Zinc in PDB 5l95: Crystal Structure of Human UBA5 in Complex with UFM1 and Amp

The structure of Crystal Structure of Human UBA5 in Complex with UFM1 and Amp, PDB code: 5l95 was solved by W.Oweis, P.Padala, R.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.00 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.875, 139.875, 99.742, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Human UBA5 in Complex with UFM1 and Amp (pdb code 5l95). 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 Human UBA5 in Complex with UFM1 and Amp, PDB code: 5l95:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human UBA5 in Complex with UFM1 and Amp


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 Human UBA5 in Complex with UFM1 and Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.6 occ:1.00 SG A:CYS226 2.3 24.3 1.0 SG A:CYS229 2.3 22.2 1.0 SG A:CYS303 2.3 23.7 1.0 SG A:CYS308 2.3 21.3 1.0 CB A:CYS303 3.0 21.9 1.0 CB A:CYS308 3.2 21.7 1.0 N A:CYS229 3.5 24.3 1.0 CB A:CYS229 3.5 20.3 1.0 CB A:CYS226 3.5 14.9 1.0 CA A:CYS229 3.7 19.1 1.0 N A:CYS226 4.0 18.6 1.0 C A:ALA228 4.2 24.9 1.0 CA A:CYS226 4.2 20.7 1.0 O A:HOH550 4.4 23.6 1.0 CA A:CYS303 4.5 26.7 1.0 C A:CYS226 4.5 24.0 1.0 O A:CYS226 4.6 27.1 1.0 CB A:ALA228 4.6 18.1 1.0 CA A:CYS308 4.7 19.8 1.0 NE2 A:GLN312 4.7 24.8 1.0 CA A:ALA228 4.8 19.7 1.0 N A:ALA228 4.8 20.0 1.0 O A:ALA228 4.8 25.0 1.0 ND2 A:ASN196 4.9 16.6 1.0 O A:ASN300 4.9 26.2 1.0 CB A:ASP305 5.0 26.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human UBA5 in Complex with UFM1 and Amp


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 Human UBA5 in Complex with UFM1 and Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:29.2 occ:1.00 SG B:CYS303 2.3 32.2 1.0 SG B:CYS229 2.3 30.8 1.0 SG B:CYS226 2.3 27.7 1.0 SG B:CYS308 2.4 31.6 1.0 CB B:CYS303 3.1 29.1 1.0 CB B:CYS308 3.2 27.8 1.0 CB B:CYS226 3.5 23.1 1.0 N B:CYS229 3.5 27.2 1.0 CB B:CYS229 3.5 29.6 1.0 CA B:CYS229 3.7 28.8 1.0 N B:CYS226 3.9 31.0 1.0 CA B:CYS226 4.1 27.1 1.0 C B:ALA228 4.2 25.0 1.0 C B:CYS226 4.5 31.9 1.0 O B:CYS226 4.5 33.5 1.0 CA B:CYS303 4.6 28.7 1.0 O B:HOH515 4.6 28.7 1.0 CA B:CYS308 4.7 33.3 1.0 CB B:ALA228 4.7 26.8 1.0 NE2 B:GLN312 4.8 31.6 1.0 N B:ALA228 4.8 28.0 1.0 CA B:ALA228 4.8 25.0 1.0 O B:ALA228 4.8 27.3 1.0 CB B:ASP305 4.9 28.1 1.0 ND2 B:ASN196 5.0 28.4 1.0

W.Oweis, P.Padala, F.Hassouna, E.Cohen-Kfir, D.R.Gibbs, E.A.Todd, C.E.Berndsen, R.Wiener. Trans-Binding Mechanism of Ubiquitin-Like Protein Activation Revealed By A UBA5-UFM1 Complex. Cell Rep V. 16 3113 2016.
ISSN: ESSN 2211-1247
PubMed: 27653677
DOI: 10.1016/J.CELREP.2016.08.067