Zinc in PDB 2y1n: Structure of C-Cbl-Zap-70 Peptide Complex

All present enzymatic activity of Structure of C-Cbl-Zap-70 Peptide Complex:
2.7.10.2;

The structure of Structure of C-Cbl-Zap-70 Peptide Complex, PDB code: 2y1n 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)	45.423 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	93.570, 93.570, 189.599, 90.00, 90.00, 120.00
R / Rfree (%)	15.82 / 18.04

The structure of Structure of C-Cbl-Zap-70 Peptide Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of C-Cbl-Zap-70 Peptide Complex (pdb code 2y1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of C-Cbl-Zap-70 Peptide Complex, PDB code: 2y1n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of C-Cbl-Zap-70 Peptide Complex


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-Zap-70 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1436 b:30.2 occ:1.00 SG A:CYS404 2.3 31.3 1.0 SG A:CYS401 2.3 28.7 1.0 SG A:CYS381 2.4 30.6 1.0 SG A:CYS384 2.4 33.7 1.0 CB A:CYS404 3.0 32.6 1.0 CB A:CYS381 3.0 28.7 1.0 CB A:CYS384 3.4 31.5 1.0 CB A:CYS401 3.5 29.2 1.0 N A:CYS384 3.6 30.8 1.0 N A:CYS401 4.0 27.9 1.0 CA A:CYS384 4.1 31.5 1.0 CA A:CYS404 4.2 35.0 1.0 N A:CYS404 4.2 33.8 1.0 CB A:ILE383 4.2 35.3 1.0 CA A:CYS401 4.3 32.7 1.0 ND2 A:ASN387 4.3 30.6 1.0 CA A:CYS381 4.5 29.9 1.0 O A:CYS401 4.6 31.7 1.0 CB A:ASN387 4.6 33.8 1.0 C A:ILE383 4.7 35.1 1.0 CG2 A:ILE383 4.7 35.5 1.0 C A:CYS401 4.8 31.7 1.0 C A:CYS381 4.8 31.8 1.0 O A:CYS381 4.8 35.3 1.0 CA A:ILE383 4.8 34.3 1.0 N A:ILE383 4.8 37.4 1.0 CG A:ASN387 4.9 35.7 1.0 O A:ASN387 5.0 29.1 1.0 OG A:SER403 5.0 39.2 1.0

Zinc binding site 2 out of 4 in the Structure of C-Cbl-Zap-70 Peptide Complex


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-Zap-70 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1437 b:27.4 occ:1.00 ND1 A:HIS398 2.1 26.0 1.0 SG A:CYS396 2.3 26.1 1.0 SG A:CYS419 2.3 25.0 1.0 SG A:CYS416 2.4 27.0 1.0 CE1 A:HIS398 3.1 30.4 1.0 CG A:HIS398 3.1 26.4 1.0 CB A:CYS416 3.1 26.0 1.0 CB A:CYS396 3.2 26.8 1.0 CB A:HIS398 3.4 26.1 1.0 CB A:CYS419 3.6 26.3 1.0 N A:CYS419 3.8 26.5 1.0 NE2 A:HIS398 4.2 30.8 1.0 CD2 A:HIS398 4.2 28.8 1.0 CA A:CYS419 4.3 29.1 1.0 CB A:PHE418 4.4 26.8 1.0 N A:HIS398 4.5 28.6 1.0 CA A:CYS396 4.5 26.2 1.0 O A:HOH2191 4.6 29.1 1.0 CA A:CYS416 4.6 27.4 1.0 CA A:HIS398 4.6 29.6 1.0 C A:PHE418 4.8 25.4 1.0 C A:CYS396 4.8 27.0 1.0 C A:CYS419 4.9 28.4 1.0 N A:PHE418 4.9 28.4 1.0 CA A:PHE418 4.9 27.0 1.0 N A:ARG420 5.0 27.4 1.0 O A:HOH2172 5.0 31.5 1.0

Zinc binding site 3 out of 4 in the Structure of C-Cbl-Zap-70 Peptide Complex


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-Zap-70 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1436 b:36.5 occ:1.00 SG C:CYS401 2.3 30.7 1.0 SG C:CYS381 2.3 38.6 1.0 SG C:CYS384 2.3 35.5 1.0 SG C:CYS404 2.5 43.6 1.0 CB C:CYS381 3.0 34.3 1.0 CB C:CYS404 3.1 40.2 1.0 CB C:CYS384 3.4 35.8 1.0 CB C:CYS401 3.5 32.0 1.0 N C:CYS384 3.7 39.6 1.0 N C:CYS404 4.0 41.8 1.0 N C:CYS401 4.1 29.9 1.0 CA C:CYS404 4.2 43.4 1.0 CA C:CYS384 4.2 37.2 1.0 CB C:ILE383 4.2 41.6 1.0 ND2 C:ASN387 4.3 40.5 1.0 CA C:CYS401 4.3 35.5 1.0 CG2 C:ILE383 4.4 43.5 1.0 CA C:CYS381 4.4 32.7 1.0 CB C:ASN387 4.5 34.6 1.0 O C:CYS401 4.7 37.2 1.0 C C:ILE383 4.7 40.5 1.0 CG C:ASN387 4.9 37.1 1.0 C C:CYS401 4.9 37.6 1.0 C C:CYS381 4.9 37.4 1.0 CA C:ILE383 4.9 39.6 1.0 N C:ASN387 4.9 35.4 1.0 N C:ILE383 5.0 37.0 1.0 O C:ASN387 5.0 31.7 1.0 O C:CYS381 5.0 36.1 1.0 N C:ALA385 5.0 38.2 1.0

Zinc binding site 4 out of 4 in the Structure of C-Cbl-Zap-70 Peptide Complex


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-Zap-70 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1437 b:31.2 occ:1.00 ND1 C:HIS398 2.2 31.7 1.0 SG C:CYS396 2.3 30.1 1.0 SG C:CYS419 2.5 32.3 1.0 SG C:CYS416 2.5 29.8 1.0 CE1 C:HIS398 3.1 33.0 1.0 CB C:CYS396 3.1 32.5 1.0 CG C:HIS398 3.2 33.1 1.0 CB C:CYS416 3.3 37.8 1.0 CB C:CYS419 3.5 31.4 1.0 CB C:HIS398 3.6 30.0 1.0 N C:CYS419 4.0 33.2 1.0 NE2 C:HIS398 4.3 33.6 1.0 CA C:CYS419 4.3 34.2 1.0 CD2 C:HIS398 4.3 34.1 1.0 N C:HIS398 4.5 29.1 1.0 CA C:CYS396 4.6 30.5 1.0 CB C:PHE418 4.6 36.5 1.0 CA C:HIS398 4.7 30.7 1.0 CA C:CYS416 4.7 35.7 1.0 O C:HOH2119 4.7 33.9 1.0 N C:PHE418 4.8 33.1 1.0 C C:CYS396 4.9 31.1 1.0 C C:PHE418 4.9 34.4 1.0 C C:CYS419 5.0 37.6 1.0 N C:ARG420 5.0 35.8 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