Zinc in PDB 6nyd: Crystal Structure of S. Cerevisiae UBC3 (CDC34)

All present enzymatic activity of Crystal Structure of S. Cerevisiae UBC3 (CDC34):
2.3.2.23;

The structure of Crystal Structure of S. Cerevisiae UBC3 (CDC34), PDB code: 6nyd was solved by S.K.Olsen, K.M.Williams, J.H.Atkison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.39 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.084, 49.022, 103.684, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.9

The binding sites of Zinc atom in the Crystal Structure of S. Cerevisiae UBC3 (CDC34) (pdb code 6nyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S. Cerevisiae UBC3 (CDC34), PDB code: 6nyd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of S. Cerevisiae UBC3 (CDC34)


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 S. Cerevisiae UBC3 (CDC34) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:44.2 occ:1.00 NE2 C:HIS100 1.9 58.9 1.0 SG C:CYS95 2.2 43.8 1.0 CE1 C:HIS100 2.7 73.3 1.0 HE1 C:HIS100 2.7 88.0 1.0 CD2 C:HIS100 3.1 57.1 1.0 HB2 C:CYS95 3.2 43.2 1.0 CB C:CYS95 3.3 36.0 1.0 HA C:CYS95 3.4 36.8 1.0 HD2 C:HIS100 3.5 68.6 1.0 CA C:CYS95 3.8 30.6 1.0 ND1 C:HIS100 3.9 79.6 1.0 HH C:TYR89 3.9 59.8 1.0 O C:HOH881 3.9 42.7 1.0 O C:HOH883 4.0 50.0 1.0 CG C:HIS100 4.1 49.9 1.0 HB3 C:CYS95 4.1 43.2 1.0 H C:ILE96 4.2 35.7 1.0 HE2 C:TYR89 4.3 42.6 1.0 C C:CYS95 4.4 30.9 1.0 N C:ILE96 4.5 29.8 1.0 HD1 C:HIS100 4.6 95.5 1.0 OH C:TYR89 4.7 49.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of S. Cerevisiae UBC3 (CDC34)


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 S. Cerevisiae UBC3 (CDC34) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:0.4 occ:1.00 O C:HOH806 2.8 54.1 1.0 OD1 C:ASP144 3.0 54.6 1.0 HE21 C:GLN155 3.1 88.1 1.0 HE22 C:GLN155 3.2 88.1 1.0 OD2 C:ASP148 3.3 45.9 1.0 OD1 C:ASP148 3.3 46.7 1.0 O C:HOH885 3.4 48.9 1.0 NE2 C:GLN155 3.4 73.4 1.0 CG C:ASP148 3.7 51.8 1.0 CG C:ASP144 3.8 55.7 1.0 OD2 C:ASP144 4.1 89.5 1.0 HD22 C:ASN152 4.2 68.4 1.0 HH C:TYR84 4.3 64.2 1.0 OH C:TYR84 4.4 53.5 1.0 CD C:GLN155 4.7 81.4 1.0 HD21 C:ASN152 4.8 68.4 1.0 ND2 C:ASN152 4.8 57.0 1.0 O C:ASP144 4.9 33.1 1.0 HG2 C:GLN155 5.0 91.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of S. Cerevisiae UBC3 (CDC34)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of S. Cerevisiae UBC3 (CDC34) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:54.3 occ:1.00 NE2 C:HIS30 1.9 53.0 1.0 OE2 C:GLU32 2.0 52.2 1.0 O C:HOH888 2.2 46.4 1.0 HE1 C:HIS30 2.6 50.5 1.0 CE1 C:HIS30 2.6 42.1 1.0 O C:HOH897 2.6 64.7 1.0 CD C:GLU32 3.0 49.4 1.0 HG2 C:GLU32 3.0 54.3 1.0 CD2 C:HIS30 3.2 46.6 1.0 CG C:GLU32 3.3 45.2 1.0 HG3 C:GLU32 3.3 54.3 1.0 HD2 C:HIS30 3.6 55.9 1.0 ND1 C:HIS30 3.8 49.6 1.0 CG C:HIS30 4.1 41.5 1.0 OE1 C:GLU32 4.1 61.1 1.0 O C:HOH830 4.2 53.7 1.0 HG3 C:PRO172 4.3 72.2 1.0 HD1 C:HIS30 4.5 59.5 1.0 HG2 C:PRO172 4.5 72.2 1.0 HD1 C:PHE175 4.6 73.6 1.0 CB C:GLU32 4.8 37.7 1.0 CG C:PRO172 4.8 60.2 1.0 O C:HOH833 4.9 60.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of S. Cerevisiae UBC3 (CDC34)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of S. Cerevisiae UBC3 (CDC34) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn704 b:85.6 occ:1.00 NE2 C:HIS56 2.1 55.8 1.0 O C:HOH889 2.2 65.4 1.0 OE1 C:GLU51 2.7 0.7 1.0 OE2 C:GLU51 3.0 0.2 1.0 CD2 C:HIS56 3.1 49.4 1.0 CE1 C:HIS56 3.1 57.4 1.0 CD C:GLU51 3.2 0.4 1.0 HD2 C:HIS56 3.2 59.3 1.0 HE1 C:HIS56 3.3 68.9 1.0 ND1 C:HIS56 4.2 55.0 1.0 CG C:HIS56 4.2 51.6 1.0 CG C:GLU51 4.7 89.9 1.0 HA C:GLU51 4.8 62.7 1.0 O C:HOH853 4.8 53.7 1.0

K.M.Williams, S.Qie, J.H.Atkison, S.Salazar-Arango, J.Alan Diehl, S.K.Olsen. Structural Insights Into E1 Recognition and the Ubiquitin-Conjugating Activity of the E2 Enzyme CDC34. Nat Commun V. 10 3296 2019.
ISSN: ESSN 2041-1723
PubMed: 31341161
DOI: 10.1038/S41467-019-11061-8