Zinc in PDB 5ypb: P62/SQSTM1 Zz Domain with His-Peptide

The structure of P62/SQSTM1 Zz Domain with His-Peptide, PDB code: 5ypb 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)	33.69 / 2.90
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	113.981, 113.981, 113.981, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 28.7

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with His-Peptide (pdb code 5ypb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the P62/SQSTM1 Zz Domain with His-Peptide, PDB code: 5ypb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the P62/SQSTM1 Zz Domain with His-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 His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:38.2 occ:1.00 SG A:CYS27 2.3 32.6 1.0 SG A:CYS7 2.3 34.2 1.0 SG A:CYS4 2.3 37.3 1.0 SG A:CYS30 2.3 42.5 1.0 H A:CYS7 3.0 46.0 1.0 HB3 A:CYS7 3.1 47.1 1.0 H A:CYS27 3.2 42.4 1.0 HB3 A:CYS4 3.2 51.9 1.0 CB A:CYS4 3.2 43.1 1.0 HB2 A:CYS30 3.3 48.8 1.0 HB3 A:CYS27 3.3 47.7 1.0 CB A:CYS7 3.3 39.1 1.0 HB2 A:CYS4 3.3 51.9 1.0 H A:CYS30 3.4 51.2 1.0 CB A:CYS27 3.4 39.6 1.0 CB A:CYS30 3.5 40.5 1.0 N A:CYS7 3.6 38.2 1.0 N A:CYS27 3.9 35.2 1.0 CA A:CYS7 4.0 38.1 1.0 HB2 A:CYS7 4.1 47.1 1.0 N A:CYS30 4.1 42.6 1.0 HB3 A:CYS30 4.1 48.8 1.0 HB2 A:CYS27 4.2 47.7 1.0 CA A:CYS27 4.2 37.8 1.0 HB A:VAL29 4.2 57.9 1.0 H A:GLY6 4.3 45.6 1.0 H C:HIS36 4.3 43.3 1.0 HA3 A:GLY6 4.3 52.8 1.0 CA A:CYS30 4.4 47.1 1.0 H A:GLY9 4.5 57.9 1.0 C A:GLY6 4.6 42.0 1.0 HA A:LEU26 4.7 48.4 1.0 CA A:CYS4 4.7 42.1 1.0 HA C:LEU35 4.7 46.4 1.0 C A:CYS27 4.8 37.0 1.0 CA A:GLY6 4.8 43.9 1.0 HA A:CYS7 4.8 45.9 1.0 C A:CYS7 4.8 42.9 1.0 HA A:CYS30 4.9 56.6 1.0 N A:GLY6 4.9 37.9 1.0 HD22 A:LEU26 4.9 44.7 1.0 H A:VAL29 4.9 51.3 1.0 O A:CYS27 4.9 40.1 1.0

Zinc binding site 2 out of 8 in the P62/SQSTM1 Zz Domain with His-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 His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:47.8 occ:1.00 NE2 A:HIS36 2.0 44.8 1.0 ND1 A:HIS39 2.0 48.6 1.0 SG A:CYS21 2.2 49.5 1.0 SG A:CYS18 2.3 47.0 1.0 H A:CYS21 2.7 61.5 1.0 HB2 A:CYS21 2.9 58.4 1.0 CD2 A:HIS36 3.0 40.6 1.0 CE1 A:HIS36 3.0 39.6 1.0 CE1 A:HIS39 3.0 53.6 1.0 CG A:HIS39 3.0 51.2 1.0 CB A:CYS21 3.1 48.6 1.0 HB3 A:HIS39 3.2 65.0 1.0 HD2 A:HIS36 3.2 48.9 1.0 HB2 A:HIS39 3.2 65.0 1.0 HE1 A:HIS36 3.2 47.6 1.0 HE1 A:HIS39 3.2 64.5 1.0 HB A:VAL20 3.3 60.4 1.0 CB A:HIS39 3.3 54.1 1.0 N A:CYS21 3.5 51.1 1.0 CB A:CYS18 3.5 41.5 1.0 HB2 A:CYS18 3.5 49.9 1.0 HB3 A:CYS18 3.7 49.9 1.0 CA A:CYS21 3.9 46.4 1.0 HB3 A:CYS21 3.9 58.4 1.0 ND1 A:HIS36 4.1 39.2 1.0 CG A:HIS36 4.1 38.0 1.0 NE2 A:HIS39 4.1 53.0 1.0 CD2 A:HIS39 4.2 53.5 1.0 CB A:VAL20 4.2 50.2 1.0 H A:VAL20 4.2 64.6 1.0 HA A:CYS21 4.4 55.8 1.0 HB3 A:TYR24 4.4 52.5 1.0 C A:VAL20 4.5 51.3 1.0 HG12 A:VAL20 4.7 71.0 1.0 HD22 B:ASN8 4.7 87.9 1.0 CA A:VAL20 4.8 50.3 1.0 HA2 B:GLY9 4.8 63.1 1.0 N A:VAL20 4.9 53.7 1.0 CA A:HIS39 4.9 50.6 1.0 CG1 A:VAL20 4.9 59.0 1.0 CA A:CYS18 4.9 42.2 1.0 HG11 A:VAL20 4.9 71.0 1.0 HD1 A:HIS36 4.9 47.2 1.0 HE2 A:HIS39 4.9 63.7 1.0 HG23 A:VAL20 5.0 55.2 1.0

Zinc binding site 3 out of 8 in the P62/SQSTM1 Zz Domain with His-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 His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:40.8 occ:1.00 SG B:CYS27 2.2 35.0 1.0 SG B:CYS30 2.3 40.9 1.0 SG B:CYS7 2.4 39.9 1.0 SG B:CYS4 2.4 38.5 1.0 H B:CYS7 3.0 54.8 1.0 H B:CYS27 3.1 41.6 1.0 HB2 B:CYS30 3.1 45.5 1.0 HB3 B:CYS7 3.1 46.2 1.0 HB3 B:CYS4 3.2 52.7 1.0 HB3 B:CYS27 3.2 50.6 1.0 CB B:CYS4 3.3 43.8 1.0 H B:CYS30 3.3 49.6 1.0 CB B:CYS7 3.3 38.4 1.0 HB2 B:CYS4 3.3 52.7 1.0 CB B:CYS30 3.4 37.8 1.0 CB B:CYS27 3.4 42.1 1.0 N B:CYS7 3.6 45.5 1.0 N B:CYS27 3.9 34.6 1.0 HB3 B:CYS30 4.0 45.5 1.0 N B:CYS30 4.1 41.2 1.0 CA B:CYS7 4.1 40.1 1.0 HB2 B:CYS7 4.1 46.2 1.0 HB2 B:CYS27 4.1 50.6 1.0 CA B:CYS27 4.2 36.7 1.0 HA3 B:GLY6 4.2 56.8 1.0 H B:GLY6 4.2 51.4 1.0 HB B:VAL29 4.3 53.7 1.0 CA B:CYS30 4.3 43.9 1.0 H B:GLY9 4.5 58.6 1.0 C B:GLY6 4.5 48.4 1.0 HA B:LEU26 4.6 44.8 1.0 CA B:GLY6 4.7 47.2 1.0 CA B:CYS4 4.7 45.2 1.0 HA B:CYS30 4.8 52.9 1.0 H A:HIS36 4.8 49.2 1.0 C B:CYS27 4.8 37.1 1.0 H B:VAL29 4.8 52.3 1.0 HA B:CYS7 4.8 48.3 1.0 N B:GLY6 4.9 42.7 1.0 C B:CYS7 4.9 45.1 1.0 HD22 B:LEU26 4.9 47.5 1.0 H B:ASN8 4.9 58.6 1.0 O B:CYS27 5.0 34.8 1.0

Zinc binding site 4 out of 8 in the P62/SQSTM1 Zz Domain with His-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 His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:45.9 occ:1.00 NE2 B:HIS36 2.0 54.7 1.0 ND1 B:HIS39 2.0 51.8 1.0 SG B:CYS21 2.3 50.6 1.0 SG B:CYS18 2.4 46.4 1.0 HB2 B:CYS21 2.8 52.6 1.0 H B:CYS21 2.8 66.2 1.0 CE1 B:HIS36 2.9 41.7 1.0 HE1 B:HIS36 3.0 50.1 1.0 CG B:HIS39 3.0 56.1 1.0 CE1 B:HIS39 3.0 50.9 1.0 CB B:CYS21 3.0 43.8 1.0 CD2 B:HIS36 3.1 44.9 1.0 HB2 B:HIS39 3.2 58.1 1.0 HB3 B:HIS39 3.2 58.1 1.0 HE1 B:HIS39 3.2 61.2 1.0 CB B:HIS39 3.3 48.3 1.0 HD2 B:HIS36 3.4 54.0 1.0 HB B:VAL20 3.4 67.0 1.0 N B:CYS21 3.5 55.0 1.0 HB2 B:CYS18 3.5 49.7 1.0 CB B:CYS18 3.5 41.3 1.0 HB3 B:CYS18 3.7 49.7 1.0 CA B:CYS21 3.8 52.9 1.0 HB3 B:CYS21 3.8 52.6 1.0 ND1 B:HIS36 4.1 41.6 1.0 NE2 B:HIS39 4.1 57.5 1.0 CD2 B:HIS39 4.2 58.2 1.0 CG B:HIS36 4.2 41.8 1.0 HB3 B:TYR24 4.3 45.1 1.0 HA B:CYS21 4.3 63.6 1.0 H B:VAL20 4.3 62.8 1.0 CB B:VAL20 4.3 55.7 1.0 C B:VAL20 4.6 52.6 1.0 HG12 B:VAL20 4.8 67.0 1.0 HD1 B:HIS36 4.8 50.0 1.0 HB2 B:TYR24 4.8 45.1 1.0 CG B:TYR24 4.8 40.6 1.0 CA B:HIS39 4.9 50.8 1.0 CB B:TYR24 4.9 37.5 1.0 CA B:VAL20 4.9 50.6 1.0 CA B:CYS18 4.9 40.2 1.0 HE2 B:HIS39 4.9 69.2 1.0 N B:VAL20 4.9 52.2 1.0 CD1 B:TYR24 5.0 40.4 1.0

Zinc binding site 5 out of 8 in the P62/SQSTM1 Zz Domain with His-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of P62/SQSTM1 Zz Domain with His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:44.3 occ:1.00 SG C:CYS4 2.2 47.5 1.0 SG C:CYS7 2.3 58.9 1.0 SG C:CYS30 2.3 40.7 1.0 SG C:CYS27 2.3 42.4 1.0 H C:CYS7 2.7 65.9 1.0 H C:CYS27 3.0 43.7 1.0 HB3 C:CYS7 3.1 69.3 1.0 HB2 C:CYS30 3.1 49.5 1.0 HB3 C:CYS4 3.1 61.5 1.0 CB C:CYS4 3.1 51.1 1.0 HB2 C:CYS4 3.2 61.5 1.0 CB C:CYS7 3.3 57.7 1.0 H C:CYS30 3.3 52.5 1.0 CB C:CYS30 3.4 41.1 1.0 HB3 C:CYS27 3.4 53.7 1.0 N C:CYS7 3.4 54.8 1.0 CB C:CYS27 3.5 44.6 1.0 N C:CYS27 3.8 36.3 1.0 CA C:CYS7 3.9 63.0 1.0 H C:GLY6 4.0 49.3 1.0 HB3 C:CYS30 4.0 49.5 1.0 N C:CYS30 4.1 43.6 1.0 HB C:VAL29 4.1 57.9 1.0 HB2 C:CYS7 4.1 69.3 1.0 H C:GLY9 4.1 76.6 1.0 CA C:CYS27 4.2 43.6 1.0 H C:ASN8 4.2 75.9 1.0 HA3 C:GLY6 4.2 55.6 1.0 HB2 C:CYS27 4.3 53.7 1.0 CA C:CYS30 4.3 38.2 1.0 C C:GLY6 4.4 44.8 1.0 HA C:LEU26 4.5 45.2 1.0 C C:CYS7 4.6 59.8 1.0 CA C:CYS4 4.6 50.0 1.0 N C:ASN8 4.6 63.1 1.0 HD22 C:LEU26 4.6 45.7 1.0 CA C:GLY6 4.6 46.2 1.0 N C:GLY6 4.7 41.0 1.0 HA C:CYS7 4.7 75.7 1.0 HA C:CYS30 4.7 46.0 1.0 C C:CYS27 4.8 38.8 1.0 O C:CYS27 4.8 41.5 1.0 N C:GLY9 4.9 63.8 1.0 HB3 C:LEU26 4.9 43.7 1.0 HA C:CYS4 4.9 60.2 1.0 C C:LEU26 4.9 41.5 1.0

Zinc binding site 6 out of 8 in the P62/SQSTM1 Zz Domain with His-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of P62/SQSTM1 Zz Domain with His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:44.3 occ:1.00 HB2 C:CYS21 1.8 65.8 1.0 HG C:CYS21 2.0 75.8 1.0 NE2 C:HIS36 2.1 38.8 1.0 ND1 C:HIS39 2.2 48.1 1.0 SG C:CYS21 2.3 63.0 1.0 SG C:CYS18 2.3 41.7 1.0 CB C:CYS21 2.4 54.7 1.0 H C:CYS21 2.6 64.0 1.0 CE1 C:HIS36 3.0 46.1 1.0 CE1 C:HIS39 3.0 46.3 1.0 HE1 C:HIS36 3.0 55.5 1.0 N C:CYS21 3.1 53.2 1.0 HE1 C:HIS39 3.1 55.7 1.0 HB3 C:CYS21 3.1 65.8 1.0 CD2 C:HIS36 3.2 43.3 1.0 CA C:CYS21 3.2 55.1 1.0 CG C:HIS39 3.3 55.0 1.0 HD2 C:HIS36 3.5 52.1 1.0 HB2 C:HIS39 3.5 56.5 1.0 CB C:CYS18 3.5 39.7 1.0 HB2 C:CYS18 3.5 47.8 1.0 HB3 C:HIS39 3.6 56.5 1.0 HB C:VAL20 3.6 56.2 1.0 HA C:CYS21 3.7 66.3 1.0 HB3 C:CYS18 3.7 47.8 1.0 CB C:HIS39 3.7 47.0 1.0 H C:VAL20 4.1 63.1 1.0 ND1 C:HIS36 4.1 46.0 1.0 NE2 C:HIS39 4.2 57.6 1.0 C C:VAL20 4.2 50.9 1.0 CG C:HIS36 4.3 41.3 1.0 CD2 C:HIS39 4.3 55.4 1.0 HB3 C:TYR24 4.4 55.5 1.0 HA2 A:GLY9 4.5 61.4 1.0 CB C:VAL20 4.5 46.7 1.0 C C:CYS21 4.5 61.6 1.0 HD3 A:PRO10 4.6 85.1 1.0 CA C:VAL20 4.7 45.1 1.0 N C:VAL20 4.8 52.5 1.0 O C:CYS21 4.8 57.6 1.0 HB2 C:TYR24 4.9 55.5 1.0 HD1 C:HIS36 4.9 55.4 1.0 CA C:CYS18 4.9 40.2 1.0 HE2 C:HIS39 4.9 69.2 1.0 CB C:TYR24 5.0 46.1 1.0

Zinc binding site 7 out of 8 in the P62/SQSTM1 Zz Domain with His-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of P62/SQSTM1 Zz Domain with His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:76.8 occ:1.00 SG D:CYS27 2.2 72.3 1.0 SG D:CYS4 2.3 84.3 1.0 SG D:CYS30 2.3 86.8 1.0 SG D:CYS7 2.4 95.0 1.0 H D:CYS27 2.9 97.5 1.0 HB3 D:CYS27 2.9 0.2 1.0 CB D:CYS27 3.1 85.9 1.0 HB3 D:CYS4 3.1 0.1 1.0 CB D:CYS4 3.2 90.0 1.0 HB2 D:CYS4 3.2 0.1 1.0 HB3 D:CYS7 3.2 0.7 1.0 HB2 D:CYS30 3.2 89.4 1.0 H D:CYS30 3.3 90.5 1.0 CB D:CYS30 3.4 74.4 1.0 CB D:CYS7 3.4 98.0 1.0 H D:CYS7 3.5 0.2 1.0 N D:CYS27 3.6 81.2 1.0 CA D:CYS27 3.9 77.3 1.0 HB2 D:CYS27 3.9 0.2 1.0 N D:CYS7 3.9 95.9 1.0 N D:CYS30 4.0 75.3 1.0 HB D:VAL29 4.1 0.8 1.0 HB3 D:CYS30 4.2 89.4 1.0 HB2 D:CYS7 4.2 0.7 1.0 CA D:CYS7 4.3 0.0 1.0 CA D:CYS30 4.3 75.6 1.0 H D:GLY6 4.4 0.0 1.0 C D:CYS27 4.4 80.9 1.0 H D:GLY9 4.5 0.5 1.0 HA D:LEU26 4.5 92.3 1.0 O D:CYS27 4.5 75.4 1.0 HA3 D:GLY6 4.6 0.4 1.0 CA D:CYS4 4.6 87.3 1.0 HA D:CYS30 4.7 90.8 1.0 H D:VAL29 4.7 96.5 1.0 HA D:CYS27 4.7 92.9 1.0 C D:GLY6 4.7 97.3 1.0 HD22 D:LEU26 4.8 93.1 1.0 C D:LEU26 4.8 76.9 1.0 HA D:CYS4 4.9 0.9 1.0

Zinc binding site 8 out of 8 in the P62/SQSTM1 Zz Domain with His-Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of P62/SQSTM1 Zz Domain with His-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:74.1 occ:1.00 ND1 D:HIS39 2.1 83.3 1.0 NE2 D:HIS36 2.1 65.5 1.0 SG D:CYS21 2.2 77.8 1.0 SG D:CYS18 2.3 62.1 1.0 H D:CYS21 2.4 97.4 1.0 HB2 D:CYS21 2.8 79.5 1.0 CE1 D:HIS36 2.8 63.4 1.0 HE1 D:HIS36 2.9 76.2 1.0 CE1 D:HIS39 2.9 82.2 1.0 HB D:VAL20 3.0 92.4 1.0 CB D:CYS21 3.0 66.2 1.0 HE1 D:HIS39 3.0 98.7 1.0 CG D:HIS39 3.2 77.1 1.0 N D:CYS21 3.2 81.0 1.0 CD2 D:HIS36 3.2 71.5 1.0 HB2 D:HIS39 3.4 85.6 1.0 CB D:CYS18 3.5 65.9 1.0 HB2 D:CYS18 3.5 79.2 1.0 HD2 D:HIS36 3.5 85.9 1.0 HB3 D:HIS39 3.5 85.6 1.0 CB D:HIS39 3.6 71.3 1.0 CA D:CYS21 3.7 71.2 1.0 HB3 D:CYS18 3.7 79.2 1.0 H D:VAL20 3.8 80.6 1.0 HB3 D:CYS21 3.9 79.5 1.0 CB D:VAL20 3.9 76.9 1.0 ND1 D:HIS36 4.0 73.8 1.0 NE2 D:HIS39 4.1 84.6 1.0 HA D:CYS21 4.2 85.6 1.0 C D:VAL20 4.2 74.1 1.0 CD2 D:HIS39 4.2 80.8 1.0 CG D:HIS36 4.3 72.8 1.0 CA D:VAL20 4.4 74.6 1.0 N D:VAL20 4.5 67.1 1.0 HG12 D:VAL20 4.5 0.5 1.0 HB3 D:TYR24 4.6 0.6 1.0 HG23 D:VAL20 4.6 93.3 1.0 CG1 D:VAL20 4.7 83.6 1.0 HD1 D:HIS36 4.8 88.7 1.0 CG2 D:VAL20 4.8 77.6 1.0 HG11 D:VAL20 4.8 0.5 1.0 HE2 D:HIS39 4.8 0.6 1.0 HG21 D:VAL20 4.8 93.3 1.0 CA D:CYS18 4.9 64.4 1.0 C D:CYS21 4.9 81.6 1.0 HB2 D:TYR24 4.9 0.6 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