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Zinc in PDB 2wx0: TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21

Protein crystallography data

The structure of TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21, PDB code: 2wx0 was solved by Y.Kulathu, M.Akutsu, A.Bremm, K.Hofmann, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.799 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.390, 73.620, 59.250, 90.00, 105.91, 90.00
R / Rfree (%) 17.36 / 23.59

Zinc Binding Sites:

The binding sites of Zinc atom in the TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21 (pdb code 2wx0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21, PDB code: 2wx0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2wx0

Go back to Zinc Binding Sites List in 2wx0
Zinc binding site 1 out of 2 in the TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1694

b:24.6
occ:1.00
SG C:CYS673 2.3 19.2 1.0
SG C:CYS687 2.4 22.6 1.0
SG C:CYS670 2.4 24.4 1.0
SG C:CYS684 2.4 21.3 1.0
CB C:CYS670 3.1 14.2 1.0
CB C:CYS684 3.1 14.7 1.0
CB C:CYS687 3.2 16.0 1.0
CB C:CYS673 3.4 21.4 1.0
N C:CYS687 3.7 23.6 1.0
N C:CYS673 3.9 31.8 1.0
CA C:CYS687 4.0 25.9 1.0
CA C:CYS673 4.2 22.3 1.0
CB C:ALA672 4.5 20.3 1.0
CB C:GLN686 4.5 27.6 1.0
CB C:PHE675 4.6 25.3 1.0
CA C:CYS670 4.6 21.7 1.0
CA C:CYS684 4.6 18.1 1.0
C C:CYS687 4.7 24.5 1.0
C C:ALA672 4.7 34.7 1.0
C C:GLN686 4.7 28.0 1.0
N C:GLU688 4.8 30.6 1.0
C C:CYS673 4.8 22.4 1.0
N C:PHE675 4.8 25.8 1.0
N C:THR674 4.9 31.4 1.0
N C:ALA672 4.9 37.8 1.0
CA C:ALA672 5.0 31.4 1.0
N C:GLN686 5.0 25.4 1.0
CA C:GLN686 5.0 24.8 1.0

Zinc binding site 2 out of 2 in 2wx0

Go back to Zinc Binding Sites List in 2wx0
Zinc binding site 2 out of 2 in the TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TAB2 Nzf Domain in Complex with LYS63-Linked Di-Ubiquitin, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1694

b:26.2
occ:1.00
SG G:CYS673 2.2 20.1 1.0
SG G:CYS687 2.3 22.8 1.0
SG G:CYS670 2.4 24.1 1.0
SG G:CYS684 2.4 25.4 1.0
CB G:CYS670 3.2 17.6 1.0
CB G:CYS684 3.2 11.8 1.0
CB G:CYS673 3.3 10.8 1.0
CB G:CYS687 3.4 12.1 1.0
N G:CYS673 3.7 25.1 1.0
N G:CYS687 3.8 23.9 1.0
CA G:CYS673 4.0 25.4 1.0
CA G:CYS687 4.1 21.4 1.0
CB G:GLN686 4.2 25.1 1.0
CB G:ALA672 4.4 20.6 1.0
CB G:MET689 4.5 31.5 1.0
C G:ALA672 4.6 34.1 1.0
CB G:PHE675 4.6 32.6 1.0
CA G:CYS670 4.6 23.0 1.0
CA G:CYS684 4.7 16.7 1.0
C G:CYS673 4.7 20.4 1.0
C G:GLN686 4.7 30.4 1.0
C G:CYS687 4.8 25.8 1.0
N G:THR674 4.8 23.1 1.0
N G:PHE675 4.8 22.7 1.0
N G:ALA672 4.8 38.7 1.0
CA G:ALA672 4.8 35.1 1.0
CA G:GLN686 4.9 26.7 1.0
N G:GLU688 4.9 22.5 1.0
N G:MET689 4.9 25.6 1.0
N G:GLN686 4.9 28.3 1.0

Reference:

Y.Kulathu, M.Akutsu, A.Bremm, K.Hofmann, D.Komander. Two-Sided Ubiquitin Binding Explains Specificity of the TAB2 Nzf Domain Nat.Struct.Mol.Biol. V. 16 1328 2009.
ISSN: ISSN 1545-9993
PubMed: 19935683
DOI: 10.1038/NSMB.1731
Page generated: Sat Sep 26 04:28:11 2020
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