Zinc in PDB 5ypa: P62/SQSTM1 Zz Domain with Lys-Peptide

The structure of P62/SQSTM1 Zz Domain with Lys-Peptide, PDB code: 5ypa 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)	21.99 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.085, 43.822, 67.219, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.5

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Lys-Peptide (pdb code 5ypa). 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 Lys-Peptide, PDB code: 5ypa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the P62/SQSTM1 Zz Domain with Lys-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 Lys-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:33.1 occ:1.00 SG A:CYS27 2.2 31.6 1.0 SG A:CYS30 2.3 31.0 1.0 SG A:CYS7 2.4 34.7 1.0 SG A:CYS4 2.4 25.4 1.0 HB3 A:CYS4 3.2 53.1 1.0 HB2 A:CYS30 3.2 49.3 1.0 H A:CYS7 3.2 44.6 1.0 HB3 A:CYS7 3.2 33.7 1.0 CB A:CYS4 3.3 44.2 1.0 H A:CYS27 3.3 49.1 1.0 HB3 A:CYS27 3.3 40.4 1.0 HB2 A:CYS4 3.4 53.1 1.0 CB A:CYS7 3.4 28.1 1.0 CB A:CYS30 3.4 41.0 1.0 CB A:CYS27 3.4 33.7 1.0 H A:CYS30 3.5 27.9 1.0 N A:CYS7 3.7 37.1 1.0 N A:CYS27 4.1 40.9 1.0 HB3 A:CYS30 4.1 49.3 1.0 HB2 A:CYS27 4.1 40.4 1.0 CA A:CYS7 4.1 30.2 1.0 N A:CYS30 4.2 23.2 1.0 HB2 A:CYS7 4.2 33.7 1.0 HA3 A:GLY6 4.2 21.6 1.0 H A:GLY6 4.3 35.0 1.0 CA A:CYS27 4.3 29.1 1.0 HB A:VAL29 4.3 36.8 1.0 H A:GLY9 4.3 57.9 1.0 CA A:CYS30 4.4 35.3 1.0 O A:HOH213 4.5 29.8 1.0 C A:GLY6 4.6 39.9 1.0 CA A:CYS4 4.7 40.8 1.0 CA A:GLY6 4.7 18.0 1.0 HA A:CYS30 4.8 42.4 1.0 H A:ASN8 4.8 50.5 1.0 HA A:LEU26 4.8 42.8 1.0 N A:GLY6 4.9 29.1 1.0 C A:CYS27 4.9 36.4 1.0 C A:CYS7 4.9 42.1 1.0 O A:CYS27 4.9 45.0 1.0 HA A:CYS7 4.9 36.3 1.0

Zinc binding site 2 out of 4 in the P62/SQSTM1 Zz Domain with Lys-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 Lys-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:40.3 occ:1.00 NE2 A:HIS36 2.0 34.0 1.0 SG A:CYS21 2.1 43.9 1.0 ND1 A:HIS39 2.2 28.4 1.0 SG A:CYS18 2.3 47.0 1.0 H A:CYS21 2.7 33.7 1.0 HB2 A:CYS21 2.7 45.5 1.0 CB A:CYS21 2.9 37.9 1.0 CD2 A:HIS36 3.0 22.8 1.0 CE1 A:HIS36 3.0 38.3 1.0 CE1 A:HIS39 3.1 16.0 1.0 HD2 A:HIS36 3.2 27.4 1.0 HE1 A:HIS39 3.2 19.2 1.0 HE1 A:HIS36 3.2 46.0 1.0 HB2 A:HIS39 3.2 24.7 1.0 CG A:HIS39 3.3 27.2 1.0 N A:CYS21 3.4 28.1 1.0 HB A:VAL20 3.5 49.5 1.0 CB A:CYS18 3.5 31.2 1.0 HB2 A:CYS18 3.6 37.4 1.0 CB A:HIS39 3.6 20.6 1.0 HB3 A:HIS39 3.7 24.7 1.0 HB3 A:CYS21 3.7 45.5 1.0 HB3 A:CYS18 3.7 37.4 1.0 CA A:CYS21 3.7 35.6 1.0 ND1 A:HIS36 4.1 34.6 1.0 CG A:HIS36 4.1 30.2 1.0 H A:VAL20 4.2 25.8 1.0 NE2 A:HIS39 4.2 40.3 1.0 HA A:CYS21 4.3 42.8 1.0 CD2 A:HIS39 4.4 54.6 1.0 CB A:VAL20 4.4 41.2 1.0 C A:VAL20 4.5 41.6 1.0 HB3 A:TYR24 4.5 46.1 1.0 HG12 A:VAL20 4.7 37.4 1.0 CD1 A:TYR24 4.7 34.6 1.0 CG A:TYR24 4.8 25.5 1.0 HD1 A:TYR24 4.8 41.6 1.0 CA A:VAL20 4.9 36.2 1.0 CA A:CYS18 4.9 47.3 1.0 HD1 A:HIS36 4.9 41.6 1.0 N A:VAL20 4.9 21.5 1.0 C A:CYS21 4.9 51.3 1.0 HA A:CYS18 5.0 56.8 1.0

Zinc binding site 3 out of 4 in the P62/SQSTM1 Zz Domain with Lys-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 Lys-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:34.3 occ:1.00 SG B:CYS4 2.3 35.9 1.0 SG B:CYS7 2.3 37.9 1.0 SG B:CYS30 2.3 32.4 1.0 SG B:CYS27 2.3 29.1 1.0 HB2 B:CYS30 3.0 46.7 1.0 H B:CYS27 3.0 37.4 1.0 HB3 B:CYS4 3.1 35.1 1.0 HB3 B:CYS7 3.1 43.2 1.0 CB B:CYS4 3.1 29.2 1.0 H B:CYS7 3.1 44.6 1.0 HB3 B:CYS27 3.2 12.1 1.0 CB B:CYS30 3.2 38.9 1.0 HB2 B:CYS4 3.3 35.1 1.0 CB B:CYS7 3.3 36.0 1.0 H B:CYS30 3.3 61.8 1.0 CB B:CYS27 3.4 10.1 1.0 N B:CYS7 3.7 37.1 1.0 N B:CYS27 3.7 31.1 1.0 HB3 B:CYS30 3.9 46.7 1.0 O B:HOH207 4.0 24.5 1.0 N B:CYS30 4.0 51.5 1.0 CA B:CYS7 4.1 32.4 1.0 HB2 B:CYS7 4.1 43.2 1.0 CA B:CYS27 4.1 34.9 1.0 H B:GLY6 4.1 40.6 1.0 HB2 B:CYS27 4.2 12.1 1.0 HA3 B:GLY6 4.2 42.6 1.0 CA B:CYS30 4.2 29.5 1.0 HB B:VAL29 4.3 48.1 1.0 H B:GLY9 4.3 37.8 1.0 HA B:LEU26 4.5 28.6 1.0 C B:GLY6 4.5 35.5 1.0 CA B:CYS4 4.6 35.4 1.0 HA B:CYS30 4.6 35.5 1.0 CA B:GLY6 4.7 35.5 1.0 C B:CYS27 4.7 43.2 1.0 O B:CYS27 4.7 30.6 1.0 N B:GLY6 4.7 33.8 1.0 HD22 B:LEU26 4.7 17.6 1.0 H B:ASN8 4.8 47.4 1.0 C B:CYS7 4.8 30.1 1.0 HA B:CYS7 4.9 39.0 1.0 HB3 B:LEU26 4.9 43.9 1.0 C B:LEU26 4.9 9.4 1.0 HA B:CYS4 4.9 42.5 1.0 HA B:CYS27 4.9 41.9 1.0 H B:VAL29 5.0 48.6 1.0

Zinc binding site 4 out of 4 in the P62/SQSTM1 Zz Domain with Lys-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 Lys-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:33.5 occ:1.00 NE2 B:HIS36 1.9 32.0 1.0 ND1 B:HIS39 2.0 45.3 1.0 SG B:CYS18 2.2 34.1 1.0 SG B:CYS21 2.3 20.4 1.0 H B:CYS21 2.7 34.3 1.0 CE1 B:HIS36 2.9 30.5 1.0 CE1 B:HIS39 2.9 28.8 1.0 HB2 B:CYS21 2.9 34.5 1.0 CD2 B:HIS36 2.9 23.4 1.0 HE1 B:HIS39 3.0 34.5 1.0 HE1 B:HIS36 3.0 36.7 1.0 CG B:HIS39 3.1 39.0 1.0 CB B:CYS21 3.1 28.8 1.0 HD2 B:HIS36 3.2 28.1 1.0 HB2 B:HIS39 3.3 48.7 1.0 HB B:VAL20 3.4 31.3 1.0 N B:CYS21 3.4 28.5 1.0 HB3 B:HIS39 3.5 48.7 1.0 CB B:HIS39 3.6 40.5 1.0 CB B:CYS18 3.6 30.9 1.0 HB2 B:CYS18 3.6 37.1 1.0 HB3 B:CYS18 3.9 37.1 1.0 CA B:CYS21 3.9 28.7 1.0 HB3 B:CYS21 3.9 34.5 1.0 ND1 B:HIS36 4.0 23.5 1.0 NE2 B:HIS39 4.0 32.9 1.0 CG B:HIS36 4.1 29.7 1.0 CD2 B:HIS39 4.2 27.9 1.0 H B:VAL20 4.2 39.7 1.0 HA B:CYS21 4.3 34.4 1.0 CB B:VAL20 4.4 26.0 1.0 C B:VAL20 4.5 23.4 1.0 HG12 B:VAL20 4.7 47.3 1.0 HD1 B:HIS36 4.8 28.3 1.0 HE2 B:HIS39 4.8 39.6 1.0 CA B:VAL20 4.8 26.3 1.0 N B:VAL20 4.8 33.1 1.0 HB3 B:TYR24 4.8 37.6 1.0 CA B:CYS18 4.9 39.9 1.0 HA B:CYS18 4.9 47.9 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