Zinc in PDB 3h8v: Human Ubiquitin-Activating Enzyme 5 in Complex with Atp

The structure of Human Ubiquitin-Activating Enzyme 5 in Complex with Atp, PDB code: 3h8v was solved by J.R.Walker, J.P.Bacik, N.Rastgoo, J.Weigelt, C.Bountra, A.M.Edwards, C.H.Arrowsmith, A.Bochkarev, S.Dhe-Paganon, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.53 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.999, 77.999, 207.005, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22.4

The binding sites of Zinc atom in the Human Ubiquitin-Activating Enzyme 5 in Complex with Atp (pdb code 3h8v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Ubiquitin-Activating Enzyme 5 in Complex with Atp, PDB code: 3h8v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Ubiquitin-Activating Enzyme 5 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Ubiquitin-Activating Enzyme 5 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.9 occ:1.00 SG A:CYS308 2.3 55.5 1.0 SG A:CYS303 2.4 57.6 1.0 SG A:CYS226 2.4 50.2 1.0 SG A:CYS229 2.4 61.1 1.0 CB A:CYS308 3.0 46.1 1.0 CB A:CYS303 3.1 63.0 1.0 CB A:CYS226 3.3 49.6 1.0 N A:CYS229 3.5 58.7 1.0 CB A:CYS229 3.6 59.6 1.0 CA A:CYS229 3.7 58.9 1.0 N A:CYS226 3.9 50.0 1.0 CA A:CYS226 4.1 49.0 1.0 O A:HOH454 4.3 37.0 1.0 C A:ALA228 4.3 58.5 1.0 CA A:CYS303 4.5 58.4 1.0 CA A:CYS308 4.6 52.6 1.0 C A:CYS226 4.6 48.9 1.0 CB A:ALA228 4.7 53.9 1.0 N A:ALA228 4.7 50.1 1.0 O A:CYS226 4.7 48.7 1.0 CA A:ALA228 4.8 50.5 1.0 ND2 A:ASN196 4.8 50.5 1.0 OE1 A:GLN312 4.9 76.8 1.0

Zinc binding site 2 out of 2 in the Human Ubiquitin-Activating Enzyme 5 in Complex with Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Ubiquitin-Activating Enzyme 5 in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:33.4 occ:1.00 SG B:CYS308 2.3 44.0 1.0 SG B:CYS303 2.4 56.6 1.0 SG B:CYS226 2.4 47.3 1.0 SG B:CYS229 2.4 48.4 1.0 CB B:CYS303 3.1 52.8 1.0 CB B:CYS308 3.1 46.8 1.0 CB B:CYS226 3.4 46.7 1.0 CB B:CYS229 3.5 46.5 1.0 N B:CYS229 3.6 50.7 1.0 CA B:CYS229 3.7 52.0 1.0 N B:CYS226 4.0 50.1 1.0 CA B:CYS226 4.2 50.4 1.0 C B:ALA228 4.3 51.0 1.0 O B:HOH409 4.5 42.2 1.0 CB B:ALA228 4.5 48.9 1.0 CA B:CYS303 4.6 47.7 1.0 C B:CYS226 4.6 48.0 1.0 CA B:CYS308 4.6 61.8 1.0 OE1 B:GLN312 4.7 81.6 1.0 O B:CYS226 4.7 54.4 1.0 N B:ALA228 4.7 51.9 1.0 CA B:ALA228 4.8 51.3 1.0 ND2 B:ASN196 4.8 46.4 1.0 CB B:ASP305 4.9 54.0 1.0 O B:ASN300 4.9 54.2 1.0 O B:ALA228 4.9 57.4 1.0

J.P.Bacik, J.R.Walker, M.Ali, A.D.Schimmer, S.Dhe-Paganon. Crystal Structure of the Human Ubiquitin-Activating Enzyme 5 (UBA5) Bound to Atp: Mechanistic Insights Into A Minimalistic E1 Enzyme. J.Biol.Chem. V. 285 20273 2010.
ISSN: ISSN 0021-9258
PubMed: 20368332
DOI: 10.1074/JBC.M110.102921