Zinc in PDB 2y1m: Structure of Native C-Cbl

The structure of Structure of Native C-Cbl, PDB code: 2y1m was solved by H.Dou, G.J.Sibbet, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.615 / 2.67
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	146.800, 148.560, 348.210, 90.00, 90.00, 90.00
R / Rfree (%)	21.84 / 26.29

The structure of Structure of Native C-Cbl 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 Native C-Cbl (pdb code 2y1m). 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 Native C-Cbl, PDB code: 2y1m:
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 Native C-Cbl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1436 b:52.1 occ:1.00 SG A:CYS381 2.3 45.5 1.0 SG A:CYS404 2.3 57.9 1.0 SG A:CYS401 2.4 45.8 1.0 SG A:CYS384 2.4 56.5 1.0 CB A:CYS381 2.9 39.7 1.0 CB A:CYS404 3.2 48.9 1.0 CB A:CYS384 3.3 54.2 1.0 CB A:CYS401 3.4 51.4 1.0 N A:CYS384 3.5 51.1 1.0 N A:CYS401 3.9 41.1 1.0 CA A:CYS384 4.0 47.5 1.0 CB A:ILE383 4.1 55.1 1.0 CA A:CYS401 4.2 43.4 1.0 N A:CYS404 4.3 56.7 1.0 CA A:CYS404 4.3 58.0 1.0 CA A:CYS381 4.4 41.3 1.0 C A:ILE383 4.5 52.5 1.0 O A:CYS401 4.5 43.9 1.0 O A:CYS381 4.7 51.0 1.0 CG2 A:ILE383 4.7 49.5 1.0 CA A:ILE383 4.7 50.7 1.0 C A:CYS401 4.7 42.6 1.0 N A:ILE383 4.7 47.1 1.0 C A:CYS381 4.7 46.8 1.0 OD1 A:ASN387 4.8 51.9 1.0 C A:CYS384 5.0 49.8 1.0 N A:ALA385 5.0 53.4 1.0 O A:ASN387 5.0 44.8 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1437 b:46.1 occ:1.00 ND1 A:HIS398 2.0 31.4 1.0 SG A:CYS416 2.2 46.4 1.0 SG A:CYS419 2.3 58.5 1.0 CE1 A:HIS398 2.6 35.8 1.0 SG A:CYS396 2.7 50.9 1.0 CB A:CYS416 3.0 47.1 1.0 CG A:HIS398 3.2 38.0 1.0 CB A:CYS396 3.2 49.2 1.0 CB A:CYS419 3.5 55.6 1.0 N A:CYS419 3.6 54.1 1.0 CB A:HIS398 3.8 37.5 1.0 NE2 A:HIS398 3.9 42.9 1.0 CA A:CYS419 4.1 55.4 1.0 CB A:PHE418 4.1 43.3 1.0 CD2 A:HIS398 4.2 37.4 1.0 CA A:CYS416 4.5 51.8 1.0 C A:PHE418 4.6 53.4 1.0 N A:PHE418 4.6 49.8 1.0 CA A:PHE418 4.6 50.2 1.0 CA A:CYS396 4.7 48.4 1.0 N A:ARG420 4.8 58.8 1.0 C A:CYS416 4.8 51.8 1.0 N A:HIS398 4.8 41.4 1.0 O A:CYS416 4.8 53.8 1.0 C A:CYS419 4.8 59.8 1.0 C A:CYS396 5.0 48.4 1.0 CA A:HIS398 5.0 41.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1436 b:51.4 occ:1.00 SG B:CYS381 2.2 48.5 1.0 SG B:CYS404 2.2 52.2 1.0 SG B:CYS401 2.5 53.9 1.0 SG B:CYS384 2.5 58.4 1.0 CB B:CYS381 2.9 41.5 1.0 CB B:CYS401 3.1 51.6 1.0 CB B:CYS404 3.4 56.9 1.0 CB B:CYS384 3.5 56.8 1.0 N B:CYS384 3.8 56.5 1.0 N B:CYS401 3.9 44.9 1.0 CA B:CYS401 4.1 47.6 1.0 CA B:CYS384 4.2 58.5 1.0 CB B:ASN387 4.3 57.0 1.0 CB B:ILE383 4.4 60.5 1.0 N B:CYS404 4.4 56.0 1.0 CA B:CYS381 4.4 44.6 1.0 CA B:CYS404 4.5 56.2 1.0 C B:CYS401 4.7 50.0 1.0 O B:CYS401 4.7 47.1 1.0 C B:CYS381 4.7 49.8 1.0 C B:ILE383 4.7 57.1 1.0 CG2 B:ILE383 4.8 45.8 1.0 O B:CYS381 4.8 47.6 1.0 N B:ASN387 4.9 60.5 1.0 N B:ILE383 4.9 45.8 1.0 OD1 B:ASN387 4.9 58.7 1.0 CA B:ILE383 4.9 55.6 1.0 O B:ASN387 4.9 58.2 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1437 b:49.8 occ:1.00 ND1 B:HIS398 2.0 36.0 1.0 SG B:CYS416 2.3 48.2 1.0 SG B:CYS419 2.4 57.9 1.0 SG B:CYS396 2.6 55.8 1.0 CE1 B:HIS398 2.9 41.0 1.0 CB B:CYS396 3.0 45.6 1.0 CG B:HIS398 3.1 41.9 1.0 CB B:CYS416 3.2 55.6 1.0 CB B:HIS398 3.4 42.4 1.0 CB B:CYS419 3.6 53.1 1.0 N B:CYS419 3.9 48.8 1.0 NE2 B:HIS398 4.1 38.2 1.0 CD2 B:HIS398 4.2 41.5 1.0 CB B:PHE418 4.2 49.4 1.0 CA B:CYS419 4.3 52.0 1.0 CA B:CYS396 4.4 51.3 1.0 N B:HIS398 4.6 45.3 1.0 CA B:CYS416 4.6 59.0 1.0 CA B:HIS398 4.7 44.2 1.0 C B:PHE418 4.7 54.4 1.0 C B:CYS396 4.7 47.8 1.0 CA B:PHE418 4.8 54.5 1.0 N B:PHE418 4.8 47.9 1.0 C B:CYS416 5.0 57.6 1.0 O B:CYS396 5.0 52.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1436 b:56.2 occ:1.00 SG C:CYS404 2.2 49.6 1.0 SG C:CYS401 2.5 73.0 1.0 SG C:CYS381 2.6 56.9 1.0 SG C:CYS384 2.8 73.1 1.0 CB C:CYS384 2.9 63.5 1.0 CB C:CYS381 3.1 42.4 1.0 CB C:CYS404 3.4 57.1 1.0 N C:CYS384 3.6 55.4 1.0 CB C:CYS401 3.9 65.3 1.0 CA C:CYS384 3.9 56.4 1.0 OD1 C:ASN387 4.1 67.4 1.0 N C:CYS404 4.3 56.2 1.0 CA C:CYS404 4.4 57.9 1.0 N C:CYS401 4.4 57.0 1.0 C C:ILE383 4.5 59.2 1.0 CB C:ILE383 4.5 62.9 1.0 CA C:CYS381 4.6 43.4 1.0 CB C:ASN387 4.6 67.8 1.0 CA C:CYS401 4.6 56.0 1.0 CG C:ASN387 4.8 73.8 1.0 C C:CYS384 4.8 59.8 1.0 N C:ILE383 4.9 53.5 1.0 N C:ALA385 4.9 59.0 1.0 CA C:ILE383 4.9 59.3 1.0 O C:CYS381 4.9 61.9 1.0 O C:CYS401 4.9 56.1 1.0 C C:CYS381 4.9 53.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1437 b:50.3 occ:1.00 ND1 C:HIS398 1.9 36.9 1.0 SG C:CYS419 2.3 48.0 1.0 SG C:CYS416 2.5 51.0 1.0 SG C:CYS396 2.5 53.7 1.0 CE1 C:HIS398 2.8 35.9 1.0 CG C:HIS398 3.0 39.5 1.0 CB C:CYS396 3.0 50.3 1.0 CB C:CYS419 3.1 49.7 1.0 CB C:HIS398 3.4 42.3 1.0 CB C:CYS416 3.5 54.0 1.0 N C:CYS419 3.8 54.4 1.0 NE2 C:HIS398 4.0 40.8 1.0 CD2 C:HIS398 4.0 41.6 1.0 CA C:CYS419 4.1 54.4 1.0 CA C:CYS396 4.4 54.9 1.0 CB C:PHE418 4.4 46.9 1.0 N C:HIS398 4.5 52.2 1.0 CA C:HIS398 4.5 55.2 1.0 C C:CYS396 4.6 48.5 1.0 O C:CYS396 4.8 43.1 1.0 C C:PHE418 4.8 58.0 1.0 CA C:CYS416 4.9 61.1 1.0 C C:CYS419 5.0 60.2 1.0 CA C:PHE418 5.0 54.7 1.0 N C:ARG420 5.0 61.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1436 b:47.1 occ:1.00 SG D:CYS401 2.3 51.5 1.0 SG D:CYS404 2.3 49.5 1.0 SG D:CYS381 2.4 42.1 1.0 SG D:CYS384 2.5 53.9 1.0 CB D:CYS381 3.0 38.8 1.0 CB D:CYS384 3.2 41.4 1.0 CB D:CYS404 3.2 46.4 1.0 CB D:CYS401 3.3 44.7 1.0 N D:CYS384 3.7 44.3 1.0 N D:CYS401 3.9 42.6 1.0 CA D:CYS384 4.0 43.7 1.0 CA D:CYS401 4.1 42.3 1.0 N D:CYS404 4.2 41.9 1.0 CB D:ASN387 4.3 45.8 1.0 CB D:ILE383 4.3 48.5 1.0 CA D:CYS404 4.3 46.0 1.0 CA D:CYS381 4.5 42.0 1.0 O D:CYS401 4.5 44.6 1.0 C D:CYS401 4.6 42.0 1.0 C D:ILE383 4.7 47.3 1.0 N D:ILE383 4.9 43.2 1.0 OD1 D:ASN387 4.9 49.2 1.0 CA D:ILE383 4.9 43.7 1.0 N D:ALA385 4.9 48.6 1.0 C D:CYS384 5.0 47.4 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1437 b:46.9 occ:1.00 ND1 D:HIS398 2.1 36.0 1.0 SG D:CYS419 2.3 48.3 1.0 SG D:CYS416 2.3 40.5 1.0 SG D:CYS396 2.4 44.1 1.0 CE1 D:HIS398 2.9 35.8 1.0 CB D:CYS416 3.1 49.3 1.0 CG D:HIS398 3.2 38.6 1.0 CB D:CYS419 3.2 48.1 1.0 CB D:CYS396 3.4 46.2 1.0 N D:CYS419 3.6 49.3 1.0 CB D:HIS398 3.7 35.5 1.0 CA D:CYS419 4.0 48.6 1.0 NE2 D:HIS398 4.1 39.3 1.0 CB D:PHE418 4.2 49.3 1.0 CD2 D:HIS398 4.3 38.4 1.0 CA D:CYS416 4.6 56.2 1.0 C D:PHE418 4.6 51.7 1.0 CG2 D:ILE393 4.6 47.6 1.0 N D:HIS398 4.7 42.9 1.0 N D:ARG420 4.7 49.8 1.0 N D:PHE418 4.7 52.2 1.0 CA D:PHE418 4.7 50.2 1.0 C D:CYS419 4.7 52.2 1.0 CA D:CYS396 4.8 51.1 1.0 CA D:HIS398 4.8 39.9 1.0 C D:CYS416 5.0 49.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1436 b:70.4 occ:1.00 SG E:CYS384 2.4 68.2 1.0 SG E:CYS404 2.4 71.2 1.0 SG E:CYS381 2.6 60.8 1.0 CB E:CYS384 2.8 79.6 1.0 CB E:CYS404 2.8 68.9 1.0 SG E:CYS401 2.8 80.5 1.0 N E:CYS384 3.3 66.9 1.0 CB E:CYS381 3.3 58.0 1.0 CG1 E:ILE383 3.4 71.9 1.0 CA E:CYS384 3.6 72.8 1.0 CB E:CYS401 3.7 68.7 1.0 CD1 E:ILE383 4.0 74.5 1.0 CA E:CYS404 4.1 74.4 1.0 N E:CYS401 4.1 59.2 1.0 N E:CYS404 4.3 70.6 1.0 OD1 E:ASN387 4.3 73.4 1.0 CA E:CYS401 4.3 64.6 1.0 C E:ILE383 4.3 67.8 1.0 O E:CYS401 4.4 62.4 1.0 C E:CYS401 4.5 69.0 1.0 CB E:ILE383 4.7 67.1 1.0 N E:ILE383 4.7 61.3 1.0 C E:CYS384 4.7 72.2 1.0 CA E:CYS381 4.8 56.6 1.0 CA E:ILE383 4.8 68.8 1.0 N E:ALA385 4.8 68.7 1.0 CB E:ASN387 4.9 71.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Native C-Cbl within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1437 b:57.0 occ:1.00 ND1 E:HIS398 2.1 51.0 1.0 SG E:CYS419 2.4 58.8 1.0 SG E:CYS396 2.5 63.2 1.0 SG E:CYS416 2.6 48.3 1.0 CB E:CYS416 2.7 61.2 1.0 CE1 E:HIS398 2.9 50.5 1.0 CG E:HIS398 3.3 53.5 1.0 CB E:CYS419 3.4 65.8 1.0 CB E:CYS396 3.5 59.3 1.0 N E:CYS419 3.5 59.8 1.0 CB E:HIS398 3.9 53.3 1.0 CA E:CYS419 4.0 58.0 1.0 NE2 E:HIS398 4.1 51.7 1.0 CA E:CYS416 4.2 74.4 1.0 CD2 E:HIS398 4.3 52.6 1.0 CB E:PHE418 4.4 56.9 1.0 C E:PHE418 4.6 64.7 1.0 CG2 E:ILE393 4.6 60.6 1.0 C E:CYS419 4.7 62.6 1.0 N E:HIS398 4.8 56.9 1.0 CA E:CYS396 4.9 66.2 1.0 N E:ARG420 4.9 65.6 1.0 N E:CYS416 4.9 78.8 1.0 CA E:PHE418 4.9 61.7 1.0 C E:CYS416 4.9 67.5 1.0 N E:PHE418 4.9 66.4 1.0 CA E:HIS398 5.0 58.0 1.0

H.Dou, L.Buetow, A.Hock, G.J.Sibbet, K.H.Vousden, D.T.Huang. Structural Basis For Autoinhibition and Phosphorylation- Dependent Activation of C-Cbl. Nat.Struct.Mol.Biol. V. 19 184 2012.
ISSN: ISSN 1545-9993
PubMed: 22266821
DOI: 10.1038/NSMB.2231