYR235 4.5 94.9 1.0 C B:ASP229 4.5 75.6 1.0 CG B:GLU240 4.5 0.8 1.0 CB B:ASN233 4.6 94.3 1.0 CG2 B:THR231 4.6 72.5 1.0 CA B:ILE236 4.6 83.7 1.0 N B:LEU230 4.7 68.7 1.0 CA B:ASN233 4.8 72.0 1.0 CA B:CYS232 4.8 73.1 1.0 C B:CYS232 4.9 76.7 1.0 CD1 B:ILE236 4.9 79.1 1.0 N B:ASP234 4.9 88.0 1.0 C B:ASN233 5.0 76.7 1.0

Calcium binding site 3 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:0.9 occ:1.00 O C:TYR235 2.3 1.0 1.0 OD1 C:ASP229 2.4 94.4 1.0 OD1 C:ASN233 2.4 0.2 1.0 OE2 C:GLU240 2.4 0.1 1.0 OG1 C:THR231 2.4 86.7 1.0 OE1 C:GLU240 2.9 0.4 1.0 CD C:GLU240 3.0 0.1 1.0 CG C:ASN233 3.3 98.4 1.0 CG C:ASP229 3.4 90.6 1.0 C C:TYR235 3.5 94.2 1.0 ND2 C:ASN233 3.6 0.4 1.0 CB C:THR231 3.7 94.2 1.0 N C:THR231 3.9 85.6 1.0 OD2 C:ASP229 4.0 84.7 1.0 N C:CYS232 4.1 93.5 1.0 N C:TYR235 4.1 0.1 1.0 N C:ASN233 4.1 82.4 1.0 CA C:THR231 4.2 87.3 1.0 CA C:TYR235 4.2 92.9 1.0 CA C:ASP229 4.3 82.5 1.0 CB C:ASP229 4.4 85.8 1.0 C C:THR231 4.4 89.0 1.0 CG C:GLU240 4.5 0.6 1.0 N C:LEU230 4.5 85.2 1.0 C C:ASP229 4.5 81.0 1.0 N C:ILE236 4.5 97.3 1.0 CB C:TYR235 4.5 0.5 1.0 CB C:ASN233 4.6 90.6 1.0 CG2 C:THR231 4.6 83.4 1.0 CA C:ILE236 4.7 96.9 1.0 CA C:ASN233 4.8 87.0 1.0 CA C:CYS232 4.9 90.0 1.0 N C:ASP234 4.9 83.4 1.0 C C:CYS232 5.0 82.7 1.0

Calcium binding site 4 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca503 b:0.1 occ:1.00 O D:TYR235 2.3 64.2 1.0 OD1 D:ASP229 2.3 80.5 1.0 OE2 D:GLU240 2.4 88.0 1.0 OG1 D:THR231 2.4 74.4 1.0 OD1 D:ASN233 2.4 0.7 1.0 OE1 D:GLU240 3.1 84.6 1.0 CD D:GLU240 3.1 88.2 1.0 CG D:ASP229 3.2 74.2 1.0 CG D:ASN233 3.3 95.4 1.0 C D:TYR235 3.5 79.3 1.0 ND2 D:ASN233 3.7 0.6 1.0 CB D:THR231 3.7 77.2 1.0 OD2 D:ASP229 3.8 77.2 1.0 N D:THR231 3.8 87.1 1.0 N D:CYS232 4.0 82.0 1.0 N D:ASN233 4.1 61.8 1.0 CA D:THR231 4.1 86.7 1.0 CA D:ASP229 4.1 79.9 1.0 N D:TYR235 4.2 78.9 1.0 C D:THR231 4.2 86.2 1.0 CB D:ASP229 4.2 68.2 1.0 CA D:TYR235 4.3 73.9 1.0 C D:ASP229 4.3 76.5 1.0 N D:LEU230 4.4 72.5 1.0 N D:ILE236 4.5 83.2 1.0 CG2 D:THR231 4.5 65.0 1.0 CB D:TYR235 4.6 70.6 1.0 CG D:GLU240 4.6 80.9 1.0 CB D:ASN233 4.6 65.3 1.0 CA D:ILE236 4.7 73.5 1.0 CA D:CYS232 4.7 75.3 1.0 CA D:ASN233 4.8 61.0 1.0 C D:CYS232 4.8 72.1 1.0 O D:ASP229 4.9 91.0 1.0 C D:LEU230 4.9 81.5 1.0 CD1 D:ILE236 5.0 72.6 1.0 N D:ASP234 5.0 61.9 1.0

Calcium binding site 5 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca503 b:0.1 occ:1.00 O E:TYR235 2.3 0.5 1.0 OG1 E:THR231 2.4 91.8 1.0 OD1 E:ASP229 2.4 0.1 1.0 OE2 E:GLU240 2.4 0.7 1.0 OD1 E:ASN233 2.4 98.5 1.0 OE1 E:GLU240 2.9 0.1 1.0 CD E:GLU240 3.0 0.9 1.0 CG E:ASN233 3.2 0.1 1.0 C E:TYR235 3.4 0.1 1.0 ND2 E:ASN233 3.5 0.2 1.0 CG E:ASP229 3.5 98.5 1.0 CB E:THR231 3.7 0.5 1.0 N E:THR231 3.9 0.9 1.0 N E:CYS232 4.2 0.1 1.0 N E:TYR235 4.2 0.6 1.0 N E:ASN233 4.2 96.2 1.0 CA E:THR231 4.2 0.8 1.0 CA E:TYR235 4.2 0.4 1.0 OD2 E:ASP229 4.3 99.7 1.0 CA E:ASP229 4.4 96.3 1.0 N E:ILE236 4.4 0.7 1.0 C E:THR231 4.4 0.9 1.0 CG2 E:THR231 4.4 94.8 1.0 CB E:ASP229 4.5 92.1 1.0 CG E:GLU240 4.5 0.8 1.0 CB E:TYR235 4.5 0.3 1.0 CA E:ILE236 4.5 0.1 1.0 N E:LEU230 4.5 94.8 1.0 CB E:ASN233 4.5 0.7 1.0 C E:ASP229 4.6 93.7 1.0 OE2 E:GLU164 4.6 0.7 1.0 CA E:ASN233 4.8 0.6 1.0 CD1 E:ILE236 5.0 96.3 1.0

Calcium binding site 6 out of 6 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca503 b:0.7 occ:1.00 O F:TYR235 2.3 0.5 1.0 OG1 F:THR231 2.4 0.3 1.0 OD1 F:ASN233 2.4 0.1 1.0 OE2 F:GLU240 2.4 0.4 1.0 OD1 F:ASP229 2.4 0.4 1.0 OE1 F:GLU240 2.9 0.8 1.0 CD F:GLU240 3.0 0.6 1.0 CG F:ASP229 3.3 0.1 1.0 CG F:ASN233 3.4 1.0 1.0 C F:TYR235 3.5 0.7 1.0 CB F:THR231 3.7 0.8 1.0 OD2 F:ASP229 3.8 91.5 1.0 N F:THR231 3.8 0.7 1.0 ND2 F:ASN233 3.9 0.4 1.0 CA F:THR231 4.2 0.9 1.0 N F:CYS232 4.2 0.6 1.0 N F:TYR235 4.2 0.7 1.0 N F:ASN233 4.2 0.7 1.0 CA F:ASP229 4.3 0.2 1.0 CA F:TYR235 4.3 0.8 1.0 CB F:ASP229 4.3 98.1 1.0 C F:THR231 4.4 0.1 1.0 N F:LEU230 4.4 99.9 1.0 N F:ILE236 4.5 97.5 1.0 C F:ASP229 4.5 0.5 1.0 CG F:GLU240 4.5 0.7 1.0 CG2 F:THR231 4.5 0.3 1.0 CB F:TYR235 4.6 0.6 1.0 CA F:ILE236 4.6 93.1 1.0 CB F:ASN233 4.6 0.4 1.0 CA F:ASN233 4.9 0.4 1.0 CD1 F:ILE236 4.9 98.5 1.0

L.Buetow, G.Tria, S.F.Ahmed, A.Hock, H.Dou, G.J.Sibbet, D.I.Svergun, D.T.Huang. Casitas B-Lineage Lymphoma Linker Helix Mutations Found in Myeloproliferative Neoplasms Affect Conformation. Bmc Biol. V. 14 76 2016.
ISSN: ESSN 1741-7007
PubMed: 27609087
DOI: 10.1186/S12915-016-0298-6