Zinc in PDB 2nvu: Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex

The structure of Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex, PDB code: 2nvu was solved by D.T.Huang, H.W.Hunt, M.Zhuang, M.D.Ohi, J.M.Holton, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.494, 156.494, 190.485, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 27.4

The structure of Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex (pdb code 2nvu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex, PDB code: 2nvu:

Zinc binding site 1 out of 1 in the Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of APPBP1-UBA3~NEDD8-NEDD8-Mgatp-UBC12(C111A), A Trapped Ubiquitin-Like Protein Activation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:61.8 occ:1.00 SG B:CYS2346 2.3 59.7 1.0 SG B:CYS2199 2.4 45.3 1.0 SG B:CYS2343 2.4 58.5 1.0 SG B:CYS2202 2.5 57.2 1.0 CB B:CYS2343 3.1 57.9 1.0 CB B:CYS2199 3.4 47.0 1.0 CB B:CYS2346 3.6 61.3 1.0 CB B:CYS2202 3.7 55.9 1.0 N B:CYS2202 3.8 54.3 1.0 N B:CYS2346 3.8 57.8 1.0 N B:CYS2199 3.9 44.8 1.0 CA B:CYS2202 4.1 55.8 1.0 CA B:CYS2199 4.2 46.4 1.0 CA B:CYS2346 4.2 60.0 1.0 CB B:GLU2201 4.5 55.4 1.0 C B:GLU2201 4.6 53.1 1.0 CA B:CYS2343 4.6 57.7 1.0 C B:CYS2199 4.6 47.5 1.0 O B:CYS2199 4.7 49.3 1.0 CB B:ALA2345 4.8 57.6 1.0 C B:ALA2345 4.8 58.9 1.0 C B:CYS2346 4.9 60.8 1.0 CA B:GLU2201 5.0 52.7 1.0 N B:GLU2201 5.0 51.9 1.0

D.T.Huang, H.W.Hunt, M.Zhuang, M.D.Ohi, J.M.Holton, B.A.Schulman. Basis For A Ubiquitin-Like Protein Thioester Switch Toggling E1-E2 Affinity. Nature V. 445 394 2007.
ISSN: ISSN 0028-0836
PubMed: 17220875
DOI: 10.1038/NATURE05490