Zinc in PDB 5ypf: P62/SQSTM1 Zz Domain with Trp-Peptide

The structure of P62/SQSTM1 Zz Domain with Trp-Peptide, PDB code: 5ypf 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)	40.65 / 2.95
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	114.964, 114.964, 114.964, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.5

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Trp-Peptide (pdb code 5ypf). 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 Trp-Peptide, PDB code: 5ypf:
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 Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:57.5 occ:1.00 HG A:CYS7 1.2 65.8 1.0 HG A:CYS27 1.4 60.7 1.0 SG A:CYS7 2.2 54.7 1.0 SG A:CYS4 2.3 41.6 1.0 SG A:CYS30 2.3 56.1 1.0 SG A:CYS27 2.3 50.4 1.0 H A:CYS7 2.5 72.5 1.0 HB3 A:CYS4 3.0 67.2 1.0 HB3 A:CYS7 3.0 62.5 1.0 CB A:CYS4 3.1 55.9 1.0 CB A:CYS7 3.1 51.9 1.0 HB2 A:CYS30 3.2 60.2 1.0 H A:CYS27 3.2 59.6 1.0 HB2 A:CYS4 3.2 67.2 1.0 N A:CYS7 3.3 60.3 1.0 HB3 A:CYS27 3.4 67.4 1.0 CB A:CYS30 3.4 50.0 1.0 H A:CYS30 3.5 59.9 1.0 CB A:CYS27 3.5 56.0 1.0 CA A:CYS7 3.8 59.0 1.0 HD22 B:LEU35 3.8 80.7 1.0 H A:GLY6 3.9 66.5 1.0 HD23 B:LEU35 4.0 80.7 1.0 N A:CYS27 4.0 49.5 1.0 HB2 A:CYS7 4.0 62.5 1.0 HB3 A:CYS30 4.1 60.2 1.0 HA3 A:GLY6 4.1 88.1 1.0 N A:CYS30 4.2 49.8 1.0 CD2 B:LEU35 4.3 67.1 1.0 HB2 A:CYS27 4.3 67.4 1.0 C A:GLY6 4.3 68.1 1.0 CA A:CYS27 4.3 48.3 1.0 HB A:VAL29 4.4 81.4 1.0 CA A:CYS30 4.4 54.7 1.0 HD21 B:LEU35 4.4 80.7 1.0 H A:ASN8 4.4 72.7 1.0 CA A:GLY6 4.5 73.3 1.0 CA A:CYS4 4.5 59.7 1.0 H A:GLY9 4.5 70.3 1.0 HA A:CYS7 4.5 70.9 1.0 H B:HIS36 4.6 67.7 1.0 N A:GLY6 4.6 55.3 1.0 C A:CYS7 4.6 55.6 1.0 HA A:LEU26 4.7 64.8 1.0 N A:ASN8 4.8 60.4 1.0 HA A:CYS30 4.8 65.8 1.0 HA A:CYS4 4.9 71.8 1.0 C A:CYS4 4.9 60.4 1.0 C A:CYS27 5.0 49.9 1.0

Zinc binding site 2 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:74.2 occ:1.00 HD1 A:HIS39 1.4 0.8 1.0 HG A:CYS21 1.7 65.0 1.0 ND1 A:HIS39 2.0 83.8 1.0 NE2 A:HIS36 2.0 45.6 1.0 HB2 A:HIS39 2.1 75.3 1.0 HB3 A:HIS39 2.2 75.3 1.0 SG A:CYS18 2.3 61.2 1.0 CB A:HIS39 2.3 62.7 1.0 CG A:HIS39 2.4 73.0 1.0 SG A:CYS21 2.6 54.0 1.0 CD2 A:HIS36 2.8 55.5 1.0 HD2 A:HIS36 2.9 66.7 1.0 H A:CYS21 3.1 92.3 1.0 CE1 A:HIS36 3.2 53.8 1.0 CE1 A:HIS39 3.3 75.0 1.0 HB A:VAL20 3.3 87.5 1.0 HB2 A:CYS21 3.4 0.1 1.0 HE1 A:HIS36 3.5 64.8 1.0 CB A:CYS21 3.6 86.7 1.0 HB2 A:CYS18 3.6 61.3 1.0 CB A:CYS18 3.7 50.9 1.0 CD2 A:HIS39 3.7 66.6 1.0 HE1 A:HIS39 3.7 90.1 1.0 N A:CYS21 3.9 76.8 1.0 CA A:HIS39 3.9 57.2 1.0 CG A:HIS36 4.1 47.5 1.0 HB3 A:CYS18 4.1 61.3 1.0 NE2 A:HIS39 4.1 69.4 1.0 ND1 A:HIS36 4.2 55.7 1.0 H A:VAL20 4.2 74.5 1.0 CB A:VAL20 4.3 72.8 1.0 HA A:HIS39 4.3 68.8 1.0 CA A:CYS21 4.4 73.8 1.0 HB3 A:CYS21 4.4 0.1 1.0 HD2 A:HIS39 4.5 80.0 1.0 N A:HIS39 4.5 64.6 1.0 H A:HIS39 4.5 77.7 1.0 C A:HIS39 4.6 60.7 1.0 HG23 A:VAL20 4.8 0.0 1.0 HA A:CYS21 4.8 88.8 1.0 HG21 A:VAL20 4.8 0.0 1.0 HG12 A:VAL20 4.9 85.0 1.0 C A:VAL20 4.9 68.8 1.0 HG11 A:VAL20 4.9 85.0 1.0 HA A:CYS18 4.9 56.0 1.0 CG2 A:VAL20 4.9 88.2 1.0 CA A:CYS18 4.9 46.6 1.0 N A:VAL20 5.0 62.0 1.0 CA A:VAL20 5.0 58.5 1.0 CG1 A:VAL20 5.0 70.7 1.0 HD1 A:HIS36 5.0 67.0 1.0 HB3 A:TYR24 5.0 55.3 1.0

Zinc binding site 3 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:51.5 occ:1.00 SG B:CYS4 2.2 50.9 1.0 SG B:CYS7 2.3 57.6 1.0 SG B:CYS30 2.3 61.0 1.0 SG B:CYS27 2.4 60.0 1.0 H B:CYS7 2.9 65.7 1.0 HB3 B:CYS4 3.1 70.1 1.0 CB B:CYS4 3.1 58.3 1.0 HB2 B:CYS30 3.1 68.3 1.0 HB2 B:CYS4 3.1 70.1 1.0 H B:CYS27 3.2 75.9 1.0 CB B:CYS30 3.3 56.8 1.0 H B:CYS30 3.3 77.0 1.0 HB3 B:CYS7 3.4 77.4 1.0 CB B:CYS7 3.4 64.3 1.0 HB3 B:CYS27 3.5 65.9 1.0 CB B:CYS27 3.6 54.8 1.0 N B:CYS7 3.7 54.6 1.0 N B:CYS27 4.0 63.1 1.0 HB3 B:CYS30 4.0 68.3 1.0 N B:CYS30 4.1 64.1 1.0 HB B:VAL29 4.2 71.4 1.0 CA B:CYS7 4.2 63.0 1.0 H B:GLY6 4.2 70.4 1.0 HB2 B:CYS7 4.2 77.4 1.0 H C:HIS36 4.3 61.9 1.0 CA B:CYS30 4.3 59.9 1.0 CA B:CYS27 4.3 53.4 1.0 HB2 B:CYS27 4.4 65.9 1.0 HD23 C:LEU35 4.4 89.1 1.0 HA3 B:GLY6 4.4 73.4 1.0 HD22 C:LEU35 4.5 89.1 1.0 CA B:CYS4 4.6 52.4 1.0 HA B:LEU26 4.7 66.8 1.0 C B:GLY6 4.7 59.0 1.0 HA B:CYS30 4.7 72.0 1.0 H B:GLY9 4.8 78.3 1.0 H B:ASN8 4.8 75.2 1.0 CA B:GLY6 4.8 61.0 1.0 N B:GLY6 4.9 58.5 1.0 HD22 B:LEU26 4.9 71.4 1.0 CD2 C:LEU35 4.9 74.1 1.0 HA B:CYS4 4.9 63.0 1.0 HA B:CYS7 4.9 75.7 1.0 C B:CYS27 4.9 44.9 1.0 H B:VAL29 5.0 78.2 1.0 HA C:LEU35 5.0 65.0 1.0 O B:CYS27 5.0 47.6 1.0

Zinc binding site 4 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:70.7 occ:1.00 HG B:CYS21 1.6 67.0 1.0 ND1 B:HIS39 2.0 67.7 1.0 NE2 B:HIS36 2.0 44.5 1.0 HB2 B:HIS39 2.1 82.9 1.0 HB3 B:HIS39 2.2 82.9 1.0 SG B:CYS18 2.2 60.5 1.0 CB B:HIS39 2.3 68.9 1.0 CG B:HIS39 2.4 69.1 1.0 SG B:CYS21 2.5 55.7 1.0 H B:CYS21 2.7 92.3 1.0 CD2 B:HIS36 2.8 60.4 1.0 HD2 B:HIS36 2.9 72.6 1.0 HB B:VAL20 3.0 75.8 1.0 HB2 B:CYS21 3.2 81.8 1.0 CE1 B:HIS36 3.2 53.2 1.0 CE1 B:HIS39 3.3 71.5 1.0 CB B:CYS21 3.4 68.0 1.0 HE1 B:HIS36 3.5 64.0 1.0 N B:CYS21 3.5 76.8 1.0 CB B:CYS18 3.6 50.0 1.0 HB2 B:CYS18 3.6 60.1 1.0 CD2 B:HIS39 3.7 65.0 1.0 HE1 B:HIS39 3.7 85.9 1.0 CA B:HIS39 3.9 61.9 1.0 HB3 B:CYS18 3.9 60.1 1.0 H B:VAL20 4.0 76.8 1.0 CB B:VAL20 4.0 63.0 1.0 CG B:HIS36 4.0 54.4 1.0 NE2 B:HIS39 4.1 72.2 1.0 CA B:CYS21 4.1 67.5 1.0 ND1 B:HIS36 4.2 47.4 1.0 HB3 B:CYS21 4.2 81.8 1.0 HA B:HIS39 4.4 74.5 1.0 HD2 B:HIS39 4.4 78.1 1.0 HA B:CYS21 4.5 81.2 1.0 C B:VAL20 4.5 63.6 1.0 HG12 B:VAL20 4.5 85.3 1.0 N B:HIS39 4.6 70.3 1.0 H B:HIS39 4.6 84.6 1.0 CA B:VAL20 4.6 66.7 1.0 N B:VAL20 4.7 63.9 1.0 C B:HIS39 4.7 59.7 1.0 HG23 B:VAL20 4.7 74.4 1.0 HG11 B:VAL20 4.7 85.3 1.0 CG1 B:VAL20 4.7 71.0 1.0 HG21 B:VAL20 4.8 74.4 1.0 CG2 B:VAL20 4.8 61.9 1.0 CA B:CYS18 4.8 56.5 1.0 HA B:CYS18 4.9 68.0 1.0 HE2 B:HIS39 4.9 86.7 1.0 HB3 B:TYR24 5.0 62.3 1.0 HA2 A:GLY9 5.0 68.7 1.0 HD1 B:HIS36 5.0 57.0 1.0

Zinc binding site 5 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:64.9 occ:1.00 SG C:CYS4 2.1 58.6 1.0 SG C:CYS7 2.1 80.5 1.0 SG C:CYS30 2.3 51.9 1.0 H C:CYS7 2.4 88.6 1.0 SG C:CYS27 2.5 62.7 1.0 HB2 C:CYS30 2.9 71.2 1.0 H C:CYS27 2.9 66.6 1.0 HB3 C:CYS7 2.9 85.0 1.0 CB C:CYS7 3.0 70.7 1.0 CB C:CYS4 3.2 59.8 1.0 CB C:CYS30 3.2 59.2 1.0 HB3 C:CYS4 3.2 71.9 1.0 N C:CYS7 3.2 73.7 1.0 HB2 C:CYS4 3.3 71.9 1.0 H C:CYS30 3.3 69.2 1.0 HB3 C:CYS27 3.5 76.6 1.0 CB C:CYS27 3.6 63.7 1.0 CA C:CYS7 3.7 67.1 1.0 N C:CYS27 3.7 55.3 1.0 HB3 C:CYS30 3.8 71.2 1.0 HB2 C:CYS7 3.9 85.0 1.0 H C:GLY6 3.9 62.6 1.0 N C:CYS30 4.0 57.5 1.0 HA3 C:GLY6 4.2 64.1 1.0 CA C:CYS27 4.2 61.2 1.0 CA C:CYS30 4.2 62.5 1.0 HA C:LEU26 4.2 72.1 1.0 H C:GLY9 4.3 0.6 1.0 H C:ASN8 4.3 86.5 1.0 C C:GLY6 4.3 59.6 1.0 HD22 C:LEU26 4.4 56.0 1.0 HB C:VAL29 4.4 73.8 1.0 HB2 C:CYS27 4.4 76.6 1.0 HA C:CYS7 4.4 80.7 1.0 C C:CYS7 4.5 75.5 1.0 CA C:CYS4 4.6 59.1 1.0 CA C:GLY6 4.6 53.3 1.0 N C:GLY6 4.6 52.1 1.0 N C:ASN8 4.6 72.0 1.0 HB3 C:LEU26 4.7 68.5 1.0 HA C:CYS30 4.7 75.2 1.0 C C:LEU26 4.8 56.8 1.0 O C:CYS27 4.8 61.0 1.0 C C:CYS27 4.8 55.3 1.0 HA C:CYS4 4.9 71.1 1.0 HD23 C:LEU26 4.9 56.0 1.0 CA C:LEU26 4.9 59.9 1.0 C C:CYS4 5.0 61.4 1.0

Zinc binding site 6 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:67.6 occ:1.00 HB2 C:HIS39 1.9 73.5 1.0 ND1 C:HIS39 2.0 54.0 1.0 NE2 C:HIS36 2.1 55.8 1.0 SG C:CYS18 2.3 47.6 1.0 CB C:HIS39 2.3 61.1 1.0 HB3 C:HIS39 2.4 73.5 1.0 CG C:HIS39 2.4 57.7 1.0 HG C:CYS21 2.5 59.5 1.0 SG C:CYS21 2.5 49.5 1.0 CD2 C:HIS36 2.9 53.6 1.0 HD2 C:HIS36 2.9 64.5 1.0 H C:CYS21 3.2 80.8 1.0 CE1 C:HIS36 3.2 66.7 1.0 CE1 C:HIS39 3.3 65.0 1.0 HB2 C:CYS21 3.3 80.8 1.0 HE1 C:HIS36 3.6 80.2 1.0 CB C:CYS21 3.6 67.2 1.0 HB C:VAL20 3.6 74.3 1.0 HB2 C:CYS18 3.7 53.4 1.0 CB C:CYS18 3.7 44.4 1.0 CD2 C:HIS39 3.7 51.9 1.0 HE1 C:HIS39 3.8 78.1 1.0 CA C:HIS39 3.9 50.1 1.0 N C:CYS21 4.0 67.2 1.0 HB3 C:CYS18 4.0 53.4 1.0 NE2 C:HIS39 4.1 65.6 1.0 CG C:HIS36 4.1 55.3 1.0 HA2 B:GLY9 4.1 84.8 1.0 HD3 B:PRO10 4.2 91.0 1.0 H C:VAL20 4.2 73.1 1.0 ND1 C:HIS36 4.2 65.3 1.0 HB3 C:CYS21 4.3 80.8 1.0 HA C:HIS39 4.4 60.3 1.0 H C:HIS39 4.4 78.9 1.0 CA C:CYS21 4.4 66.1 1.0 N C:HIS39 4.4 65.6 1.0 HD2 C:HIS39 4.5 62.4 1.0 HD2 B:PRO10 4.5 91.0 1.0 CB C:VAL20 4.6 61.8 1.0 C C:HIS39 4.6 56.7 1.0 HA3 B:GLY9 4.8 84.8 1.0 CD B:PRO10 4.8 75.7 1.0 HA C:CYS21 4.8 79.5 1.0 CA B:GLY9 4.9 70.6 1.0 HA C:CYS18 4.9 57.1 1.0 CA C:CYS18 4.9 47.4 1.0 HE2 C:HIS39 4.9 78.9 1.0 N C:VAL20 5.0 60.8 1.0

Zinc binding site 7 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:86.7 occ:1.00 HG D:CYS4 1.2 0.7 1.0 SG D:CYS7 2.2 0.1 1.0 SG D:CYS27 2.3 81.8 1.0 SG D:CYS30 2.3 0.6 1.0 SG D:CYS4 2.3 92.1 1.0 HG D:CYS7 2.5 0.2 1.0 HG D:CYS27 2.6 98.4 1.0 H D:CYS7 2.7 0.5 1.0 H D:CYS27 2.7 99.1 1.0 HB2 D:CYS30 3.1 0.7 1.0 HB3 D:CYS7 3.1 0.6 1.0 H D:CYS30 3.2 0.2 1.0 CB D:CYS7 3.2 95.4 1.0 HB3 D:CYS27 3.2 0.9 1.0 CB D:CYS30 3.3 0.4 1.0 CB D:CYS27 3.3 90.7 1.0 HB2 D:CYS4 3.5 1.0 1.0 N D:CYS7 3.5 0.4 1.0 CB D:CYS4 3.5 94.8 1.0 N D:CYS27 3.5 82.5 1.0 HB3 D:CYS4 3.7 1.0 1.0 N D:CYS30 3.9 88.4 1.0 CA D:CYS7 3.9 0.2 1.0 CA D:CYS27 4.0 84.5 1.0 HB D:VAL29 4.0 0.9 1.0 HB3 D:CYS30 4.0 0.7 1.0 HB2 D:CYS7 4.0 0.6 1.0 HB2 D:CYS27 4.1 0.9 1.0 CA D:CYS30 4.2 96.6 1.0 HA D:LEU26 4.2 93.4 1.0 H D:GLY9 4.3 0.4 1.0 H D:GLY6 4.3 0.2 1.0 HA3 D:GLY6 4.4 0.8 1.0 C D:GLY6 4.6 0.9 1.0 HD22 D:LEU26 4.6 0.3 1.0 C D:CYS27 4.6 88.9 1.0 HA D:CYS30 4.6 0.1 1.0 H D:ASN8 4.6 0.5 1.0 O D:CYS27 4.7 88.1 1.0 HB3 D:LEU26 4.7 0.2 1.0 C D:LEU26 4.7 79.8 1.0 HA D:CYS7 4.7 0.4 1.0 H D:VAL29 4.7 0.9 1.0 C D:CYS7 4.8 0.3 1.0 HA D:CYS27 4.8 0.6 1.0 CA D:GLY6 4.8 95.5 1.0 CA D:LEU26 4.9 77.7 1.0 CA D:CYS4 4.9 96.5 1.0 N D:ASN8 4.9 0.3 1.0 CB D:VAL29 4.9 0.6 1.0 N D:GLY6 4.9 94.2 1.0

Zinc binding site 8 out of 8 in the P62/SQSTM1 Zz Domain with Trp-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 Trp-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:92.1 occ:1.00 HG D:CYS18 1.2 79.2 1.0 NE2 D:HIS36 2.1 60.1 1.0 ND1 D:HIS39 2.1 0.3 1.0 SG D:CYS18 2.4 65.8 1.0 SG D:CYS21 2.4 80.1 1.0 CE1 D:HIS36 2.9 64.4 1.0 HB2 D:CYS21 2.9 82.3 1.0 CE1 D:HIS39 2.9 99.5 1.0 HE1 D:HIS36 2.9 77.5 1.0 H D:CYS21 3.0 0.7 1.0 HE1 D:HIS39 3.0 0.5 1.0 CB D:CYS21 3.2 68.5 1.0 CG D:HIS39 3.2 91.3 1.0 CD2 D:HIS36 3.2 70.2 1.0 HB2 D:HIS39 3.4 99.4 1.0 HD2 D:HIS36 3.5 84.5 1.0 HB2 D:CYS18 3.6 91.6 1.0 CB D:CYS18 3.6 76.2 1.0 HB3 D:HIS39 3.6 99.4 1.0 HB D:VAL20 3.6 0.7 1.0 CB D:HIS39 3.7 82.7 1.0 N D:CYS21 3.7 95.4 1.0 HB3 D:CYS18 3.8 91.6 1.0 HB3 D:CYS21 4.0 82.3 1.0 ND1 D:HIS36 4.1 73.1 1.0 NE2 D:HIS39 4.1 97.0 1.0 CA D:CYS21 4.1 84.1 1.0 H D:VAL20 4.2 80.9 1.0 CG D:HIS36 4.2 72.9 1.0 CD2 D:HIS39 4.2 93.9 1.0 HA D:CYS21 4.6 0.1 1.0 CB D:VAL20 4.6 90.5 1.0 HB3 D:TYR24 4.6 88.7 1.0 HD1 D:HIS36 4.8 87.8 1.0 HE2 D:HIS39 4.8 0.6 1.0 C D:VAL20 4.8 81.6 1.0 CA D:CYS18 4.9 66.0 1.0 N D:VAL20 5.0 67.3 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