Atomistry » Zinc » PDB 5o1j-5of9 » 5o76
Atomistry »
  Zinc »
    PDB 5o1j-5of9 »
      5o76 »

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

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy