Zinc in PDB 5vnz: Structure of A TRAF6-UBC13~Ub Complex

All present enzymatic activity of Structure of A TRAF6-UBC13~Ub Complex:
2.3.2.23; 2.3.2.27;

The structure of Structure of A TRAF6-UBC13~Ub Complex, PDB code: 5vnz was solved by A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.45 / 3.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	138.360, 170.551, 97.312, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 29.4

The binding sites of Zinc atom in the Structure of A TRAF6-UBC13~Ub Complex (pdb code 5vnz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A TRAF6-UBC13~Ub Complex, PDB code: 5vnz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of A TRAF6-UBC13~Ub 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 A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:0.2 occ:1.00 SG A:CYS91 2.3 0.2 1.0 SG A:CYS74 2.3 0.7 1.0 SG A:CYS94 2.3 0.1 1.0 SG A:CYS71 2.3 0.5 1.0 CB A:CYS71 3.3 0.4 1.0 CB A:CYS91 3.3 0.1 1.0 CB A:CYS94 3.4 1.0 1.0 CB A:CYS74 3.4 0.2 1.0 N A:CYS74 3.8 0.2 1.0 CA A:CYS74 4.2 0.6 1.0 N A:CYS91 4.2 0.2 1.0 N A:GLY56 4.3 0.8 1.0 CA A:CYS91 4.4 0.1 1.0 CB A:ILE73 4.6 0.8 1.0 CA A:GLY56 4.7 0.3 1.0 C A:GLN55 4.7 0.1 1.0 CA A:CYS71 4.7 0.1 1.0 CA A:CYS94 4.8 0.4 1.0 C A:ILE73 4.8 0.6 1.0

Zinc binding site 2 out of 6 in the Structure of A TRAF6-UBC13~Ub 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 A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:0.0 occ:1.00 NE2 A:HIS88 1.9 0.2 1.0 SG A:CYS106 2.3 0.9 1.0 SG A:CYS86 2.3 0.1 1.0 OD1 A:ASP109 2.4 0.2 1.0 OD2 A:ASP109 2.8 0.1 1.0 CE1 A:HIS88 2.9 0.4 1.0 CG A:ASP109 2.9 0.8 1.0 CD2 A:HIS88 2.9 0.8 1.0 CB A:CYS106 3.3 0.7 1.0 CB A:CYS86 3.4 0.3 1.0 CG2 A:VAL108 3.7 0.8 1.0 ND1 A:HIS88 3.9 0.4 1.0 CG A:HIS88 4.0 0.6 1.0 CB A:ASP109 4.3 0.4 1.0 N A:ASP109 4.4 0.4 1.0 CG A:GLU111 4.6 0.4 1.0 OG1 A:THR84 4.6 0.5 1.0 CA A:CYS106 4.7 0.4 1.0 CA A:CYS86 4.7 0.5 1.0 CB A:GLU111 4.8 0.0 1.0 C A:CYS86 4.8 0.4 1.0 CA A:ASP109 4.9 0.9 1.0 O A:CYS106 4.9 0.1 1.0 O C:GLY35 4.9 0.0 1.0 C A:CYS106 4.9 0.8 1.0

Zinc binding site 3 out of 6 in the Structure of A TRAF6-UBC13~Ub 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 A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:0.2 occ:1.00 NE2 A:HIS152 2.2 0.6 1.0 SG A:CYS135 2.3 0.0 1.0 SG A:CYS140 2.3 0.7 1.0 SG A:CYS156 2.3 0.6 1.0 CE1 A:HIS152 3.0 0.8 1.0 CD2 A:HIS152 3.2 0.1 1.0 CB A:CYS135 3.3 0.3 1.0 CB A:CYS140 3.4 0.1 1.0 CB A:CYS156 3.4 0.4 1.0 CA A:CYS156 4.1 0.4 1.0 ND1 A:HIS152 4.2 0.1 1.0 CG A:HIS152 4.3 0.5 1.0 ND2 A:ASN137 4.6 0.6 1.0 CA A:CYS135 4.7 0.9 1.0 CA A:CYS140 4.8 0.3 1.0 N A:ARG157 4.9 0.3 1.0 CB A:GLU142 5.0 0.9 1.0

Zinc binding site 4 out of 6 in the Structure of A TRAF6-UBC13~Ub 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 A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:0.1 occ:1.00 SG D:CYS91 2.3 0.0 1.0 SG D:CYS74 2.3 1.0 1.0 SG D:CYS94 2.3 0.1 1.0 SG D:CYS71 2.3 0.5 1.0 CB D:CYS71 3.3 0.4 1.0 CB D:CYS91 3.3 0.3 1.0 CB D:CYS94 3.4 0.4 1.0 CB D:CYS74 3.4 0.6 1.0 N D:CYS74 3.8 0.8 1.0 CA D:CYS74 4.2 0.0 1.0 N D:CYS91 4.2 0.4 1.0 N D:GLY56 4.2 0.3 1.0 CA D:CYS91 4.4 0.1 1.0 CB D:ILE73 4.6 0.7 1.0 CA D:GLY56 4.7 1.0 1.0 C D:GLN55 4.7 0.8 1.0 CA D:CYS71 4.7 0.0 1.0 CA D:CYS94 4.8 0.4 1.0 C D:ILE73 4.8 0.9 1.0

Zinc binding site 5 out of 6 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:0.7 occ:1.00 NE2 D:HIS88 1.9 0.2 1.0 SG D:CYS106 2.3 0.2 1.0 SG D:CYS86 2.3 0.3 1.0 OD1 D:ASP109 2.4 0.6 1.0 OD2 D:ASP109 2.8 0.1 1.0 CE1 D:HIS88 2.9 0.5 1.0 CG D:ASP109 2.9 0.1 1.0 CD2 D:HIS88 2.9 0.1 1.0 CB D:CYS106 3.3 0.6 1.0 CB D:CYS86 3.4 0.6 1.0 CG2 D:VAL108 3.7 0.3 1.0 ND1 D:HIS88 3.9 0.0 1.0 CG D:HIS88 4.0 0.0 1.0 CB D:ASP109 4.3 0.1 1.0 N D:ASP109 4.4 0.7 1.0 CG D:GLU111 4.6 0.7 1.0 OG1 D:THR84 4.6 0.5 1.0 CA D:CYS106 4.7 0.8 1.0 CA D:CYS86 4.7 0.9 1.0 CB D:GLU111 4.8 0.5 1.0 C D:CYS86 4.8 0.4 1.0 CA D:ASP109 4.9 0.3 1.0 O D:CYS106 4.9 0.3 1.0 C D:CYS106 4.9 0.9 1.0

Zinc binding site 6 out of 6 in the Structure of A TRAF6-UBC13~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A TRAF6-UBC13~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:0.1 occ:1.00 NE2 D:HIS152 2.2 0.4 1.0 SG D:CYS156 2.3 0.6 1.0 SG D:CYS140 2.3 0.6 1.0 SG D:CYS135 2.4 0.4 1.0 CE1 D:HIS152 3.0 0.1 1.0 CD2 D:HIS152 3.2 0.4 1.0 CB D:CYS140 3.4 1.0 1.0 CB D:CYS135 3.4 0.6 1.0 CB D:CYS156 3.4 0.0 1.0 ND1 D:HIS152 4.1 0.2 1.0 CA D:CYS156 4.2 0.5 1.0 CG D:HIS152 4.3 0.7 1.0 ND2 D:ASN137 4.5 0.2 1.0 CA D:CYS135 4.8 0.5 1.0 OE1 D:GLU142 4.8 0.9 1.0 CA D:CYS140 4.8 0.5 1.0 N D:ARG157 4.9 0.0 1.0 CD D:GLU142 4.9 0.5 1.0

A.J.Middleton, R.Budhidarmo, A.Das, J.Zhu, M.Foglizzo, P.D.Mace, C.L.Day. The Activity of Traf Ring Homo- and Heterodimers Is Regulated By Zinc Finger 1. Nat Commun V. 8 1788 2017.
ISSN: ESSN 2041-1723
PubMed: 29176576
DOI: 10.1038/S41467-017-01665-3