Zinc in PDB 5yp8: P62/SQSTM1 Zz Domain with Arg-Peptide

The structure of P62/SQSTM1 Zz Domain with Arg-Peptide, PDB code: 5yp8 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)	19.81 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.981, 43.948, 66.596, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.4

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Arg-Peptide (pdb code 5yp8). 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 Arg-Peptide, PDB code: 5yp8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the P62/SQSTM1 Zz Domain with Arg-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 Arg-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:26.9 occ:1.00 SG A:CYS27 2.2 29.9 1.0 SG A:CYS30 2.2 28.2 1.0 SG A:CYS4 2.3 25.0 1.0 SG A:CYS7 2.3 30.0 1.0 H A:CYS7 3.0 36.5 1.0 HB2 A:CYS30 3.1 31.8 1.0 HB3 A:CYS7 3.1 37.5 1.0 HB3 A:CYS4 3.1 31.3 1.0 H A:CYS27 3.2 27.9 1.0 CB A:CYS4 3.2 26.1 1.0 CB A:CYS7 3.3 31.3 1.0 CB A:CYS30 3.3 26.5 1.0 HB2 A:CYS4 3.3 31.3 1.0 H A:CYS30 3.4 34.4 1.0 HB3 A:CYS27 3.5 31.8 1.0 CB A:CYS27 3.5 26.5 1.0 N A:CYS7 3.6 30.4 1.0 N A:CYS27 3.9 23.2 1.0 O A:HOH225 4.0 36.1 1.0 HB3 A:CYS30 4.0 31.8 1.0 O A:HOH230 4.0 39.8 1.0 CA A:CYS7 4.0 30.5 1.0 N A:CYS30 4.1 28.6 1.0 HA3 A:GLY6 4.1 35.9 1.0 HB2 A:CYS7 4.1 37.5 1.0 H A:GLY6 4.1 33.5 1.0 HB2 A:CYS27 4.3 31.8 1.0 CA A:CYS27 4.3 24.6 1.0 CA A:CYS30 4.3 26.3 1.0 H A:GLY9 4.3 33.5 1.0 HB A:VAL29 4.4 41.5 1.0 C A:GLY6 4.4 31.2 1.0 CA A:GLY6 4.6 29.9 1.0 HA A:LEU26 4.6 26.5 1.0 CA A:CYS4 4.6 24.2 1.0 HA A:CYS30 4.7 31.5 1.0 N A:GLY6 4.7 27.9 1.0 H A:ASN8 4.8 33.8 1.0 O A:CYS27 4.8 27.1 1.0 HA A:CYS7 4.8 36.6 1.0 C A:CYS7 4.8 30.5 1.0 HD22 A:LEU26 4.8 30.3 1.0 C A:CYS27 4.8 24.6 1.0 HA A:CYS4 5.0 29.1 1.0

Zinc binding site 2 out of 4 in the P62/SQSTM1 Zz Domain with Arg-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 Arg-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:25.8 occ:1.00 NE2 A:HIS36 2.0 25.0 1.0 ND1 A:HIS39 2.0 27.3 1.0 SG A:CYS18 2.3 24.4 1.0 SG A:CYS21 2.3 28.0 1.0 H A:CYS21 2.9 29.0 1.0 CE1 A:HIS36 2.9 26.1 1.0 CE1 A:HIS39 3.0 28.3 1.0 HE1 A:HIS36 3.0 31.3 1.0 HB2 A:HIS39 3.0 33.7 1.0 HB2 A:CYS21 3.1 30.3 1.0 CD2 A:HIS36 3.1 25.1 1.0 CG A:HIS39 3.1 28.0 1.0 HE1 A:HIS39 3.1 34.0 1.0 CB A:CYS21 3.3 25.2 1.0 HD2 A:HIS36 3.3 30.1 1.0 HB2 A:CYS18 3.4 28.9 1.0 CB A:CYS18 3.4 24.1 1.0 CB A:HIS39 3.4 28.1 1.0 HB A:VAL20 3.5 34.7 1.0 HB3 A:HIS39 3.5 33.7 1.0 N A:CYS21 3.6 24.1 1.0 HB3 A:CYS18 3.6 28.9 1.0 ND1 A:HIS36 4.0 25.1 1.0 HB3 A:CYS21 4.1 30.3 1.0 CA A:CYS21 4.1 24.1 1.0 NE2 A:HIS39 4.1 30.0 1.0 CG A:HIS36 4.2 25.1 1.0 H A:VAL20 4.2 31.0 1.0 CD2 A:HIS39 4.2 30.3 1.0 CB A:VAL20 4.4 28.9 1.0 HA A:CYS21 4.5 28.9 1.0 C A:VAL20 4.7 25.2 1.0 CA A:CYS18 4.7 22.1 1.0 HA A:CYS18 4.8 26.5 1.0 HD1 A:HIS36 4.8 30.1 1.0 HG12 A:VAL20 4.8 37.2 1.0 HB3 A:TYR24 4.9 29.9 1.0 N A:VAL20 4.9 25.9 1.0 CA A:VAL20 4.9 27.7 1.0 HE2 A:HIS39 4.9 36.0 1.0 CA A:HIS39 4.9 28.4 1.0

Zinc binding site 3 out of 4 in the P62/SQSTM1 Zz Domain with Arg-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 Arg-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:30.4 occ:1.00 SG B:CYS7 2.3 32.1 1.0 SG B:CYS30 2.3 32.1 1.0 SG B:CYS27 2.4 26.8 1.0 SG B:CYS4 2.4 27.4 1.0 HB2 B:CYS30 3.0 35.3 1.0 HB3 B:CYS7 3.0 38.1 1.0 H B:CYS7 3.1 43.2 1.0 H B:CYS27 3.2 29.4 1.0 HB3 B:CYS4 3.2 31.9 1.0 CB B:CYS7 3.3 31.7 1.0 CB B:CYS30 3.3 29.4 1.0 CB B:CYS4 3.3 26.6 1.0 HB3 B:CYS27 3.3 30.0 1.0 HB2 B:CYS4 3.4 31.9 1.0 H B:CYS30 3.4 34.4 1.0 CB B:CYS27 3.5 25.0 1.0 N B:CYS7 3.6 36.0 1.0 HB3 B:CYS30 3.9 35.3 1.0 N B:CYS27 4.0 24.5 1.0 HB2 B:CYS7 4.0 38.1 1.0 O B:HOH214 4.0 67.4 1.0 CA B:CYS7 4.1 33.5 1.0 N B:CYS30 4.1 28.7 1.0 HA3 B:GLY6 4.1 41.5 1.0 H B:GLY6 4.2 40.0 1.0 HB2 B:CYS27 4.2 30.0 1.0 CA B:CYS27 4.2 25.5 1.0 CA B:CYS30 4.3 29.7 1.0 HB B:VAL29 4.3 37.3 1.0 C B:GLY6 4.4 38.0 1.0 H B:GLY9 4.5 39.7 1.0 CA B:GLY6 4.6 34.6 1.0 HA B:LEU26 4.6 27.7 1.0 HA B:CYS30 4.7 35.7 1.0 CA B:CYS4 4.7 26.1 1.0 N B:GLY6 4.8 33.3 1.0 C B:CYS27 4.8 24.3 1.0 HA B:CYS7 4.8 40.3 1.0 O B:CYS27 4.8 25.1 1.0 HD22 B:LEU26 4.8 32.6 1.0 H B:ASN8 4.9 40.4 1.0 C B:CYS7 4.9 33.4 1.0 H B:VAL29 5.0 33.4 1.0

Zinc binding site 4 out of 4 in the P62/SQSTM1 Zz Domain with Arg-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 Arg-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:33.5 occ:1.00 ND1 B:HIS39 2.0 38.8 1.0 NE2 B:HIS36 2.0 31.3 1.0 SG B:CYS18 2.2 31.1 1.0 SG B:CYS21 2.4 38.7 1.0 H B:CYS21 2.9 39.7 1.0 CE1 B:HIS39 2.9 41.1 1.0 CE1 B:HIS36 2.9 30.9 1.0 HE1 B:HIS36 3.0 37.1 1.0 CG B:HIS39 3.0 36.6 1.0 HE1 B:HIS39 3.0 49.4 1.0 CD2 B:HIS36 3.1 30.0 1.0 HB2 B:CYS21 3.2 45.8 1.0 HB2 B:HIS39 3.2 46.6 1.0 HB2 B:CYS18 3.3 36.0 1.0 CB B:CYS18 3.3 30.0 1.0 CB B:CYS21 3.3 38.2 1.0 HD2 B:HIS36 3.4 36.0 1.0 HB3 B:HIS39 3.4 46.6 1.0 CB B:HIS39 3.4 38.9 1.0 HB B:VAL20 3.5 50.0 1.0 HB3 B:CYS18 3.5 36.0 1.0 N B:CYS21 3.6 33.1 1.0 NE2 B:HIS39 4.0 42.2 1.0 ND1 B:HIS36 4.0 30.7 1.0 CA B:CYS21 4.1 34.3 1.0 CD2 B:HIS39 4.1 41.5 1.0 H B:VAL20 4.1 41.8 1.0 HB3 B:CYS21 4.2 45.8 1.0 CG B:HIS36 4.2 30.3 1.0 HB3 B:TYR24 4.3 35.2 1.0 CB B:VAL20 4.4 41.6 1.0 HA B:CYS21 4.5 41.1 1.0 C B:VAL20 4.7 32.9 1.0 CA B:CYS18 4.7 27.0 1.0 HE2 B:HIS39 4.8 50.6 1.0 HA B:CYS18 4.8 32.4 1.0 CG B:TYR24 4.8 31.5 1.0 HD1 B:HIS36 4.8 36.9 1.0 CD2 B:TYR24 4.8 32.4 1.0 HD2 B:TYR24 4.8 38.9 1.0 N B:VAL20 4.9 34.8 1.0 CB B:TYR24 4.9 29.4 1.0 HG12 B:VAL20 4.9 53.6 1.0 HB2 B:TYR24 4.9 35.2 1.0 CA B:VAL20 4.9 35.9 1.0 HD2 B:HIS39 5.0 49.8 1.0 CA B:HIS39 5.0 36.9 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