Zinc in PDB 6fnn: Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex

All present enzymatic activity of Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex:
3.4.19.12;

The structure of Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex, PDB code: 6fnn was solved by A.C.D.Fuchs, R.Albrecht, J.Martin, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.90 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.674, 94.571, 170.855, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.1

The binding sites of Zinc atom in the Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex (pdb code 6fnn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex, PDB code: 6fnn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:48.5 occ:0.33 O C:GLY78 1.8 50.1 1.0 OD2 A:ASP96 2.0 37.7 1.0 NE2 A:HIS83 2.0 37.4 1.0 NE2 A:HIS85 2.1 35.9 0.5 CE1 A:HIS83 2.5 33.7 1.0 CG A:ASP96 2.7 36.0 1.0 OD1 A:ASP96 2.8 34.0 1.0 C C:GLY78 2.9 52.9 1.0 CD2 A:HIS85 3.0 34.5 0.5 CE1 A:HIS85 3.2 37.9 0.5 CD2 A:HIS83 3.2 34.6 1.0 N C:GLY78 3.4 43.6 1.0 OG A:SER93 3.6 36.9 1.0 OXT C:GLY78 3.7 57.8 1.0 CA C:GLY78 3.8 49.5 1.0 ND1 A:HIS83 3.8 37.3 1.0 CD2 A:HIS85 3.8 41.2 0.5 NE2 A:HIS85 3.9 44.4 0.5 CB A:ASP96 4.1 29.7 1.0 CG A:HIS83 4.1 32.4 1.0 CG A:HIS85 4.1 35.6 0.5 ND1 A:HIS85 4.2 37.5 0.5 O A:PHE91 4.2 33.5 1.0 CB A:SER93 4.2 37.1 1.0 N A:SER93 4.3 34.3 1.0 C C:GLY77 4.5 38.3 1.0 CG A:HIS85 4.6 40.3 0.5 OE1 A:GLU24 4.6 34.0 1.0 CA C:GLY77 4.6 34.8 1.0 CE1 A:HIS85 4.7 46.3 0.5 CA A:SER93 4.9 36.7 1.0 CG1 A:VAL114 5.0 28.3 1.0

Zinc binding site 2 out of 2 in the Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Caldiarchaeum Subterraneum Ubiquitin:RPN11-Homolog Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:51.3 occ:0.33 O D:GLY78 1.7 50.6 1.0 OD2 B:ASP96 1.8 43.2 1.0 O D:HOH311 2.1 49.6 1.0 NE2 B:HIS83 2.3 39.9 1.0 CG B:ASP96 2.6 38.4 1.0 CE1 B:HIS83 2.6 35.5 1.0 OD1 B:ASP96 2.7 37.1 1.0 C D:GLY78 2.9 52.1 1.0 OG B:SER93 3.4 37.0 1.0 N D:GLY78 3.4 44.7 1.0 OXT D:GLY78 3.6 55.1 1.0 CD2 B:HIS83 3.7 36.5 1.0 CA D:GLY78 3.7 50.0 1.0 ND1 B:HIS83 3.8 37.1 1.0 CB B:SER93 3.9 37.9 1.0 N B:SER93 3.9 36.6 1.0 O B:PHE91 4.0 38.5 1.0 CB B:ASP96 4.0 35.0 1.0 CG B:HIS83 4.4 33.1 1.0 C D:GLY77 4.5 40.5 1.0 CA B:SER93 4.5 38.7 1.0 CA D:GLY77 4.7 36.8 1.0 OE1 B:GLU24 4.7 37.1 1.0 CA B:LEU92 4.8 37.9 1.0 C B:LEU92 4.8 37.7 1.0 CG B:HIS85 4.9 50.1 1.0 CD2 B:HIS85 4.9 53.6 1.0

A.C.D.Fuchs, L.Maldoner, M.Wojtynek, M.D.Hartmann, J.Martin. RPN11-Mediated Ubiquitin Processing in An Ancestral Archaeal Ubiquitination System. Nat Commun V. 9 2696 2018.
ISSN: ESSN 2041-1723
PubMed: 30002364
DOI: 10.1038/S41467-018-05198-1