Zinc in PDB 5yph: P62/SQSTM1 Zz Domain with Ile-Peptide

The structure of P62/SQSTM1 Zz Domain with Ile-Peptide, PDB code: 5yph was solved by D.H.Kwon, L.Kim, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.91 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.658, 33.381, 35.019, 90.00, 103.61, 90.00
R / Rfree (%)	14.7 / 18.7

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Ile-Peptide (pdb code 5yph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the P62/SQSTM1 Zz Domain with Ile-Peptide, PDB code: 5yph:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the P62/SQSTM1 Zz Domain with Ile-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P62/SQSTM1 Zz Domain with Ile-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:12.1 occ:1.00 SG A:CYS7 2.3 12.0 1.0 SG A:CYS4 2.3 8.3 1.0 SG A:CYS30 2.4 9.9 1.0 SG A:CYS27 2.4 10.4 1.0 CB A:CYS30 3.2 11.1 1.0 CB A:CYS4 3.3 8.5 1.0 CB A:CYS7 3.3 12.3 1.0 CB A:CYS27 3.6 11.0 1.0 N A:CYS7 3.6 12.8 1.0 CA A:CYS7 4.0 10.4 1.0 N A:CYS27 4.1 10.5 1.0 N A:CYS30 4.1 12.4 1.0 CA A:CYS30 4.2 11.4 1.0 C A:GLY6 4.3 11.6 1.0 CA A:CYS27 4.4 8.7 1.0 CA A:GLY6 4.5 10.0 1.0 N A:GLY6 4.7 10.4 1.0 CA A:CYS4 4.7 8.3 1.0 C A:CYS7 4.7 13.9 1.0 O A:CYS27 4.9 11.0 1.0 C A:CYS27 4.9 10.2 1.0 N A:GLY9 4.9 14.4 1.0 N A:ASN8 4.9 11.6 1.0

Zinc binding site 2 out of 4 in the P62/SQSTM1 Zz Domain with Ile-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P62/SQSTM1 Zz Domain with Ile-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:11.5 occ:1.00 NE2 A:HIS36 2.0 8.5 1.0 ND1 A:HIS39 2.1 11.0 1.0 SG A:CYS21 2.3 11.3 1.0 SG A:CYS18 2.3 9.4 1.0 CD2 A:HIS36 3.0 9.2 1.0 CE1 A:HIS36 3.0 9.8 1.0 CE1 A:HIS39 3.0 11.8 1.0 CG A:HIS39 3.2 9.4 1.0 CB A:CYS21 3.2 14.5 1.0 CB A:CYS18 3.5 10.2 1.0 CB A:HIS39 3.5 10.2 1.0 N A:CYS21 3.7 11.4 1.0 CA A:CYS21 4.1 12.4 1.0 ND1 A:HIS36 4.1 11.3 1.0 CG A:HIS36 4.1 8.4 1.0 NE2 A:HIS39 4.2 12.9 1.0 CD2 A:HIS39 4.3 11.0 1.0 CB A:VAL20 4.4 10.7 1.0 OD2 B:ASP23 4.7 14.6 1.0 C A:VAL20 4.7 14.9 1.0 CA A:CYS18 4.8 8.8 1.0 N A:VAL20 4.9 9.7 1.0 CA A:VAL20 4.9 13.2 1.0 O B:HOH232 5.0 12.3 1.0

Zinc binding site 3 out of 4 in the P62/SQSTM1 Zz Domain with Ile-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of P62/SQSTM1 Zz Domain with Ile-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:12.8 occ:1.00 SG B:CYS7 2.3 11.9 1.0 SG B:CYS4 2.3 9.1 1.0 SG B:CYS27 2.3 12.9 1.0 SG B:CYS30 2.4 11.1 1.0 CB B:CYS7 3.2 14.2 1.0 CB B:CYS4 3.3 8.9 1.0 CB B:CYS30 3.3 11.1 1.0 CB B:CYS27 3.5 12.2 1.0 N B:CYS7 3.6 10.8 1.0 N B:CYS27 4.0 9.8 1.0 CA B:CYS7 4.0 12.8 1.0 N B:CYS30 4.1 11.9 1.0 CA B:CYS27 4.3 11.4 1.0 CA B:CYS30 4.3 11.3 1.0 C B:GLY6 4.3 13.1 1.0 CA B:GLY6 4.6 9.9 1.0 N B:GLY6 4.6 9.9 1.0 CA B:CYS4 4.7 8.4 1.0 O B:HOH249 4.8 30.9 1.0 C B:CYS7 4.8 13.0 1.0 C B:CYS27 4.8 12.6 1.0 O B:CYS27 4.9 13.2 1.0

Zinc binding site 4 out of 4 in the P62/SQSTM1 Zz Domain with Ile-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of P62/SQSTM1 Zz Domain with Ile-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:12.5 occ:1.00 NE2 B:HIS36 2.0 9.7 1.0 ND1 B:HIS39 2.1 11.0 1.0 SG B:CYS21 2.2 12.2 1.0 SG B:CYS18 2.3 10.3 1.0 CE1 B:HIS36 3.0 9.1 1.0 CD2 B:HIS36 3.0 11.3 1.0 CE1 B:HIS39 3.0 14.9 1.0 CG B:HIS39 3.2 9.4 1.0 CB B:CYS21 3.2 10.4 1.0 CB B:CYS18 3.4 10.4 1.0 CB B:HIS39 3.5 12.6 1.0 N B:CYS21 3.6 11.0 1.0 CA B:CYS21 4.0 10.4 1.0 ND1 B:HIS36 4.1 10.1 1.0 CG B:HIS36 4.1 12.0 1.0 NE2 B:HIS39 4.2 13.0 1.0 CD2 B:HIS39 4.3 12.5 1.0 CB B:VAL20 4.4 12.6 1.0 C B:VAL20 4.7 11.6 1.0 CA B:CYS18 4.8 11.4 1.0 N B:VAL20 4.9 12.7 1.0 CA B:VAL20 4.9 11.2 1.0 CB B:TYR24 4.9 10.2 1.0 CG1 B:VAL20 4.9 14.2 1.0

D.H.Kwon, O.H.Park, L.Kim, Y.O.Jung, Y.Park, H.Jeong, J.Hyun, Y.K.Kim, H.K.Song. Insights Into Degradation Mechanism of N-End Rule Substrates By P62/SQSTM1 Autophagy Adapter. Nat Commun V. 9 3291 2018.
ISSN: ESSN 2041-1723
PubMed: 30120248
DOI: 10.1038/S41467-018-05825-X