Zinc in PDB 3hct: Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group

All present enzymatic activity of Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group:
6.3.2.19;

The structure of Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group, PDB code: 3hct was solved by Q.Yin, S.-C.Lin, B.Lamothe, M.Lu, Y.-C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.985, 42.798, 49.118, 104.61, 99.59, 108.60
R / Rfree (%)	21.2 / 27.8

The binding sites of Zinc atom in the Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group (pdb code 3hct). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group, PDB code: 3hct:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group


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 TRAF6 in Complex with UBC13 in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.4 occ:1.00 SG A:CYS70 2.3 19.4 1.0 SG A:CYS90 2.4 23.8 1.0 SG A:CYS73 2.4 25.0 1.0 SG A:CYS93 2.4 25.1 1.0 CB A:CYS90 3.0 21.7 1.0 CB A:CYS70 3.0 21.6 1.0 CB A:CYS93 3.2 26.5 1.0 CB A:CYS73 3.3 26.0 1.0 N A:CYS73 3.8 24.0 1.0 N A:CYS90 4.0 23.7 1.0 CA A:CYS90 4.1 22.6 1.0 CA A:CYS73 4.1 25.7 1.0 N A:GLY55 4.2 41.1 1.0 N A:GLN54 4.3 45.2 1.0 CA A:CYS70 4.5 21.4 1.0 CA A:GLY55 4.5 39.8 1.0 CB A:ILE72 4.6 27.1 1.0 CA A:CYS93 4.7 26.0 1.0 C A:ILE72 4.8 25.5 1.0 C A:GLN54 4.8 43.8 1.0 N A:CYS93 5.0 27.2 1.0 C A:CYS73 5.0 24.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group


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 TRAF6 in Complex with UBC13 in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.2 occ:1.00 ND1 A:HIS87 2.2 21.5 1.0 SG A:CYS105 2.3 22.5 1.0 SG A:CYS85 2.4 28.8 1.0 OD1 A:ASP108 2.6 32.1 1.0 OD2 A:ASP108 2.6 30.1 1.0 CG A:ASP108 2.8 31.5 1.0 CE1 A:HIS87 3.0 21.4 1.0 CB A:CYS105 3.1 21.5 1.0 CG A:HIS87 3.2 22.6 1.0 CB A:CYS85 3.3 28.2 1.0 CB A:HIS87 3.7 21.1 1.0 OG1 A:THR83 3.9 23.3 1.0 NE2 A:HIS87 4.1 23.5 1.0 CB A:ASP108 4.1 30.6 1.0 N A:ASP108 4.2 30.3 1.0 O A:CYS85 4.2 24.2 1.0 CD2 A:HIS87 4.2 22.7 1.0 C A:CYS85 4.4 25.4 1.0 CA A:CYS85 4.4 25.5 1.0 CB A:VAL107 4.5 29.6 1.0 N A:HIS87 4.5 23.1 1.0 CA A:CYS105 4.5 23.4 1.0 CG A:GLU110 4.7 35.1 1.0 CA A:ASP108 4.7 30.9 1.0 CA A:HIS87 4.7 20.8 1.0 CB A:GLU110 4.8 32.4 1.0 C A:CYS105 5.0 24.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of TRAF6 in Complex with UBC13 in the P1 Space Group


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 TRAF6 in Complex with UBC13 in the P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:83.2 occ:1.00 NE2 A:HIS151 2.7 83.0 1.0 SG A:CYS134 2.8 69.6 1.0 SG A:CYS139 2.8 72.6 1.0 CB A:CYS139 2.9 75.6 1.0 CD2 A:HIS151 3.2 82.6 1.0 CB A:CYS134 3.3 69.1 1.0 CE1 A:HIS151 3.7 82.9 1.0 CG A:HIS151 4.2 82.5 1.0 SG A:CYS155 4.2 0.7 1.0 O A:HIS151 4.4 83.5 1.0 ND1 A:HIS151 4.4 82.8 1.0 CA A:CYS139 4.5 76.4 1.0 CA A:CYS134 4.7 67.7 1.0

Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu. E2 Interaction and Dimerization in the Crystal Structure of TRAF6. Nat.Struct.Mol.Biol. V. 16 658 2009.
ISSN: ISSN 1545-9993
PubMed: 19465916
DOI: 10.1038/NSMB.1605