Zinc in PDB 5ype: P62/SQSTM1 Zz Domain with Tyr-Peptide

The structure of P62/SQSTM1 Zz Domain with Tyr-Peptide, PDB code: 5ype 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)	40.50 / 2.85
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	114.541, 114.541, 114.541, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 26.9

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Tyr-Peptide (pdb code 5ype). 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 Tyr-Peptide, PDB code: 5ype:
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 Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:28.3 occ:1.00 SG A:CYS7 2.2 20.9 1.0 SG A:CYS27 2.3 36.0 1.0 SG A:CYS4 2.3 29.5 1.0 SG A:CYS30 2.4 24.4 1.0 H A:CYS7 2.7 39.3 1.0 HB3 A:CYS4 3.1 33.7 1.0 H A:CYS27 3.1 35.1 1.0 HB3 A:CYS7 3.2 38.3 1.0 HB2 A:CYS30 3.2 41.3 1.0 CB A:CYS4 3.2 28.1 1.0 HB3 A:CYS27 3.2 36.0 1.0 CB A:CYS7 3.3 31.9 1.0 HB2 A:CYS4 3.3 33.7 1.0 CB A:CYS27 3.4 30.0 1.0 CB A:CYS30 3.4 34.4 1.0 H A:CYS30 3.5 39.1 1.0 N A:CYS7 3.5 32.7 1.0 N A:CYS27 3.9 29.3 1.0 CA A:CYS7 4.0 26.6 1.0 HB3 A:CYS30 4.1 41.3 1.0 HB2 A:CYS7 4.1 38.3 1.0 H A:GLY6 4.1 34.6 1.0 HB2 A:CYS27 4.1 36.0 1.0 N A:CYS30 4.2 32.6 1.0 CA A:CYS27 4.2 28.0 1.0 HA3 A:GLY6 4.2 36.2 1.0 H C:HIS36 4.3 40.2 1.0 HB A:VAL29 4.3 33.9 1.0 CA A:CYS30 4.4 29.7 1.0 C A:GLY6 4.5 32.0 1.0 HA A:LEU26 4.6 34.2 1.0 H A:ASN8 4.6 36.0 1.0 CA A:CYS4 4.7 29.1 1.0 CA A:GLY6 4.7 30.1 1.0 HA A:CYS7 4.7 31.9 1.0 H A:GLY9 4.8 36.4 1.0 N A:GLY6 4.8 28.8 1.0 HA C:LEU35 4.8 29.9 1.0 HA A:CYS30 4.8 35.7 1.0 C A:CYS7 4.8 27.0 1.0 HD22 A:LEU26 4.9 39.3 1.0 C A:CYS27 4.9 26.7 1.0

Zinc binding site 2 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:35.1 occ:1.00 NE2 A:HIS36 2.0 27.2 1.0 ND1 A:HIS39 2.1 38.5 1.0 SG A:CYS21 2.2 37.3 1.0 SG A:CYS18 2.3 37.0 1.0 HB2 A:CYS21 2.5 50.4 1.0 H A:CYS21 2.5 45.7 1.0 CB A:CYS21 2.8 42.0 1.0 CE1 A:HIS36 2.9 27.3 1.0 CD2 A:HIS36 3.0 32.3 1.0 CE1 A:HIS39 3.0 34.3 1.0 CG A:HIS39 3.1 39.5 1.0 HE1 A:HIS36 3.1 32.8 1.0 HB2 A:HIS39 3.2 43.4 1.0 HD2 A:HIS36 3.2 38.8 1.0 HE1 A:HIS39 3.2 41.2 1.0 N A:CYS21 3.3 38.1 1.0 HB3 A:HIS39 3.3 43.4 1.0 CB A:HIS39 3.4 36.2 1.0 HB A:VAL20 3.4 40.1 1.0 CB A:CYS18 3.5 33.8 1.0 HB2 A:CYS18 3.6 40.5 1.0 CA A:CYS21 3.6 42.9 1.0 HB3 A:CYS21 3.6 50.4 1.0 HB3 A:CYS18 3.7 40.5 1.0 ND1 A:HIS36 4.1 27.1 1.0 HA A:CYS21 4.1 51.5 1.0 CG A:HIS36 4.1 31.3 1.0 NE2 A:HIS39 4.2 35.1 1.0 H A:VAL20 4.2 49.0 1.0 CD2 A:HIS39 4.2 36.5 1.0 CB A:VAL20 4.3 33.4 1.0 C A:VAL20 4.4 37.0 1.0 HB3 A:TYR24 4.5 35.3 1.0 HG12 A:VAL20 4.6 38.7 1.0 CA A:VAL20 4.8 38.8 1.0 N A:VAL20 4.8 40.8 1.0 C A:CYS21 4.8 40.8 1.0 HD1 A:HIS36 4.8 32.5 1.0 CA A:CYS18 4.9 38.4 1.0 CA A:HIS39 4.9 42.4 1.0 HA2 B:GLY9 4.9 37.3 1.0 HE2 A:HIS39 4.9 42.1 1.0 CG1 A:VAL20 4.9 32.2 1.0

Zinc binding site 3 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:30.3 occ:1.00 SG B:CYS30 2.3 35.2 1.0 SG B:CYS27 2.3 25.0 1.0 SG B:CYS7 2.3 23.0 1.0 SG B:CYS4 2.4 24.8 1.0 H B:CYS7 2.9 31.3 1.0 HB2 B:CYS30 2.9 34.2 1.0 H B:CYS30 3.0 35.6 1.0 H B:CYS27 3.1 36.8 1.0 CB B:CYS30 3.2 28.5 1.0 HB3 B:CYS7 3.2 33.9 1.0 CB B:CYS4 3.3 33.2 1.0 CB B:CYS7 3.4 28.3 1.0 HB2 B:CYS4 3.4 39.8 1.0 HB3 B:CYS4 3.4 39.8 1.0 HB3 B:CYS27 3.4 31.1 1.0 CB B:CYS27 3.5 25.9 1.0 N B:CYS7 3.6 26.1 1.0 N B:CYS30 3.8 29.7 1.0 N B:CYS27 3.9 30.7 1.0 HB3 B:CYS30 3.9 34.2 1.0 HB B:VAL29 4.0 42.2 1.0 CA B:CYS30 4.1 36.3 1.0 CA B:CYS7 4.1 27.3 1.0 HB2 B:CYS7 4.1 33.9 1.0 CA B:CYS27 4.2 28.1 1.0 HB2 B:CYS27 4.3 31.1 1.0 H B:GLY6 4.3 34.7 1.0 HA3 B:GLY6 4.4 35.2 1.0 HA B:CYS30 4.5 43.6 1.0 HA B:LEU26 4.6 36.3 1.0 C B:GLY6 4.7 32.4 1.0 H A:HIS36 4.7 40.0 1.0 C B:CYS27 4.7 27.5 1.0 H B:VAL29 4.7 38.7 1.0 O B:CYS27 4.8 30.1 1.0 H B:GLY9 4.8 38.5 1.0 CA B:CYS4 4.8 35.3 1.0 H B:ASN8 4.8 42.0 1.0 HA B:CYS7 4.8 32.7 1.0 CA B:GLY6 4.8 29.3 1.0 HD22 B:LEU26 4.9 38.1 1.0 CB B:VAL29 4.9 35.2 1.0 N B:GLY6 4.9 28.9 1.0 C B:VAL29 4.9 33.3 1.0 HB3 B:LEU26 4.9 31.9 1.0 C B:CYS7 5.0 32.6 1.0 HA A:LEU35 5.0 42.2 1.0

Zinc binding site 4 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:40.5 occ:1.00 NE2 B:HIS36 2.0 32.8 1.0 ND1 B:HIS39 2.1 34.9 1.0 SG B:CYS21 2.3 41.7 1.0 SG B:CYS18 2.3 31.5 1.0 HB2 B:CYS21 2.5 34.2 1.0 H B:CYS21 2.6 44.6 1.0 CB B:CYS21 2.9 28.5 1.0 CE1 B:HIS36 2.9 30.2 1.0 CG B:HIS39 3.1 40.5 1.0 HE1 B:HIS36 3.1 36.2 1.0 CD2 B:HIS36 3.1 33.2 1.0 HB2 B:HIS39 3.1 37.2 1.0 CE1 B:HIS39 3.1 34.0 1.0 HE1 B:HIS39 3.3 40.8 1.0 HB3 B:HIS39 3.3 37.2 1.0 HD2 B:HIS36 3.3 39.8 1.0 N B:CYS21 3.3 37.2 1.0 CB B:HIS39 3.4 31.0 1.0 HB2 B:CYS18 3.4 34.0 1.0 CB B:CYS18 3.5 28.3 1.0 HB B:VAL20 3.5 44.5 1.0 HB3 B:CYS18 3.6 34.0 1.0 HB3 B:CYS21 3.7 34.2 1.0 CA B:CYS21 3.7 34.1 1.0 ND1 B:HIS36 4.1 30.2 1.0 CG B:HIS36 4.2 28.0 1.0 H B:VAL20 4.2 50.4 1.0 NE2 B:HIS39 4.2 38.4 1.0 HA B:CYS21 4.2 40.9 1.0 CD2 B:HIS39 4.2 38.8 1.0 HB3 B:TYR24 4.3 28.5 1.0 CB B:VAL20 4.4 37.1 1.0 C B:VAL20 4.5 35.4 1.0 HG12 B:VAL20 4.8 40.5 1.0 HD1 B:HIS36 4.8 36.2 1.0 HB2 B:TYR24 4.8 28.5 1.0 CA B:VAL20 4.8 35.3 1.0 N B:VAL20 4.8 42.0 1.0 CA B:CYS18 4.8 32.9 1.0 C B:CYS21 4.9 33.4 1.0 CA B:HIS39 4.9 35.8 1.0 CB B:TYR24 4.9 23.8 1.0 CG B:TYR24 4.9 25.1 1.0 HD1 B:TYR24 4.9 33.7 1.0 CD1 B:TYR24 5.0 28.1 1.0 HE2 B:HIS39 5.0 46.0 1.0 HA B:CYS18 5.0 39.5 1.0

Zinc binding site 5 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:34.4 occ:1.00 ND1 C:HIS39 2.0 26.3 1.0 NE2 C:HIS36 2.1 30.7 1.0 SG C:CYS21 2.3 43.4 1.0 SG C:CYS18 2.3 23.3 1.0 H C:CYS21 2.7 43.3 1.0 HB2 C:CYS21 2.8 41.9 1.0 CE1 C:HIS36 2.9 33.6 1.0 CE1 C:HIS39 3.0 31.5 1.0 HB2 C:HIS39 3.0 38.8 1.0 CB C:CYS21 3.0 34.9 1.0 CG C:HIS39 3.0 35.4 1.0 HE1 C:HIS36 3.0 40.4 1.0 CD2 C:HIS36 3.2 29.1 1.0 HE1 C:HIS39 3.2 37.8 1.0 CB C:HIS39 3.4 32.3 1.0 HB3 C:HIS39 3.4 38.8 1.0 HD2 C:HIS36 3.4 35.0 1.0 N C:CYS21 3.4 36.1 1.0 HB C:VAL20 3.5 42.0 1.0 CB C:CYS18 3.6 27.6 1.0 HB2 C:CYS18 3.6 33.1 1.0 CA C:CYS21 3.8 41.1 1.0 HB3 C:CYS18 3.8 33.1 1.0 HB3 C:CYS21 3.8 41.9 1.0 H C:VAL20 4.1 50.2 1.0 ND1 C:HIS36 4.1 32.6 1.0 NE2 C:HIS39 4.1 35.2 1.0 CD2 C:HIS39 4.2 35.6 1.0 HA2 A:GLY9 4.2 38.3 1.0 CG C:HIS36 4.2 33.3 1.0 HA C:CYS21 4.3 49.4 1.0 HD3 A:PRO10 4.4 52.3 1.0 CB C:VAL20 4.4 35.0 1.0 C C:VAL20 4.5 30.9 1.0 HB3 C:TYR24 4.8 41.7 1.0 N C:VAL20 4.8 41.8 1.0 HG12 C:VAL20 4.8 40.5 1.0 CA C:VAL20 4.8 34.9 1.0 HD2 A:PRO10 4.9 52.3 1.0 HD1 C:HIS36 4.9 39.2 1.0 CA C:HIS39 4.9 26.5 1.0 HE2 C:HIS39 4.9 42.2 1.0 CA C:CYS18 4.9 27.9 1.0 HA3 A:GLY9 5.0 38.3 1.0

Zinc binding site 6 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:35.9 occ:1.00 HB3 C:CYS7 1.4 59.5 1.0 CB C:CYS7 2.2 49.6 1.0 H C:CYS7 2.3 58.2 1.0 SG C:CYS4 2.3 31.4 1.0 SG C:CYS30 2.4 25.2 1.0 SG C:CYS27 2.5 37.8 1.0 SG C:CYS7 2.6 59.7 1.0 HB2 C:CYS7 2.9 59.5 1.0 N C:CYS7 2.9 48.5 1.0 CA C:CYS7 3.1 46.9 1.0 HB3 C:CYS4 3.1 55.0 1.0 H C:CYS27 3.2 39.7 1.0 CB C:CYS4 3.2 45.8 1.0 HB2 C:CYS30 3.3 35.4 1.0 HB2 C:CYS4 3.4 55.0 1.0 H C:CYS30 3.5 31.9 1.0 HB3 C:CYS27 3.5 42.6 1.0 CB C:CYS30 3.5 29.5 1.0 CB C:CYS27 3.6 35.5 1.0 HA C:CYS7 3.8 56.3 1.0 H C:GLY9 3.9 75.9 1.0 C C:CYS7 3.9 49.1 1.0 N C:CYS27 4.0 33.0 1.0 H C:ASN8 4.1 62.5 1.0 H C:GLY6 4.1 33.2 1.0 C C:GLY6 4.2 38.6 1.0 HB3 C:CYS30 4.2 35.4 1.0 N C:CYS30 4.2 26.6 1.0 HB C:VAL29 4.2 39.7 1.0 N C:ASN8 4.3 52.1 1.0 HA3 C:GLY6 4.4 43.6 1.0 HB2 C:CYS27 4.4 42.6 1.0 CA C:CYS27 4.4 32.4 1.0 CA C:CYS30 4.5 28.3 1.0 HA C:LEU26 4.6 33.2 1.0 CA C:CYS4 4.7 39.8 1.0 CA C:GLY6 4.7 36.3 1.0 HD22 C:LEU26 4.7 31.2 1.0 N C:GLY9 4.7 63.3 1.0 O C:CYS7 4.8 52.6 1.0 N C:GLY6 4.8 27.7 1.0 HA C:CYS30 4.9 33.9 1.0

Zinc binding site 7 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:78.0 occ:1.00 SG D:CYS7 2.2 88.2 1.0 SG D:CYS4 2.3 81.7 1.0 SG D:CYS27 2.3 61.8 1.0 SG D:CYS30 2.3 74.5 1.0 H D:CYS27 2.7 76.3 1.0 H D:CYS7 2.9 0.1 1.0 HB2 D:CYS30 3.1 81.0 1.0 HB3 D:CYS7 3.2 0.9 1.0 HB2 D:CYS4 3.2 98.7 1.0 HB3 D:CYS27 3.2 80.6 1.0 CB D:CYS4 3.3 82.2 1.0 H D:CYS30 3.3 83.3 1.0 CB D:CYS27 3.3 67.2 1.0 CB D:CYS30 3.3 67.5 1.0 CB D:CYS7 3.3 84.1 1.0 HB3 D:CYS4 3.4 98.7 1.0 N D:CYS27 3.5 63.6 1.0 N D:CYS7 3.7 93.4 1.0 CA D:CYS27 4.0 63.1 1.0 N D:CYS30 4.0 69.5 1.0 HB3 D:CYS30 4.0 81.0 1.0 HB2 D:CYS7 4.1 0.9 1.0 CA D:CYS7 4.1 91.4 1.0 HB2 D:CYS27 4.2 80.6 1.0 HA D:LEU26 4.2 75.4 1.0 HB D:VAL29 4.2 0.0 1.0 CA D:CYS30 4.3 71.2 1.0 H D:GLY6 4.3 97.3 1.0 H D:GLY9 4.4 0.5 1.0 HD22 D:LEU26 4.4 73.7 1.0 HA3 D:GLY6 4.5 99.7 1.0 HB3 D:LEU26 4.6 81.2 1.0 C D:CYS27 4.6 67.2 1.0 C D:LEU26 4.6 65.6 1.0 O D:CYS27 4.7 67.1 1.0 CA D:CYS4 4.7 82.3 1.0 HA D:CYS30 4.7 85.4 1.0 C D:GLY6 4.7 94.4 1.0 HA D:CYS27 4.8 75.7 1.0 CA D:LEU26 4.8 62.8 1.0 H D:ASN8 4.8 0.3 1.0 H D:VAL29 4.8 95.4 1.0 HA D:CYS7 4.9 0.7 1.0 HD23 D:LEU26 4.9 73.7 1.0 C D:CYS7 4.9 95.0 1.0 HA D:CYS4 4.9 98.8 1.0 CA D:GLY6 4.9 83.1 1.0 N D:GLY6 5.0 81.1 1.0

Zinc binding site 8 out of 8 in the P62/SQSTM1 Zz Domain with Tyr-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 Tyr-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:55.4 occ:1.00 NE2 D:HIS36 2.1 45.8 1.0 ND1 D:HIS39 2.1 72.6 1.0 SG D:CYS18 2.3 41.6 1.0 SG D:CYS21 2.4 54.6 1.0 H D:CYS21 2.6 70.8 1.0 HB2 D:CYS21 2.7 57.8 1.0 CE1 D:HIS36 2.8 48.2 1.0 HE1 D:HIS36 2.9 57.9 1.0 CE1 D:HIS39 3.0 64.8 1.0 CB D:CYS21 3.0 48.2 1.0 HE1 D:HIS39 3.1 77.7 1.0 CG D:HIS39 3.2 62.0 1.0 CD2 D:HIS36 3.2 53.1 1.0 HB D:VAL20 3.4 70.2 1.0 HB2 D:HIS39 3.4 57.7 1.0 N D:CYS21 3.4 59.0 1.0 HD2 D:HIS36 3.5 63.7 1.0 HB3 D:HIS39 3.5 57.7 1.0 CB D:HIS39 3.6 48.1 1.0 CB D:CYS18 3.6 47.8 1.0 HB2 D:CYS18 3.7 57.3 1.0 CA D:CYS21 3.8 53.5 1.0 HB3 D:CYS21 3.8 57.8 1.0 HB3 D:CYS18 3.9 57.3 1.0 ND1 D:HIS36 4.0 54.9 1.0 H D:VAL20 4.1 57.5 1.0 NE2 D:HIS39 4.1 64.4 1.0 CG D:HIS36 4.2 58.8 1.0 CD2 D:HIS39 4.3 63.9 1.0 HA D:CYS21 4.3 64.2 1.0 CB D:VAL20 4.3 58.5 1.0 C D:VAL20 4.5 53.4 1.0 HG12 D:VAL20 4.7 78.5 1.0 HB3 D:TYR24 4.7 70.6 1.0 N D:VAL20 4.7 48.0 1.0 CA D:VAL20 4.8 58.2 1.0 HD1 D:HIS36 4.8 65.9 1.0 HE2 D:HIS39 4.9 77.3 1.0 CG1 D:VAL20 5.0 65.4 1.0 CA D:CYS18 5.0 46.4 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