Zinc 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:

Calcium

(Ca)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of C-Cbl Y371F (pdb code 5j3x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of C-Cbl Y371F, PDB code: 5j3x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:82.7 occ:1.00 SG A:CYS401 2.3 89.6 1.0 SG A:CYS404 2.3 84.7 1.0 SG A:CYS384 2.4 0.8 1.0 SG A:CYS381 2.4 81.8 1.0 CB A:CYS381 3.3 81.2 1.0 CB A:CYS404 3.4 68.7 1.0 CB A:CYS384 3.4 87.1 1.0 CB A:CYS401 3.6 67.8 1.0 N A:CYS384 3.7 82.1 1.0 N A:CYS401 4.1 67.5 1.0 CA A:CYS384 4.2 96.8 1.0 CA A:CYS401 4.3 67.5 1.0 CB A:ILE383 4.4 79.1 1.0 N A:CYS404 4.4 76.7 1.0 CA A:CYS404 4.4 77.2 1.0 CA A:CYS381 4.7 71.5 1.0 C A:ILE383 4.7 86.7 1.0 O A:CYS401 4.8 74.5 1.0 N A:ILE383 4.8 71.4 1.0 C A:CYS401 4.8 79.5 1.0 O A:ASN387 4.9 88.5 1.0 CA A:ILE383 4.9 80.5 1.0 C A:CYS381 4.9 83.6 1.0 N A:ALA385 5.0 87.4 1.0

Zinc binding site 2 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.5 occ:1.00 ND1 A:HIS398 2.0 70.2 1.0 SG A:CYS416 2.3 93.8 1.0 SG A:CYS419 2.3 72.2 1.0 SG A:CYS396 2.4 0.8 1.0 CE1 A:HIS398 2.8 77.0 1.0 CB A:CYS416 3.1 87.5 1.0 CG A:HIS398 3.1 69.6 1.0 CB A:CYS396 3.1 91.2 1.0 CB A:CYS419 3.6 96.3 1.0 CB A:HIS398 3.6 69.0 1.0 N A:CYS419 3.8 74.3 1.0 NE2 A:HIS398 4.0 70.5 1.0 CD2 A:HIS398 4.1 69.8 1.0 CA A:CYS419 4.3 85.9 1.0 CB A:PHE418 4.3 70.2 1.0 CA A:CYS396 4.5 92.4 1.0 CA A:CYS416 4.6 92.5 1.0 N A:HIS398 4.7 72.3 1.0 CA A:HIS398 4.8 81.9 1.0 C A:PHE418 4.8 83.8 1.0 C A:CYS396 4.9 86.3 1.0 N A:PHE418 4.9 91.6 1.0 CA A:PHE418 4.9 76.3 1.0 C A:CYS419 5.0 95.6 1.0 N A:ARG420 5.0 95.2 1.0

Zinc binding site 3 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:93.0 occ:1.00 SG B:CYS401 2.3 0.6 1.0 SG B:CYS404 2.3 96.7 1.0 SG B:CYS384 2.3 0.3 1.0 SG B:CYS381 2.4 92.9 1.0 CB B:CYS404 3.2 96.2 1.0 CB B:CYS381 3.3 94.1 1.0 CB B:CYS384 3.4 97.6 1.0 CB B:CYS401 3.5 98.7 1.0 N B:CYS384 3.7 96.3 1.0 N B:CYS401 4.0 91.7 1.0 CA B:CYS384 4.2 97.5 1.0 CA B:CYS401 4.3 92.2 1.0 N B:CYS404 4.3 97.1 1.0 CB B:ILE383 4.3 99.1 1.0 CA B:CYS404 4.4 97.4 1.0 CA B:CYS381 4.6 91.1 1.0 O B:CYS401 4.7 93.6 1.0 C B:ILE383 4.8 96.5 1.0 C B:CYS401 4.8 93.1 1.0 O B:CYS381 4.8 92.9 1.0 C B:CYS381 4.9 91.9 1.0 N B:ILE383 4.9 96.7 1.0 CA B:ILE383 4.9 0.8 1.0

Zinc binding site 4 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:93.0 occ:1.00 ND1 B:HIS398 2.1 90.3 1.0 SG B:CYS396 2.3 0.1 1.0 SG B:CYS419 2.3 98.8 1.0 SG B:CYS416 2.7 99.0 1.0 CE1 B:HIS398 2.8 90.2 1.0 CG B:HIS398 3.2 89.3 1.0 CB B:CYS396 3.2 92.8 1.0 CB B:CYS416 3.3 94.3 1.0 CB B:CYS419 3.6 0.5 1.0 CB B:HIS398 3.7 89.3 1.0 N B:CYS419 3.8 99.7 1.0 NE2 B:HIS398 4.0 89.2 1.0 CD2 B:HIS398 4.2 88.7 1.0 CA B:CYS419 4.3 0.9 1.0 CB B:PHE418 4.4 96.8 1.0 CA B:CYS396 4.6 0.7 1.0 N B:HIS398 4.7 88.2 1.0 CA B:CYS416 4.8 95.7 1.0 C B:PHE418 4.8 0.6 1.0 CA B:HIS398 4.9 88.4 1.0 C B:CYS396 4.9 0.4 1.0 N B:PHE418 4.9 0.1 1.0 CA B:PHE418 5.0 96.7 1.0

Zinc binding site 5 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.6 occ:1.00 SG C:CYS404 2.3 0.0 1.0 SG C:CYS401 2.3 0.5 1.0 SG C:CYS384 2.3 0.6 1.0 SG C:CYS381 2.4 0.8 1.0 CB C:CYS384 3.2 0.8 1.0 CB C:CYS404 3.3 0.1 1.0 CB C:CYS381 3.3 0.5 1.0 CB C:CYS401 3.5 0.1 1.0 N C:CYS384 3.6 0.7 1.0 CA C:CYS384 4.0 0.1 1.0 N C:CYS401 4.1 0.8 1.0 CB C:ILE383 4.3 0.8 1.0 CA C:CYS401 4.3 0.3 1.0 N C:CYS404 4.4 0.0 1.0 CA C:CYS404 4.4 0.9 1.0 C C:ILE383 4.6 0.6 1.0 O C:CYS401 4.7 0.5 1.0 CA C:CYS381 4.7 0.7 1.0 ND2 C:ASN387 4.8 0.9 1.0 N C:ILE383 4.8 0.8 1.0 C C:CYS401 4.8 0.6 1.0 CA C:ILE383 4.8 0.1 1.0 CB C:ASN387 4.9 0.9 1.0 C C:CYS381 4.9 0.9 1.0 N C:ALA385 4.9 0.5 1.0 C C:CYS384 5.0 0.2 1.0

Zinc binding site 6 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:0.7 occ:1.00 ND1 C:HIS398 2.1 97.3 1.0 SG C:CYS419 2.3 99.1 1.0 SG C:CYS416 2.4 0.1 1.0 SG C:CYS396 2.4 0.9 1.0 CE1 C:HIS398 2.9 95.7 1.0 CB C:CYS416 3.0 0.8 1.0 CG C:HIS398 3.1 97.6 1.0 CB C:CYS396 3.1 99.4 1.0 CB C:CYS419 3.5 0.3 1.0 CB C:HIS398 3.5 99.5 1.0 N C:CYS419 3.8 0.6 1.0 NE2 C:HIS398 4.0 94.9 1.0 CD2 C:HIS398 4.1 96.1 1.0 CA C:CYS419 4.2 96.9 1.0 CB C:PHE418 4.5 97.2 1.0 CA C:CYS416 4.5 0.8 1.0 CA C:CYS396 4.6 0.9 1.0 N C:HIS398 4.7 0.6 1.0 CA C:HIS398 4.8 0.6 1.0 C C:PHE418 4.9 0.5 1.0 N C:PHE418 4.9 0.0 1.0 C C:CYS396 4.9 0.8 1.0 N C:ARG420 4.9 0.2 1.0 C C:CYS419 5.0 0.0 1.0 CA C:PHE418 5.0 0.1 1.0

Zinc binding site 7 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:84.3 occ:1.00 SG D:CYS404 2.3 82.0 1.0 SG D:CYS401 2.3 77.9 1.0 SG D:CYS384 2.3 95.4 1.0 SG D:CYS381 2.4 95.0 1.0 CB D:CYS381 3.2 67.9 1.0 CB D:CYS404 3.3 77.1 1.0 CB D:CYS384 3.4 86.7 1.0 CB D:CYS401 3.5 74.5 1.0 N D:CYS384 3.8 71.6 1.0 N D:CYS401 4.0 68.3 1.0 CA D:CYS384 4.2 85.1 1.0 CA D:CYS401 4.3 63.7 1.0 N D:CYS404 4.3 77.1 1.0 CB D:ILE383 4.4 76.4 1.0 CA D:CYS404 4.4 79.5 1.0 CA D:CYS381 4.6 69.3 1.0 O D:CYS401 4.6 81.2 1.0 C D:ILE383 4.7 85.8 1.0 N D:ILE383 4.8 79.1 1.0 C D:CYS401 4.8 84.9 1.0 C D:CYS381 4.8 98.7 1.0 CA D:ILE383 4.9 83.6 1.0 O D:CYS381 4.9 72.2 1.0 CB D:ASN387 5.0 70.2 1.0 ND2 D:ASN387 5.0 95.0 1.0

Zinc binding site 8 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:78.1 occ:1.00 ND1 D:HIS398 2.1 77.8 1.0 SG D:CYS416 2.3 79.4 1.0 SG D:CYS396 2.4 95.8 1.0 SG D:CYS419 2.4 73.9 1.0 CE1 D:HIS398 2.9 79.4 1.0 CB D:CYS396 3.1 72.1 1.0 CB D:CYS416 3.1 71.9 1.0 CG D:HIS398 3.1 84.5 1.0 CB D:CYS419 3.5 86.8 1.0 CB D:HIS398 3.6 90.3 1.0 N D:CYS419 3.7 72.3 1.0 NE2 D:HIS398 4.0 71.1 1.0 CD2 D:HIS398 4.1 69.2 1.0 CA D:CYS419 4.2 84.7 1.0 CB D:PHE418 4.3 74.7 1.0 CA D:CYS396 4.5 75.4 1.0 CA D:CYS416 4.6 82.7 1.0 C D:PHE418 4.7 72.9 1.0 N D:HIS398 4.7 65.8 1.0 CA D:HIS398 4.8 82.7 1.0 N D:PHE418 4.8 84.3 1.0 CA D:PHE418 4.9 74.8 1.0 N D:ARG420 4.9 93.6 1.0 C D:CYS419 4.9 96.1 1.0 C D:CYS396 4.9 77.5 1.0

Zinc binding site 9 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:0.8 occ:1.00 SG E:CYS404 2.3 0.2 1.0 SG E:CYS401 2.3 0.4 1.0 SG E:CYS384 2.3 0.2 1.0 SG E:CYS381 2.4 0.2 1.0 CB E:CYS381 3.2 0.1 1.0 CB E:CYS404 3.2 0.1 1.0 CB E:CYS384 3.2 0.2 1.0 CB E:CYS401 3.6 0.2 1.0 N E:CYS384 3.7 0.9 1.0 N E:CYS401 4.1 0.8 1.0 CA E:CYS384 4.1 0.4 1.0 CA E:CYS401 4.3 0.9 1.0 CA E:CYS404 4.4 0.3 1.0 N E:CYS404 4.4 0.7 1.0 CB E:ILE383 4.5 0.5 1.0 CA E:CYS381 4.6 0.0 1.0 O E:CYS401 4.7 0.7 1.0 C E:ILE383 4.7 0.5 1.0 O E:ASN387 4.8 0.8 1.0 C E:CYS401 4.8 0.9 1.0 N E:ILE383 4.8 0.6 1.0 CB E:ASN387 4.9 0.1 1.0 C E:CYS381 4.9 0.0 1.0 ND2 E:ASN387 4.9 0.2 1.0 N E:ALA385 4.9 0.6 1.0 CA E:ILE383 4.9 0.6 1.0 C E:CYS384 5.0 1.0 1.0

Zinc binding site 10 out of 12 in the Structure of C-Cbl Y371F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of C-Cbl Y371F within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:0.7 occ:1.00 ND1 E:HIS398 2.1 0.1 1.0 SG E:CYS419 2.3 0.1 1.0 SG E:CYS416 2.4 0.2 1.0 SG E:CYS396 2.4 0.7 1.0 CE1 E:HIS398 2.9 0.6 1.0 CB E:CYS416 3.1 0.7 1.0 CG E:HIS398 3.1 0.6 1.0 CB E:CYS396 3.2 0.2 1.0 CB E:CYS419 3.5 0.4 1.0 CB E:HIS398 3.6 0.9 1.0 N E:CYS419 3.7 0.5 1.0 NE2 E:HIS398 4.0 0.1 1.0 CD2 E:HIS398 4.1 0.2 1.0 CA E:CYS419 4.1 0.3 1.0 CB E:PHE418 4.4 0.1 1.0 CA E:CYS416 4.6 0.7 1.0 CA E:CYS396 4.6 0.8 1.0 N E:HIS398 4.8 0.1 1.0 C E:PHE418 4.8 0.1 1.0 CA E:HIS398 4.8 0.6 1.0 N E:PHE418 4.9 0.5 1.0 C E:CYS419 4.9 0.7 1.0 CA E:PHE418 4.9 0.2 1.0 N E:ARG420 4.9 0.9 1.0 C E:CYS396 5.0 0.3 1.0 CG2 E:ILE393 5.0 0.9 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