Zinc in PDB 6khz: P62/SQSTM1 Zz Domain with Gly-Peptide

The structure of P62/SQSTM1 Zz Domain with Gly-Peptide, PDB code: 6khz 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)	40.30 / 2.80
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	113.979, 113.979, 113.979, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 28.7

The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Gly-Peptide (pdb code 6khz). 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 Gly-Peptide, PDB code: 6khz:
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 Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:49.3 occ:1.00 HG A:CYS128 1.2 50.1 1.0 SG A:CYS154 2.3 52.0 1.0 SG A:CYS131 2.3 48.8 1.0 SG A:CYS151 2.3 37.4 1.0 SG A:CYS128 2.3 41.7 1.0 HB2 A:CYS154 2.9 49.9 1.0 HB3 A:CYS131 2.9 60.3 1.0 H A:CYS131 2.9 61.2 1.0 CB A:CYS131 3.1 50.2 1.0 CB A:CYS154 3.1 41.5 1.0 H A:CYS151 3.2 48.0 1.0 HB3 A:CYS151 3.2 45.9 1.0 H A:CYS154 3.2 51.8 1.0 HB3 A:CYS128 3.3 50.8 1.0 CB A:CYS128 3.4 42.3 1.0 N A:CYS131 3.4 51.0 1.0 CB A:CYS151 3.4 38.2 1.0 HB2 A:CYS128 3.5 50.8 1.0 HD22 B:LEU159 3.8 74.9 1.0 HB3 A:CYS154 3.8 49.9 1.0 CA A:CYS131 3.9 53.1 1.0 N A:CYS154 3.9 43.1 1.0 HD23 B:LEU159 3.9 74.9 1.0 HB2 A:CYS131 3.9 60.3 1.0 N A:CYS151 4.0 39.9 1.0 HA3 A:GLY130 4.0 67.1 1.0 H A:GLY130 4.0 65.3 1.0 HB2 A:CYS151 4.1 45.9 1.0 C A:GLY130 4.1 56.7 1.0 CA A:CYS154 4.1 44.4 1.0 CD2 B:LEU159 4.2 62.4 1.0 CA A:CYS151 4.2 36.6 1.0 HD21 B:LEU159 4.2 74.9 1.0 HB A:VAL153 4.3 57.1 1.0 CA A:GLY130 4.4 55.9 1.0 HA A:CYS154 4.6 53.3 1.0 HA A:CYS131 4.6 63.9 1.0 N A:GLY130 4.6 54.4 1.0 H A:GLY133 4.7 61.0 1.0 HA A:LEU150 4.8 47.8 1.0 CA A:CYS128 4.8 47.8 1.0 H A:ASN132 4.8 60.4 1.0 C A:CYS131 4.8 48.3 1.0 H B:HIS160 4.8 64.6 1.0 H A:VAL153 4.9 52.1 1.0 C A:CYS151 4.9 35.9 1.0 HD22 A:LEU150 4.9 50.8 1.0

Zinc binding site 2 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:50.9 occ:1.00 HG A:CYS145 1.4 52.7 1.0 NE2 A:HIS160 2.0 49.5 1.0 ND1 A:HIS163 2.1 55.8 1.0 SG A:CYS142 2.3 47.3 1.0 SG A:CYS145 2.3 43.9 1.0 H A:CYS145 2.7 68.4 1.0 HB2 A:CYS145 3.0 63.3 1.0 CE1 A:HIS160 3.0 37.7 1.0 CG A:HIS163 3.0 57.8 1.0 CD2 A:HIS160 3.0 48.7 1.0 HB3 A:HIS163 3.1 54.2 1.0 CE1 A:HIS163 3.1 52.6 1.0 HB2 A:HIS163 3.1 54.2 1.0 CB A:CYS145 3.2 52.7 1.0 HE1 A:HIS160 3.2 45.3 1.0 HD2 A:HIS160 3.2 58.5 1.0 HB2 A:CYS142 3.3 51.9 1.0 CB A:HIS163 3.3 45.1 1.0 HE1 A:HIS163 3.3 63.2 1.0 HB A:VAL144 3.3 68.3 1.0 CB A:CYS142 3.3 43.2 1.0 N A:CYS145 3.5 56.9 1.0 HB3 A:CYS142 3.6 51.9 1.0 CA A:CYS145 3.9 47.5 1.0 HB3 A:CYS145 4.0 63.3 1.0 ND1 A:HIS160 4.1 42.2 1.0 CG A:HIS160 4.1 35.2 1.0 CD2 A:HIS163 4.2 52.0 1.0 NE2 A:HIS163 4.2 54.2 1.0 H A:VAL144 4.2 64.5 1.0 CB A:VAL144 4.3 56.8 1.0 HB3 A:TYR148 4.3 46.4 1.0 HA A:CYS145 4.4 57.0 1.0 C A:VAL144 4.6 52.9 1.0 HD1 A:TYR148 4.7 54.0 1.0 CA A:CYS142 4.7 43.0 1.0 CD1 A:TYR148 4.7 44.9 1.0 CA A:HIS163 4.8 45.6 1.0 CA A:VAL144 4.8 48.1 1.0 HG23 A:VAL144 4.8 67.8 1.0 CG A:TYR148 4.8 40.3 1.0 N A:VAL144 4.9 53.7 1.0 HA A:CYS142 4.9 51.7 1.0 HD1 A:HIS160 4.9 50.7 1.0 CB A:TYR148 4.9 38.6 1.0 HG12 A:VAL144 4.9 70.4 1.0 HE2 A:HIS163 5.0 65.1 1.0 HB2 A:TYR148 5.0 46.4 1.0 HD2 A:HIS163 5.0 62.5 1.0

Zinc binding site 3 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:47.2 occ:1.00 HG B:CYS131 1.3 62.6 1.0 HG B:CYS151 1.5 52.4 1.0 SG B:CYS151 2.3 43.6 1.0 SG B:CYS131 2.3 52.1 1.0 SG B:CYS154 2.3 45.0 1.0 SG B:CYS128 2.3 49.2 1.0 HB2 B:CYS154 3.0 58.1 1.0 HB3 B:CYS128 3.1 60.4 1.0 H B:CYS151 3.1 66.1 1.0 CB B:CYS128 3.2 50.2 1.0 HB3 B:CYS151 3.2 42.8 1.0 CB B:CYS154 3.3 48.4 1.0 HB2 B:CYS128 3.4 60.4 1.0 H B:CYS131 3.4 56.6 1.0 CB B:CYS151 3.4 35.6 1.0 H B:CYS154 3.4 62.6 1.0 HB3 B:CYS131 3.5 59.3 1.0 CB B:CYS131 3.6 49.3 1.0 N B:CYS131 3.8 47.1 1.0 N B:CYS151 3.9 55.0 1.0 HB3 B:CYS154 3.9 58.1 1.0 H B:GLY130 4.0 66.1 1.0 HA3 B:GLY130 4.0 63.8 1.0 N B:CYS154 4.1 52.1 1.0 HB2 B:CYS151 4.1 42.8 1.0 H C:HIS160 4.2 56.9 1.0 CA B:CYS151 4.2 37.4 1.0 CA B:CYS131 4.3 49.8 1.0 HB B:VAL153 4.3 60.3 1.0 CA B:CYS154 4.3 45.0 1.0 HB2 B:CYS131 4.3 59.3 1.0 C B:GLY130 4.4 49.4 1.0 HD22 C:LEU159 4.4 77.7 1.0 HD23 C:LEU159 4.5 77.7 1.0 CA B:GLY130 4.5 53.1 1.0 N B:GLY130 4.6 55.0 1.0 CA B:CYS128 4.6 45.0 1.0 HA B:LEU150 4.7 53.5 1.0 H B:GLY133 4.7 55.9 1.0 HA B:CYS154 4.7 54.0 1.0 C B:CYS151 4.9 35.6 1.0 HD22 B:LEU150 4.9 64.7 1.0 HA C:LEU159 4.9 53.8 1.0 O B:CYS151 4.9 48.0 1.0 CD2 C:LEU159 4.9 64.7 1.0

Zinc binding site 4 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:52.5 occ:1.00 HD1 B:HIS163 1.3 68.6 1.0 HG B:CYS145 1.4 58.9 1.0 NE2 B:HIS160 2.0 40.3 1.0 ND1 B:HIS163 2.1 57.1 1.0 SG B:CYS145 2.3 49.1 1.0 SG B:CYS142 2.3 45.8 1.0 H B:CYS145 2.7 57.1 1.0 CD2 B:HIS160 2.9 42.1 1.0 HD2 B:HIS160 2.9 50.6 1.0 HB2 B:CYS145 3.0 51.8 1.0 CE1 B:HIS163 3.0 54.3 1.0 CG B:HIS163 3.1 47.3 1.0 CE1 B:HIS160 3.1 39.9 1.0 HB B:VAL144 3.2 46.4 1.0 CB B:CYS145 3.2 43.1 1.0 HE1 B:HIS163 3.2 65.2 1.0 HB2 B:HIS163 3.2 61.2 1.0 HB3 B:HIS163 3.2 61.2 1.0 HB2 B:CYS142 3.4 51.3 1.0 CB B:HIS163 3.4 50.9 1.0 CB B:CYS142 3.4 42.7 1.0 HE1 B:HIS160 3.4 47.9 1.0 N B:CYS145 3.4 47.5 1.0 HB3 B:CYS142 3.6 51.3 1.0 CA B:CYS145 3.9 44.8 1.0 HB3 B:CYS145 4.0 51.8 1.0 CG B:HIS160 4.1 51.2 1.0 H B:VAL144 4.1 58.8 1.0 NE2 B:HIS163 4.1 54.8 1.0 CB B:VAL144 4.1 38.6 1.0 ND1 B:HIS160 4.1 39.9 1.0 CD2 B:HIS163 4.2 52.0 1.0 HA B:CYS145 4.4 53.8 1.0 HB3 B:TYR148 4.4 52.9 1.0 C B:VAL144 4.5 49.6 1.0 HG12 B:VAL144 4.7 58.5 1.0 CA B:VAL144 4.7 42.4 1.0 N B:VAL144 4.8 48.9 1.0 CA B:CYS142 4.8 46.4 1.0 HG23 B:VAL144 4.8 57.5 1.0 CG1 B:VAL144 4.8 48.7 1.0 HG11 B:VAL144 4.9 58.5 1.0 CA B:HIS163 4.9 53.0 1.0 HA2 A:GLY133 4.9 54.8 1.0 HD1 B:TYR148 4.9 47.6 1.0 CG2 B:VAL144 5.0 47.9 1.0 HD1 B:HIS160 5.0 48.0 1.0 HG21 B:VAL144 5.0 57.5 1.0 HA B:CYS142 5.0 55.7 1.0

Zinc binding site 5 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:53.3 occ:1.00 HG C:CYS128 1.1 53.5 1.0 SG C:CYS128 2.2 44.5 1.0 SG C:CYS154 2.2 56.1 1.0 SG C:CYS151 2.3 49.6 1.0 SG C:CYS131 2.4 63.1 1.0 HB2 C:CYS154 3.0 55.1 1.0 HB3 C:CYS128 3.1 59.8 1.0 H C:CYS151 3.1 60.2 1.0 CB C:CYS128 3.1 49.8 1.0 H C:CYS131 3.2 70.7 1.0 CB C:CYS154 3.3 45.9 1.0 HB3 C:CYS131 3.3 64.4 1.0 HB2 C:CYS128 3.3 59.8 1.0 H C:CYS154 3.4 56.8 1.0 CB C:CYS131 3.4 53.6 1.0 HB3 C:CYS151 3.5 46.8 1.0 CB C:CYS151 3.6 39.0 1.0 N C:CYS131 3.6 58.9 1.0 N C:CYS151 3.9 50.1 1.0 HB3 C:CYS154 3.9 55.1 1.0 H C:GLY130 3.9 46.5 1.0 HA3 C:GLY130 4.0 56.1 1.0 CA C:CYS131 4.1 57.8 1.0 N C:CYS154 4.1 47.3 1.0 H C:GLY133 4.2 89.1 1.0 HB2 C:CYS131 4.2 64.4 1.0 HB C:VAL153 4.2 52.1 1.0 CA C:CYS151 4.3 39.7 1.0 C C:GLY130 4.3 48.3 1.0 CA C:CYS154 4.3 44.9 1.0 HB2 C:CYS151 4.3 46.8 1.0 HA C:LEU150 4.4 58.0 1.0 CA C:GLY130 4.5 46.7 1.0 N C:GLY130 4.6 38.7 1.0 CA C:CYS128 4.6 47.4 1.0 HD22 C:LEU150 4.6 62.0 1.0 HA C:CYS154 4.7 53.9 1.0 H C:ASN132 4.7 70.1 1.0 C C:CYS131 4.8 58.6 1.0 HA C:CYS131 4.9 69.4 1.0 O C:CYS151 4.9 51.0 1.0 C C:CYS151 4.9 46.2 1.0 HA C:CYS128 4.9 56.9 1.0 C C:LEU150 5.0 61.1 1.0 N C:ASN132 5.0 58.4 1.0 HB3 C:LEU150 5.0 55.3 1.0 C C:CYS128 5.0 57.1 1.0

Zinc binding site 6 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:56.8 occ:1.00 HG C:CYS142 1.2 53.2 1.0 NE2 C:HIS160 2.0 57.4 1.0 ND1 C:HIS163 2.0 58.3 1.0 SG C:CYS142 2.2 44.2 1.0 SG C:CYS145 2.3 54.1 1.0 CE1 C:HIS160 2.9 50.5 1.0 HB2 C:HIS163 2.9 58.5 1.0 HE1 C:HIS160 3.0 60.7 1.0 CG C:HIS163 3.0 57.4 1.0 H C:CYS145 3.0 68.4 1.0 HB2 C:CYS145 3.0 78.9 1.0 CE1 C:HIS163 3.1 53.9 1.0 CD2 C:HIS160 3.1 49.2 1.0 CB C:CYS145 3.2 65.7 1.0 CB C:HIS163 3.3 48.7 1.0 HB3 C:HIS163 3.3 58.5 1.0 HE1 C:HIS163 3.3 64.7 1.0 HD2 C:HIS160 3.4 59.2 1.0 HB2 C:CYS142 3.5 50.5 1.0 CB C:CYS142 3.5 42.0 1.0 HB C:VAL144 3.6 75.4 1.0 N C:CYS145 3.7 56.9 1.0 HB3 C:CYS142 3.7 50.5 1.0 HB3 C:CYS145 4.0 78.9 1.0 ND1 C:HIS160 4.0 47.4 1.0 CA C:CYS145 4.1 67.7 1.0 H C:VAL144 4.1 69.8 1.0 CD2 C:HIS163 4.1 50.8 1.0 NE2 C:HIS163 4.1 53.7 1.0 CG C:HIS160 4.2 46.3 1.0 HA2 B:GLY133 4.2 62.4 1.0 HD3 B:PRO134 4.5 77.4 1.0 HA C:CYS145 4.5 81.3 1.0 CB C:VAL144 4.6 62.8 1.0 O B:ASN132 4.7 55.0 1.0 HB3 C:TYR148 4.7 69.0 1.0 C C:VAL144 4.7 56.2 1.0 HD2 B:PRO134 4.8 77.4 1.0 CA C:HIS163 4.8 44.4 1.0 HD1 C:HIS160 4.8 56.9 1.0 CA C:CYS142 4.8 44.0 1.0 N C:VAL144 4.8 58.1 1.0 HA C:CYS142 4.9 52.8 1.0 HE2 C:HIS163 4.9 64.5 1.0 CA C:VAL144 4.9 64.5 1.0 HD2 C:HIS163 5.0 61.0 1.0

Zinc binding site 7 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:70.3 occ:1.00 SG D:CYS151 2.3 78.3 1.0 SG D:CYS128 2.3 70.5 1.0 SG D:CYS131 2.3 92.1 1.0 SG D:CYS154 2.3 74.3 1.0 H D:CYS151 2.9 81.9 1.0 H D:CYS131 2.9 91.0 1.0 HB3 D:CYS131 3.0 0.7 1.0 HB3 D:CYS151 3.2 84.7 1.0 CB D:CYS131 3.2 86.4 1.0 H D:CYS154 3.3 72.6 1.0 CB D:CYS151 3.3 70.5 1.0 HB2 D:CYS154 3.4 80.1 1.0 N D:CYS131 3.5 75.8 1.0 CB D:CYS154 3.5 66.7 1.0 CB D:CYS128 3.5 84.5 1.0 HB3 D:CYS128 3.6 0.5 1.0 N D:CYS151 3.6 68.2 1.0 HB2 D:CYS128 3.7 0.5 1.0 HB D:VAL153 3.9 96.1 1.0 CA D:CYS131 3.9 81.7 1.0 N D:CYS154 4.0 60.5 1.0 CA D:CYS151 4.0 60.7 1.0 HB2 D:CYS131 4.0 0.7 1.0 HA3 D:GLY130 4.1 0.1 1.0 HB2 D:CYS151 4.1 84.7 1.0 H D:GLY133 4.2 0.9 1.0 H D:GLY130 4.2 93.0 1.0 HB3 D:CYS154 4.2 80.1 1.0 HA D:LEU150 4.4 88.0 1.0 CA D:CYS154 4.4 67.4 1.0 C D:GLY130 4.4 79.5 1.0 CA D:GLY130 4.6 83.4 1.0 C D:CYS151 4.6 58.9 1.0 C D:CYS131 4.7 90.7 1.0 O D:CYS151 4.7 53.1 1.0 HA D:CYS154 4.7 81.0 1.0 H D:VAL153 4.7 74.7 1.0 HA D:CYS131 4.7 98.1 1.0 H D:ASN132 4.8 0.2 1.0 C D:LEU150 4.8 67.3 1.0 N D:GLY130 4.8 77.5 1.0 CB D:VAL153 4.8 80.0 1.0 HA D:CYS151 4.9 72.9 1.0 HD22 D:LEU150 4.9 93.1 1.0 CA D:CYS128 4.9 85.5 1.0 HB3 D:LEU150 4.9 88.6 1.0 HA3 D:GLY133 5.0 0.9 1.0 N D:ASN132 5.0 96.8 1.0 N D:GLY133 5.0 99.0 1.0

Zinc binding site 8 out of 8 in the P62/SQSTM1 Zz Domain with Gly-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 Gly-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:90.4 occ:1.00 HG D:CYS145 1.5 76.8 1.0 NE2 D:HIS160 2.0 61.8 1.0 ND1 D:HIS163 2.0 78.3 1.0 SG D:CYS142 2.3 70.1 1.0 SG D:CYS145 2.3 64.0 1.0 CE1 D:HIS160 2.9 51.7 1.0 HE1 D:HIS160 3.0 62.2 1.0 CE1 D:HIS163 3.0 70.6 1.0 H D:CYS145 3.0 81.9 1.0 CG D:HIS163 3.1 78.2 1.0 HE1 D:HIS163 3.1 84.8 1.0 HB2 D:CYS145 3.1 74.6 1.0 HB2 D:HIS163 3.2 89.3 1.0 CD2 D:HIS160 3.2 61.9 1.0 HB2 D:CYS142 3.3 75.1 1.0 CB D:CYS145 3.3 62.1 1.0 CB D:CYS142 3.4 62.5 1.0 HD2 D:HIS160 3.4 74.3 1.0 CB D:HIS163 3.5 74.3 1.0 HB3 D:HIS163 3.5 89.3 1.0 HB3 D:CYS142 3.7 75.1 1.0 N D:CYS145 3.7 68.2 1.0 HB D:VAL144 3.8 83.2 1.0 ND1 D:HIS160 4.1 68.2 1.0 HB3 D:CYS145 4.1 74.6 1.0 NE2 D:HIS163 4.1 79.2 1.0 H D:VAL144 4.1 85.9 1.0 CA D:CYS145 4.2 66.9 1.0 CD2 D:HIS163 4.2 80.8 1.0 CG D:HIS160 4.2 66.5 1.0 HA D:CYS145 4.7 80.4 1.0 HB3 D:TYR148 4.7 97.8 1.0 CB D:VAL144 4.7 69.2 1.0 CA D:CYS142 4.7 55.2 1.0 HA D:CYS142 4.8 66.3 1.0 HD1 D:HIS160 4.8 82.0 1.0 C D:VAL144 4.8 63.0 1.0 HE2 D:HIS163 4.9 95.1 1.0 N D:VAL144 4.9 71.5 1.0 CA D:HIS163 5.0 71.3 1.0

L.Kim, D.H.Kwon, J.Heo, M.R.Park, H.K.Song. Use of the LC3B-Fusion Technique For Biochemical and Structural Studies of Proteins Involved in the N-Degron Pathway. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 31919097
DOI: 10.1074/JBC.RA119.010912