Zinc in PDB 3oj3: Crystal Structure of the A20 ZNF4 and Ubiquitin Complex

The structure of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex, PDB code: 3oj3 was solved by I.Bosanac, S.G.Hymowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.830, 170.030, 66.239, 90.00, 90.10, 90.00
R / Rfree (%)	20.3 / 22.6

The binding sites of Zinc atom in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex (pdb code 3oj3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex, PDB code: 3oj3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn901 b:46.0 occ:1.00 SG I:CYS612 2.1 44.8 1.0 SG I:CYS627 2.4 58.9 1.0 SG I:CYS607 2.4 49.9 1.0 SG I:CYS624 2.7 44.0 1.0 CB I:CYS612 3.0 60.6 1.0 CB I:CYS607 3.1 45.3 1.0 CB I:CYS627 3.3 49.9 1.0 CB I:CYS624 3.6 38.9 1.0 N I:CYS624 4.2 47.5 1.0 CA I:CYS612 4.4 58.5 1.0 CA I:CYS624 4.5 42.1 1.0 CB I:LYS609 4.5 57.5 1.0 CA I:CYS627 4.6 42.6 1.0 CA I:CYS607 4.6 51.4 1.0 N I:CYS627 4.6 50.4 1.0 CB I:TYR614 4.8 39.0 1.0 CD I:LYS609 5.0 78.0 1.0 CD2 I:TYR614 5.0 40.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn902 b:53.2 occ:1.00 SG J:CYS612 2.1 47.5 1.0 SG J:CYS627 2.4 60.2 1.0 SG J:CYS607 2.4 49.6 1.0 SG J:CYS624 2.5 50.8 1.0 CB J:CYS607 3.2 45.5 1.0 CB J:CYS612 3.2 56.2 1.0 CB J:CYS627 3.3 46.9 1.0 CB J:CYS624 3.5 39.7 1.0 N J:CYS624 4.1 55.9 1.0 CA J:CYS624 4.4 48.9 1.0 CA J:CYS627 4.5 46.5 1.0 CA J:CYS612 4.6 56.8 1.0 N J:CYS627 4.6 53.5 1.0 CA J:CYS607 4.6 51.1 1.0 CB J:LYS609 4.7 59.0 1.0 CB J:TYR614 4.7 39.3 1.0 CD2 J:TYR614 4.9 42.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn903 b:53.2 occ:1.00 SG K:CYS607 2.1 46.5 1.0 SG K:CYS612 2.4 56.5 1.0 SG K:CYS627 2.4 70.2 1.0 SG K:CYS624 2.5 46.5 1.0 CB K:CYS607 2.9 48.5 1.0 CB K:CYS627 3.2 46.8 1.0 CB K:CYS624 3.2 41.7 1.0 O C:HOH82 3.3 53.0 1.0 CB K:CYS612 3.4 55.1 1.0 N K:CYS624 3.7 51.6 1.0 CA K:CYS624 4.0 49.3 1.0 CA K:CYS627 4.4 47.1 1.0 CA K:CYS607 4.4 54.9 1.0 N K:CYS627 4.5 49.7 1.0 CB K:TYR614 4.7 41.4 1.0 CB K:LYS609 4.7 59.1 1.0 C K:CYS624 4.7 46.7 1.0 CA K:CYS612 4.8 59.2 1.0 O K:CYS624 4.8 53.9 1.0 C K:PHE623 4.9 47.0 1.0 C K:CYS607 5.0 64.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn904 b:48.8 occ:1.00 SG L:CYS612 2.3 39.8 1.0 SG L:CYS627 2.4 64.2 1.0 SG L:CYS607 2.5 52.8 1.0 SG L:CYS624 2.6 39.9 1.0 CB L:CYS607 3.2 48.1 1.0 CB L:CYS627 3.3 46.2 1.0 CB L:CYS612 3.3 56.6 1.0 CB L:CYS624 3.4 43.3 1.0 N L:CYS624 4.0 48.9 1.0 CA L:CYS624 4.2 48.3 1.0 CA L:CYS627 4.4 43.6 1.0 N L:CYS627 4.4 51.4 1.0 CB L:TYR614 4.7 39.6 1.0 CA L:CYS612 4.7 53.1 1.0 CA L:CYS607 4.7 49.8 1.0 CB L:LYS609 4.8 61.1 1.0 CD2 L:TYR614 4.9 40.7 1.0 C L:CYS624 4.9 49.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn905 b:50.2 occ:1.00 SG M:CYS612 2.2 52.7 1.0 SG M:CYS627 2.3 53.7 1.0 SG M:CYS607 2.3 44.4 1.0 SG M:CYS624 2.8 43.2 1.0 CB M:CYS607 3.1 55.0 1.0 CB M:CYS612 3.1 56.1 1.0 CB M:CYS627 3.1 47.0 1.0 O E:HOH127 3.6 51.1 1.0 CB M:CYS624 3.7 42.4 1.0 N M:CYS624 4.1 52.4 1.0 CB M:LYS609 4.3 58.9 1.0 CA M:CYS627 4.4 43.5 1.0 CA M:CYS624 4.5 48.2 1.0 CA M:CYS612 4.5 58.8 1.0 CA M:CYS607 4.6 56.0 1.0 N M:CYS627 4.6 48.7 1.0 CD M:LYS609 4.8 79.5 1.0 CG M:LYS609 5.0 60.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn906 b:55.1 occ:1.00 SG N:CYS612 2.1 54.4 1.0 SG N:CYS627 2.4 55.9 1.0 SG N:CYS607 2.4 53.1 1.0 SG N:CYS624 2.7 44.9 1.0 CB N:CYS612 3.1 58.2 1.0 CB N:CYS607 3.2 49.2 1.0 CB N:CYS627 3.2 51.0 1.0 CB N:CYS624 3.6 40.8 1.0 N N:CYS624 4.1 48.0 1.0 CA N:CYS624 4.5 46.0 1.0 CA N:CYS627 4.5 46.8 1.0 CB N:LYS609 4.5 57.0 1.0 CA N:CYS612 4.5 57.0 1.0 N N:CYS627 4.6 47.9 1.0 CA N:CYS607 4.7 53.5 1.0 CB N:TYR614 4.8 41.9 1.0 CD N:LYS609 4.9 77.3 1.0 CD2 N:TYR614 5.0 40.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn907 b:73.6 occ:1.00 SG O:CYS607 2.2 71.1 1.0 SG O:CYS612 2.3 50.4 1.0 SG O:CYS627 2.3 69.5 1.0 SG O:CYS624 2.5 55.1 1.0 CB O:CYS624 2.8 36.7 1.0 CB O:CYS627 3.3 58.0 1.0 CB O:CYS612 3.3 61.7 1.0 CB O:CYS607 3.4 66.3 1.0 N O:CYS624 3.5 62.2 1.0 CA O:CYS624 3.7 54.2 1.0 CB O:LYS609 4.2 74.4 1.0 C O:CYS624 4.4 48.5 1.0 O O:CYS624 4.5 41.8 1.0 N O:CYS627 4.5 59.5 1.0 O G:HOH81 4.5 38.9 1.0 CA O:CYS627 4.5 54.5 1.0 C O:PHE623 4.7 65.6 1.0 CA O:CYS612 4.7 64.2 1.0 CA O:CYS607 4.8 64.8 1.0 CD O:LYS609 4.8 75.1 1.0 N O:LYS609 5.0 70.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the A20 ZNF4 and Ubiquitin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the A20 ZNF4 and Ubiquitin Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn908 b:60.6 occ:1.00 SG P:CYS607 2.2 54.8 1.0 SG P:CYS612 2.3 55.0 1.0 SG P:CYS627 2.4 61.0 1.0 SG P:CYS624 2.7 41.4 1.0 CB P:CYS607 2.9 52.0 1.0 CB P:CYS627 3.2 48.2 1.0 CB P:CYS612 3.2 60.3 1.0 CB P:CYS624 3.5 43.3 1.0 N P:CYS624 3.9 48.0 1.0 O H:HOH77 4.1 48.5 1.0 CA P:CYS624 4.3 49.1 1.0 CB P:LYS609 4.4 58.0 1.0 CA P:CYS607 4.4 51.9 1.0 CA P:CYS627 4.5 45.9 1.0 N P:CYS627 4.6 50.8 1.0 CA P:CYS612 4.6 56.5 1.0 O E:HOH79 4.6 53.0 1.0 C P:CYS607 4.9 60.2 1.0 CB P:TYR614 4.9 41.8 1.0 CD P:LYS609 4.9 76.4 1.0 N P:LYS609 5.0 57.9 1.0 C P:CYS624 5.0 50.3 1.0

I.Bosanac, I.E.Wertz, B.Pan, C.Yu, S.Kusam, C.Lam, L.Phu, Q.Phung, B.Maurer, D.Arnott, D.S.Kirkpatrick, V.M.Dixit, S.G.Hymowitz. Ubiquitin Binding to A20 ZNF4 Is Required For Modulation of Nf-Kb Signaling Mol.Cell V. 40 548 2010.
ISSN: ISSN 1097-2765
PubMed: 21095585
DOI: 10.1016/J.MOLCEL.2010.10.009