Zinc in PDB 5yp7: P62/SQSTM1 Zz Domain

The structure of P62/SQSTM1 Zz Domain, PDB code: 5yp7 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)	33.82 / 1.42
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.749, 43.345, 54.070, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 20.7

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain (pdb code 5yp7). 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, PDB code: 5yp7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the P62/SQSTM1 Zz Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.8 occ:1.00 SG A:CYS154 2.3 20.9 1.0 SG A:CYS151 2.3 19.8 1.0 SG A:CYS131 2.4 19.2 1.0 SG A:CYS128 2.4 17.4 1.0 HB2 A:CYS154 2.9 24.4 1.0 HB3 A:CYS131 3.1 28.4 1.0 HB3 A:CYS128 3.2 22.3 1.0 CB A:CYS154 3.2 20.3 1.0 CB A:CYS128 3.2 18.6 1.0 H A:CYS151 3.2 21.2 1.0 H A:CYS131 3.2 21.4 1.0 CB A:CYS131 3.3 23.6 1.0 HB2 A:CYS128 3.3 22.3 1.0 H A:CYS154 3.3 23.1 1.0 HB3 A:CYS151 3.4 21.7 1.0 CB A:CYS151 3.5 18.1 1.0 N A:CYS131 3.7 17.9 1.0 HB3 A:CYS154 3.9 24.4 1.0 N A:CYS151 4.0 17.7 1.0 N A:CYS154 4.0 19.2 1.0 HB2 A:CYS131 4.1 28.4 1.0 O A:HOH307 4.1 31.1 1.0 CA A:CYS131 4.1 19.1 1.0 HA3 A:GLY130 4.1 26.9 1.0 HD2 D:LYS157 4.1 31.5 1.0 CA A:CYS154 4.2 19.4 1.0 CA A:CYS151 4.3 17.9 1.0 HB2 A:CYS151 4.3 21.7 1.0 H A:GLY133 4.4 22.5 1.0 H A:GLY130 4.4 24.8 1.0 HB A:VAL153 4.4 22.6 1.0 HD22 A:LEU150 4.5 26.1 1.0 C A:GLY130 4.5 24.9 1.0 HG13 D:VAL153 4.5 30.3 1.0 HG11 D:VAL153 4.6 30.3 1.0 HA A:CYS154 4.6 23.2 1.0 HZ2 D:LYS157 4.6 35.4 1.0 CA A:CYS128 4.7 16.7 1.0 CA A:GLY130 4.7 22.4 1.0 HA A:LEU150 4.7 19.8 1.0 O A:CYS151 4.7 18.2 1.0 C A:CYS151 4.8 19.9 1.0 N A:GLY130 4.9 20.7 1.0 HA A:CYS131 4.9 22.9 1.0 H A:ASN132 4.9 21.3 1.0 C A:CYS131 4.9 20.0 1.0 H A:VAL153 5.0 25.9 1.0 HA A:CYS128 5.0 20.0 1.0 CG1 D:VAL153 5.0 25.2 1.0

Zinc binding site 2 out of 4 in the P62/SQSTM1 Zz Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:20.4 occ:1.00 NE2 A:HIS160 2.0 18.5 1.0 ND1 A:HIS163 2.1 21.1 1.0 SG A:CYS142 2.2 19.4 1.0 SG A:CYS145 2.3 21.3 1.0 CE1 A:HIS160 2.9 18.6 1.0 CE1 A:HIS163 3.0 19.7 1.0 CD2 A:HIS160 3.0 22.2 1.0 H A:CYS145 3.0 30.9 1.0 HB2 A:CYS145 3.0 28.6 1.0 HE1 A:HIS163 3.1 23.6 1.0 HE1 A:HIS160 3.1 22.4 1.0 CG A:HIS163 3.2 20.4 1.0 HD2 A:HIS160 3.2 26.6 1.0 CB A:CYS145 3.3 23.9 1.0 HB2 A:HIS163 3.3 24.1 1.0 HB A:VAL144 3.4 35.3 1.0 CB A:CYS142 3.4 20.4 1.0 HB2 A:CYS142 3.4 24.4 1.0 HB3 A:HIS163 3.5 24.1 1.0 CB A:HIS163 3.6 20.1 1.0 HB3 A:CYS142 3.6 24.4 1.0 N A:CYS145 3.7 25.7 1.0 HB3 A:CYS145 4.0 28.6 1.0 ND1 A:HIS160 4.1 19.7 1.0 CA A:CYS145 4.1 23.0 1.0 CG A:HIS160 4.1 22.8 1.0 NE2 A:HIS163 4.1 20.0 1.0 H A:VAL144 4.2 33.3 1.0 CD2 A:HIS163 4.2 20.6 1.0 HB3 A:TYR148 4.3 26.1 1.0 CB A:VAL144 4.3 29.4 1.0 HA A:CYS145 4.5 27.6 1.0 C A:VAL144 4.7 30.6 1.0 CA A:CYS142 4.7 18.5 1.0 HD1 A:TYR148 4.8 25.5 1.0 HD1 A:HIS160 4.8 23.7 1.0 HA A:CYS142 4.8 22.2 1.0 HG12 A:VAL144 4.9 37.5 1.0 CD1 A:TYR148 4.9 21.2 1.0 HE2 A:HIS163 4.9 24.0 1.0 N A:VAL144 4.9 27.7 1.0 CA A:VAL144 4.9 27.7 1.0 CB A:TYR148 4.9 21.8 1.0 CG A:TYR148 4.9 18.6 1.0 HB2 A:TYR148 4.9 26.1 1.0 HG23 A:VAL144 5.0 39.7 1.0

Zinc binding site 3 out of 4 in the P62/SQSTM1 Zz Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:23.4 occ:1.00 SG D:CYS131 2.3 26.3 1.0 SG D:CYS154 2.3 22.8 1.0 SG D:CYS151 2.4 22.9 1.0 SG D:CYS128 2.4 25.4 1.0 HB2 D:CYS154 3.1 21.9 1.0 H D:CYS151 3.1 26.3 1.0 HB3 D:CYS131 3.2 32.1 1.0 HB3 D:CYS128 3.2 28.7 1.0 CB D:CYS128 3.2 23.9 1.0 H D:CYS131 3.3 32.2 1.0 HB2 D:CYS128 3.3 28.7 1.0 CB D:CYS154 3.3 18.3 1.0 CB D:CYS131 3.3 26.8 1.0 H D:CYS154 3.4 24.1 1.0 HB3 D:CYS151 3.5 24.8 1.0 CB D:CYS151 3.6 20.7 1.0 N D:CYS131 3.7 26.8 1.0 N D:CYS151 3.9 21.9 1.0 HD22 D:LEU150 4.0 35.9 1.0 HB3 D:CYS154 4.0 21.9 1.0 O D:HOH317 4.1 28.1 1.0 N D:CYS154 4.1 20.1 1.0 HB2 D:CYS131 4.1 32.1 1.0 HA3 D:GLY130 4.1 42.6 1.0 CA D:CYS131 4.1 27.8 1.0 H D:GLY133 4.2 30.1 1.0 CA D:CYS151 4.3 24.2 1.0 CA D:CYS154 4.3 21.2 1.0 H D:GLY130 4.3 32.9 1.0 HB2 D:CYS151 4.3 24.8 1.0 O A:HOH339 4.4 36.6 1.0 O D:HOH314 4.4 29.1 1.0 C D:GLY130 4.5 37.0 1.0 HA D:LEU150 4.6 22.0 1.0 HB D:VAL153 4.6 32.5 1.0 HA D:CYS154 4.6 25.4 1.0 CA D:GLY130 4.7 35.5 1.0 CA D:CYS128 4.7 24.8 1.0 HD23 D:LEU150 4.7 35.9 1.0 O D:CYS151 4.8 21.1 1.0 C D:CYS151 4.8 20.3 1.0 CD2 D:LEU150 4.8 29.9 1.0 N D:GLY130 4.8 27.4 1.0 H D:ASN132 4.9 31.5 1.0 C D:CYS131 4.9 25.7 1.0 HA D:CYS131 4.9 33.4 1.0 HA D:CYS128 5.0 29.7 1.0 HD22 D:LEU159 5.0 55.2 1.0

Zinc binding site 4 out of 4 in the P62/SQSTM1 Zz Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:21.0 occ:1.00 NE2 D:HIS160 2.0 19.6 1.0 ND1 D:HIS163 2.1 20.5 1.0 SG D:CYS142 2.3 20.5 1.0 SG D:CYS145 2.3 22.9 1.0 CE1 D:HIS163 3.0 20.2 1.0 CE1 D:HIS160 3.0 20.8 1.0 HB2 D:CYS145 3.0 27.7 1.0 CD2 D:HIS160 3.0 21.9 1.0 H D:CYS145 3.0 35.7 1.0 HE1 D:HIS163 3.1 24.2 1.0 HE1 D:HIS160 3.2 25.0 1.0 HD2 D:HIS160 3.2 26.3 1.0 CG D:HIS163 3.2 21.3 1.0 CB D:CYS145 3.2 23.1 1.0 HB2 D:CYS142 3.4 25.6 1.0 CB D:CYS142 3.4 21.3 1.0 HB2 D:HIS163 3.4 23.3 1.0 HB D:VAL144 3.4 50.1 1.0 HB3 D:HIS163 3.6 23.3 1.0 HB3 D:CYS142 3.6 25.6 1.0 CB D:HIS163 3.6 19.4 1.0 N D:CYS145 3.7 29.8 1.0 HB3 D:CYS145 4.0 27.7 1.0 CA D:CYS145 4.1 25.9 1.0 ND1 D:HIS160 4.1 23.2 1.0 CG D:HIS160 4.2 19.8 1.0 NE2 D:HIS163 4.2 23.3 1.0 H D:VAL144 4.2 35.6 1.0 CD2 D:HIS163 4.3 21.5 1.0 CB D:VAL144 4.4 41.7 1.0 HB3 D:TYR148 4.5 35.8 1.0 HA D:CYS145 4.5 31.1 1.0 C D:VAL144 4.7 38.5 1.0 CA D:CYS142 4.7 19.6 1.0 HA D:CYS142 4.8 23.5 1.0 HG23 D:VAL144 4.9 59.0 1.0 HD1 D:HIS160 4.9 27.8 1.0 N D:VAL144 4.9 29.7 1.0 HE2 D:HIS163 4.9 28.0 1.0 CA D:VAL144 4.9 40.9 1.0 HG12 D:VAL144 5.0 56.9 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