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Zinc in PDB 5o76: Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant

Enzymatic activity of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant

All present enzymatic activity of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant:
2.3.2.27;

Protein crystallography data

The structure of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant, PDB code: 5o76 was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.34 / 2.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.790, 101.281, 117.339, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.8

Other elements in 5o76:

The structure of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant (pdb code 5o76). 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 PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant, PDB code: 5o76:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5o76

Go back to Zinc Binding Sites List in 5o76
Zinc binding site 1 out of 4 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:51.0
occ:1.00
 SG A:CYS384 2.2 44.6 1.0
SG A:CYS401 2.3 46.1 1.0
SG A:CYS381 2.3 39.7 1.0
SG A:CYS404 2.5 47.3 1.0
CB A:CYS384 3.0 41.6 1.0
CB A:CYS381 3.2 36.0 1.0
N A:CYS384 3.5 41.7 1.0
CB A:CYS404 3.5 42.4 1.0
CB A:CYS401 3.5 42.0 1.0
CA A:CYS384 3.8 41.7 1.0
N A:CYS401 4.0 41.7 1.0
CA A:CYS401 4.3 41.5 1.0
N A:CYS404 4.4 43.7 1.0
CA A:CYS381 4.5 35.4 1.0
C A:ILE383 4.5 46.0 1.0
CA A:CYS404 4.6 42.7 1.0
CB A:ILE383 4.6 43.1 1.0
N A:ALA385 4.6 40.1 1.0
C A:CYS384 4.7 45.7 1.0
O A:CYS401 4.7 44.9 1.0
C A:CYS381 4.7 38.2 1.0
N A:ILE383 4.8 39.5 1.0
CA A:ILE383 4.8 40.4 1.0
O A:CYS381 4.8 37.2 1.0
C A:CYS401 4.9 45.6 1.0

Zinc binding site 2 out of 4 in 5o76

Go back to Zinc Binding Sites List in 5o76
Zinc binding site 2 out of 4 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:47.6
occ:1.00
 ND1 A:HIS398 2.0 45.0 1.0
SG A:CYS416 2.2 50.8 1.0
SG A:CYS396 2.3 45.5 1.0
SG A:CYS419 2.6 55.0 1.0
CG A:HIS398 3.0 43.6 1.0
CE1 A:HIS398 3.0 44.6 1.0
CB A:CYS416 3.0 47.1 1.0
CB A:CYS396 3.2 41.8 1.0
CB A:HIS398 3.3 40.2 1.0
CB A:CYS419 3.8 52.1 1.0
N A:CYS419 4.0 51.3 1.0
NE2 A:HIS398 4.1 45.4 1.0
CD2 A:HIS398 4.1 45.5 1.0
HG21 A:ILE393 4.4 45.8 1.0
N A:HIS398 4.4 39.3 1.0
CA A:CYS419 4.4 52.0 1.0
CA A:HIS398 4.5 39.5 1.0
CA A:CYS416 4.5 47.5 1.0
CA A:CYS396 4.6 41.3 1.0
CB A:PHE418 4.7 49.9 1.0
HG13 A:ILE393 4.7 45.9 1.0
HG22 A:ILE393 4.8 44.9 1.0
C A:PHE418 4.8 54.2 1.0
CB A:CYS421 4.9 55.2 1.0
C A:CYS396 4.9 44.5 1.0
N A:PHE418 5.0 47.2 1.0
CG2 A:ILE393 5.0 45.0 1.0
C A:CYS416 5.0 51.4 1.0

Zinc binding site 3 out of 4 in 5o76

Go back to Zinc Binding Sites List in 5o76
Zinc binding site 3 out of 4 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:53.0
occ:1.00
 SG C:CYS384 2.3 53.6 1.0
SG C:CYS401 2.4 51.5 1.0
SG C:CYS381 2.4 46.8 1.0
SG C:CYS404 2.5 57.9 1.0
CB C:CYS381 3.2 43.5 1.0
CB C:CYS384 3.3 49.4 1.0
CB C:CYS401 3.3 47.8 1.0
CB C:CYS404 3.3 53.3 1.0
N C:CYS384 3.8 48.7 1.0
HD22 C:ASN387 4.0 58.5 1.0
N C:CYS401 4.0 46.0 1.0
CA C:CYS384 4.1 48.9 1.0
CA C:CYS401 4.1 46.9 1.0
O C:HOH653 4.2 63.8 1.0
N C:CYS404 4.3 53.1 1.0
CA C:CYS404 4.4 52.7 1.0
O C:CYS401 4.5 49.4 1.0
CA C:CYS381 4.6 43.5 1.0
C C:CYS401 4.6 51.2 1.0
CB C:ILE383 4.8 49.9 1.0
C C:ILE383 4.8 51.2 1.0
N C:ALA385 4.9 48.0 1.0
ND2 C:ASN387 4.9 59.2 1.0
C C:CYS384 5.0 52.7 1.0
C C:CYS381 5.0 48.7 1.0
CB C:ASN387 5.0 48.0 1.0
HG22 C:ILE383 5.0 50.8 1.0

Zinc binding site 4 out of 4 in 5o76

Go back to Zinc Binding Sites List in 5o76
Zinc binding site 4 out of 4 in the Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of PHOSPHOY371 C-Cbl in Complex with ZAP70-Peptide and Ubv.Pcbl Ubiquitin Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:52.3
occ:1.00
 SG C:CYS396 2.2 66.0 1.0
ND1 C:HIS398 2.2 48.7 1.0
SG C:CYS416 2.9 68.2 1.0
CB C:CYS396 2.9 60.3 1.0
CG C:HIS398 3.2 46.9 1.0
CE1 C:HIS398 3.2 48.6 1.0
CB C:CYS416 3.2 63.1 1.0
CB C:HIS398 3.4 43.2 1.0
O C:CYS419 3.8 65.3 1.0
N C:CYS419 3.8 60.2 1.0
CB C:CYS419 4.0 64.6 1.0
CA C:CYS419 4.3 62.4 1.0
CD2 C:HIS398 4.3 48.8 1.0
NE2 C:HIS398 4.3 49.2 1.0
CA C:CYS396 4.3 59.0 1.0
C C:CYS419 4.5 65.3 1.0
HG22 C:ILE393 4.5 52.5 1.0
CB C:PHE418 4.5 55.0 1.0
HG21 C:ILE393 4.5 51.4 1.0
CA C:CYS416 4.6 60.9 1.0
CA C:HIS398 4.7 43.5 1.0
HD12 C:ILE393 4.7 59.3 1.0
N C:HIS398 4.7 45.0 1.0
C C:PHE418 4.8 61.6 1.0
C C:CYS396 4.8 60.0 1.0
N C:PHE418 4.9 53.4 1.0
CA C:PHE418 4.9 54.0 1.0
O C:HOH634 4.9 34.3 1.0
CG2 C:ILE393 4.9 51.7 1.0
CB C:CYS421 5.0 58.2 1.0

Reference:

M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, G.J.Sibbet, B.O.Smith, W.Zhang, S.S.Sidhu, D.T.Huang. A General Strategy For Discovery of Inhibitors and Activators of Ring and U-Box E3 Ligases with Ubiquitin Variants. Mol. Cell V. 68 456 2017.
ISSN: ISSN 1097-4164
PubMed: 29053960
DOI: 10.1016/J.MOLCEL.2017.09.027
Page generated: Sun Oct 27 23:16:53 2024

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