Zinc in PDB 5d1k: Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7

All present enzymatic activity of Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7:
6.3.2.19;

The structure of Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7, PDB code: 5d1k was solved by Y.-H.Liang, S.Li, A.M.Weissman, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.34 / 1.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.470, 45.658, 67.954, 90.00, 118.09, 90.00
R / Rfree (%)	17 / 20.2

The binding sites of Zinc atom in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (pdb code 5d1k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7, PDB code: 5d1k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7


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 UBCH5B in Complex with the Ring-U5BR Fragment of AO7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.8 occ:1.00 ND1 B:HIS158 2.3 22.4 1.0 SG B:CYS138 2.3 20.5 1.0 SG B:CYS161 2.3 21.8 1.0 SG B:CYS135 2.4 17.7 1.0 CB B:CYS135 3.0 18.6 1.0 CE1 B:HIS158 3.2 21.7 1.0 CB B:CYS138 3.2 21.7 1.0 CG B:HIS158 3.2 17.6 1.0 CB B:CYS161 3.3 20.0 1.0 CB B:HIS158 3.5 16.1 1.0 N B:CYS138 3.7 17.8 1.0 N B:HIS158 4.0 17.2 1.0 CA B:CYS138 4.1 19.3 1.0 NE2 B:HIS158 4.3 20.5 1.0 CD2 B:HIS158 4.4 18.4 1.0 CA B:HIS158 4.4 16.1 1.0 CA B:CYS135 4.4 20.0 1.0 O B:CYS135 4.7 23.0 1.0 CB B:ILE137 4.7 15.8 1.0 NE2 B:GLN220 4.7 31.9 1.0 CA B:CYS161 4.7 17.2 1.0 C B:CYS135 4.8 20.8 1.0 C B:ILE137 4.8 19.9 1.0 O B:HOH493 5.0 37.0 1.0 C B:CYS138 5.0 23.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7


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 UBCH5B in Complex with the Ring-U5BR Fragment of AO7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.9 occ:1.00 ND1 B:HIS155 2.1 16.3 1.0 SG B:CYS198 2.3 16.6 1.0 SG B:CYS153 2.3 15.9 1.0 SG B:CYS201 2.4 18.4 1.0 CE1 B:HIS155 2.8 20.7 1.0 CB B:CYS198 3.1 14.8 1.0 CG B:HIS155 3.2 14.0 1.0 CB B:CYS153 3.3 16.5 1.0 CB B:CYS201 3.6 18.3 1.0 CB B:HIS155 3.8 15.4 1.0 N B:CYS201 3.9 16.5 1.0 NE2 B:HIS155 4.0 20.5 1.0 O B:CYS153 4.0 14.5 1.0 OG1 B:THR151 4.2 15.8 1.0 CD2 B:HIS155 4.2 20.1 1.0 CA B:CYS201 4.3 20.7 1.0 CB B:VAL200 4.3 18.7 1.0 C B:CYS153 4.4 14.0 1.0 CA B:CYS153 4.4 13.6 1.0 CA B:CYS198 4.6 17.3 1.0 O B:HOH413 4.7 31.9 1.0 C B:VAL200 4.8 22.3 1.0 CB B:GLU203 4.8 19.6 0.4 CG1 B:VAL200 4.8 19.7 1.0 C B:CYS201 4.9 20.6 1.0 CA B:VAL200 4.9 21.9 1.0 N B:VAL200 4.9 20.7 1.0 N B:HIS155 4.9 15.4 1.0 CB B:GLU203 4.9 19.7 0.6 N B:ARG202 5.0 19.6 1.0

S.Li, Y.H.Liang, J.Mariano, M.B.Metzger, D.K.Stringer, V.A.Hristova, J.Li, P.A.Randazzo, Y.C.Tsai, X.Ji, A.M.Weissman. Insights Into Ubiquitination From the Unique Clamp-Like Binding of the Ring E3 AO7 to the E2 UBCH5B. J.Biol.Chem. V. 290 30225 2015.
ISSN: ESSN 1083-351X
PubMed: 26475854
DOI: 10.1074/JBC.M115.685867