Zinc in PDB 5ypg: P62/SQSTM1 Zz Domain with Leu-Peptide

The structure of P62/SQSTM1 Zz Domain with Leu-Peptide, PDB code: 5ypg 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)	27.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.534, 44.279, 68.151, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 29.3

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

Zinc binding site 1 out of 4 in the P62/SQSTM1 Zz Domain with Leu-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 Leu-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:36.0 occ:1.00 SG A:CYS30 2.3 43.7 1.0 SG A:CYS4 2.3 27.5 1.0 SG A:CYS7 2.3 40.2 1.0 SG A:CYS27 2.3 28.4 1.0 H A:CYS7 2.9 38.7 1.0 HB2 A:CYS30 3.0 35.7 1.0 HB3 A:CYS4 3.1 35.0 1.0 CB A:CYS4 3.1 29.1 1.0 HB2 A:CYS4 3.2 35.0 1.0 H A:CYS27 3.2 32.0 1.0 CB A:CYS30 3.2 29.7 1.0 HB3 A:CYS7 3.3 54.4 1.0 H A:CYS30 3.3 40.8 1.0 CB A:CYS7 3.4 45.3 1.0 N A:CYS7 3.6 32.2 1.0 CB A:CYS27 3.7 32.8 1.0 HB3 A:CYS27 3.7 39.3 1.0 HB3 A:CYS30 3.9 35.7 1.0 N A:CYS30 4.0 34.0 1.0 N A:CYS27 4.0 26.7 1.0 CA A:CYS7 4.1 34.3 1.0 HA3 A:GLY6 4.1 43.3 1.0 HB A:VAL29 4.1 47.6 1.0 H A:GLY6 4.1 33.6 1.0 CA A:CYS30 4.2 30.6 1.0 HB2 A:CYS7 4.2 54.4 1.0 H A:GLY9 4.3 45.6 1.0 CA A:CYS27 4.4 25.8 1.0 HB2 A:CYS27 4.4 39.3 1.0 C A:GLY6 4.5 40.8 1.0 HA A:CYS30 4.5 36.7 1.0 HA A:LEU26 4.6 27.4 1.0 CA A:CYS4 4.6 25.9 1.0 CA A:GLY6 4.6 36.1 1.0 N A:GLY6 4.8 28.1 1.0 HA A:CYS7 4.9 41.2 1.0 C A:CYS7 4.9 38.5 1.0 H A:ASN8 4.9 39.2 1.0 O A:CYS27 4.9 36.5 1.0 HD22 A:LEU26 4.9 37.7 1.0 C A:CYS27 4.9 30.5 1.0 HB3 A:LEU26 4.9 32.9 1.0 HA A:CYS4 4.9 31.1 1.0

Zinc binding site 2 out of 4 in the P62/SQSTM1 Zz Domain with Leu-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 Leu-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:30.8 occ:1.00 HE2 A:HIS36 1.1 34.0 1.0 NE2 A:HIS36 2.0 28.4 1.0 ND1 A:HIS39 2.0 33.5 1.0 SG A:CYS18 2.3 28.9 1.0 SG A:CYS21 2.3 36.6 1.0 HB2 A:CYS21 2.7 42.7 1.0 H A:CYS21 2.8 39.9 1.0 CE1 A:HIS36 3.0 31.6 1.0 HB2 A:HIS39 3.0 39.1 1.0 CD2 A:HIS36 3.0 28.6 1.0 CG A:HIS39 3.0 37.1 1.0 CE1 A:HIS39 3.0 35.3 1.0 CB A:CYS21 3.0 35.6 1.0 HE1 A:HIS36 3.2 37.9 1.0 HD2 A:HIS36 3.2 34.3 1.0 HE1 A:HIS39 3.2 42.4 1.0 CB A:HIS39 3.3 32.6 1.0 HB3 A:HIS39 3.3 39.1 1.0 N A:CYS21 3.5 33.2 1.0 CB A:CYS18 3.5 31.6 1.0 HB2 A:CYS18 3.5 37.9 1.0 HB A:VAL20 3.6 42.7 1.0 HB3 A:CYS18 3.7 37.9 1.0 HB3 A:CYS21 3.8 42.7 1.0 CA A:CYS21 3.8 28.1 1.0 ND1 A:HIS36 4.1 35.6 1.0 CG A:HIS36 4.1 37.0 1.0 NE2 A:HIS39 4.1 39.1 1.0 CD2 A:HIS39 4.1 40.0 1.0 H A:VAL20 4.2 35.4 1.0 HA A:CYS21 4.3 33.7 1.0 CB A:VAL20 4.5 35.6 1.0 C A:VAL20 4.6 33.8 1.0 CA A:HIS39 4.8 33.8 1.0 CA A:CYS18 4.8 27.5 1.0 N A:VAL20 4.9 29.5 1.0 HB3 A:TYR24 4.9 30.5 1.0 CA A:VAL20 4.9 35.6 1.0 HE2 A:HIS39 4.9 46.9 1.0 HA A:CYS18 4.9 33.0 1.0 HG12 A:VAL20 5.0 60.5 1.0 HD2 A:HIS39 5.0 48.0 1.0

Zinc binding site 3 out of 4 in the P62/SQSTM1 Zz Domain with Leu-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 Leu-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:33.7 occ:1.00 HG B:CYS21 1.5 52.2 1.0 NE2 B:HIS36 2.0 30.7 1.0 ND1 B:HIS39 2.1 28.5 1.0 SG B:CYS21 2.3 43.5 1.0 SG B:CYS18 2.3 33.0 1.0 H B:CYS21 2.7 53.7 1.0 HB2 B:CYS21 2.7 47.1 1.0 CE1 B:HIS36 3.0 37.5 1.0 CE1 B:HIS39 3.0 31.9 1.0 CB B:CYS21 3.0 39.2 1.0 CD2 B:HIS36 3.0 30.9 1.0 CG B:HIS39 3.1 40.8 1.0 HE1 B:HIS39 3.1 38.3 1.0 HE1 B:HIS36 3.1 45.1 1.0 HB2 B:HIS39 3.2 43.7 1.0 HD2 B:HIS36 3.2 37.0 1.0 N B:CYS21 3.4 44.7 1.0 HB2 B:CYS18 3.4 40.8 1.0 HB3 B:HIS39 3.5 43.7 1.0 CB B:CYS18 3.5 34.0 1.0 CB B:HIS39 3.5 36.4 1.0 HB B:VAL20 3.5 55.8 1.0 HB3 B:CYS18 3.7 40.8 1.0 CA B:CYS21 3.8 40.8 1.0 HB3 B:CYS21 3.8 47.1 1.0 ND1 B:HIS36 4.1 32.3 1.0 NE2 B:HIS39 4.1 37.8 1.0 CG B:HIS36 4.1 32.7 1.0 CD2 B:HIS39 4.2 34.2 1.0 H B:VAL20 4.2 42.9 1.0 HA B:CYS21 4.2 49.0 1.0 CB B:VAL20 4.4 46.5 1.0 C B:VAL20 4.5 43.4 1.0 HB3 B:TYR24 4.7 49.4 1.0 HG12 B:VAL20 4.7 58.9 1.0 HD1 B:TYR24 4.7 42.0 1.0 CD1 B:TYR24 4.8 35.0 1.0 CA B:CYS18 4.8 35.2 1.0 CA B:VAL20 4.8 44.3 1.0 HD1 B:HIS36 4.9 38.8 1.0 N B:VAL20 4.9 35.8 1.0 HE2 B:HIS39 4.9 45.4 1.0 HA B:CYS18 4.9 42.2 1.0 CA B:HIS39 5.0 33.3 1.0

Zinc binding site 4 out of 4 in the P62/SQSTM1 Zz Domain with Leu-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 Leu-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:35.5 occ:1.00 SG B:CYS27 2.2 29.0 1.0 SG B:CYS30 2.3 30.5 1.0 SG B:CYS4 2.3 34.7 1.0 SG B:CYS7 2.3 36.2 1.0 H B:CYS7 2.8 50.7 1.0 HB2 B:CYS30 2.8 36.4 1.0 HB3 B:CYS7 3.1 48.1 1.0 H B:CYS27 3.1 31.9 1.0 HB3 B:CYS4 3.1 32.6 1.0 CB B:CYS30 3.1 30.3 1.0 CB B:CYS4 3.2 27.2 1.0 HB2 B:CYS4 3.3 32.6 1.0 CB B:CYS7 3.3 40.1 1.0 H B:CYS30 3.3 38.5 1.0 HB3 B:CYS27 3.4 33.2 1.0 N B:CYS7 3.4 42.3 1.0 CB B:CYS27 3.5 27.7 1.0 HB3 B:CYS30 3.8 36.4 1.0 N B:CYS27 3.9 26.6 1.0 N B:CYS30 3.9 32.1 1.0 CA B:CYS7 4.0 41.2 1.0 HA3 B:GLY6 4.0 47.5 1.0 H B:GLY6 4.1 44.5 1.0 HB2 B:CYS7 4.1 48.1 1.0 CA B:CYS30 4.1 35.8 1.0 HB B:VAL29 4.1 60.0 1.0 HB2 B:CYS27 4.2 33.2 1.0 CA B:CYS27 4.3 33.1 1.0 C B:GLY6 4.4 47.3 1.0 H B:GLY9 4.4 34.5 1.0 CA B:GLY6 4.5 39.6 1.0 HA B:CYS30 4.5 43.0 1.0 HA B:LEU26 4.6 31.4 1.0 CA B:CYS4 4.7 33.0 1.0 N B:GLY6 4.7 37.1 1.0 HA B:CYS7 4.7 49.5 1.0 C B:CYS7 4.8 40.7 1.0 H B:ASN8 4.8 44.7 1.0 C B:CYS27 4.9 33.0 1.0 O B:CYS27 4.9 27.3 1.0 HA B:CYS4 5.0 39.6 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