Zinc in PDB 5d1m: Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (P199A)

All present enzymatic activity of Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (P199A):
6.3.2.19;

The structure of Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (P199A), PDB code: 5d1m 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)	30.40 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.696, 47.415, 67.975, 90.00, 118.32, 90.00
R / Rfree (%)	18.8 / 22.3

The binding sites of Zinc atom in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (P199A) (pdb code 5d1m). 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 (P199A), PDB code: 5d1m:
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 (P199A)


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 (P199A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.6 occ:1.00 SG B:CYS138 2.3 19.1 1.0 ND1 B:HIS158 2.3 18.9 1.0 SG B:CYS135 2.4 16.7 1.0 SG B:CYS161 2.4 19.1 1.0 CB B:CYS135 3.0 17.2 1.0 CB B:CYS138 3.2 19.4 1.0 CG B:HIS158 3.3 18.7 1.0 CE1 B:HIS158 3.3 23.1 1.0 CB B:CYS161 3.4 17.4 1.0 CB B:HIS158 3.5 16.3 1.0 N B:CYS138 3.8 16.9 1.0 N B:HIS158 3.9 16.5 1.0 CA B:CYS138 4.1 15.3 1.0 CA B:HIS158 4.3 17.2 1.0 NE2 B:HIS158 4.4 21.3 1.0 CD2 B:HIS158 4.4 19.9 1.0 CA B:CYS135 4.5 15.7 1.0 O B:CYS135 4.7 20.4 1.0 CA B:CYS161 4.8 16.2 1.0 C B:CYS135 4.8 16.8 1.0 NE2 B:GLN220 4.9 33.3 1.0 C B:ILE137 4.9 18.0 1.0 CB B:ILE137 4.9 16.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of UBCH5B in Complex with the Ring-U5BR Fragment of AO7 (P199A)


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 (P199A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.2 occ:1.00 ND1 B:HIS155 2.2 19.6 1.0 SG B:CYS198 2.3 16.8 1.0 SG B:CYS153 2.3 16.4 1.0 SG B:CYS201 2.4 17.1 1.0 CE1 B:HIS155 2.9 18.9 1.0 CB B:CYS198 3.2 15.7 1.0 CB B:CYS153 3.4 16.4 1.0 CG B:HIS155 3.4 15.8 1.0 CB B:CYS201 3.7 15.4 1.0 N B:CYS201 3.9 16.1 1.0 CB B:HIS155 4.0 16.0 1.0 NE2 B:HIS155 4.1 22.1 1.0 O B:CYS153 4.2 16.5 1.0 CB B:VAL200 4.3 17.0 1.0 OG1 B:THR151 4.3 15.5 1.0 CA B:CYS201 4.3 17.3 1.0 CD2 B:HIS155 4.4 20.0 1.0 C B:CYS153 4.5 16.5 1.0 CA B:CYS153 4.5 16.4 1.0 CA B:CYS198 4.7 17.9 1.0 CG1 B:VAL200 4.8 18.3 1.0 O B:HOH429 4.8 21.5 0.5 C B:VAL200 4.8 20.9 1.0 CA B:VAL200 4.9 19.3 1.0 N B:VAL200 4.9 18.9 1.0 CB B:GLU203 5.0 18.2 0.3 O B:HOH401 5.0 29.1 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