Zinc in PDB 6miu: Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide

The structure of Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide, PDB code: 6miu was solved by J.Ahn, Y.Zhang, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.31 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.990, 27.864, 38.994, 90.06, 90.45, 110.30
R / Rfree (%)	15.5 / 21.2

The binding sites of Zinc atom in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide (pdb code 6miu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide, PDB code: 6miu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.1 occ:1.00 SG A:CYS151 2.2 16.2 1.0 SG A:CYS128 2.3 16.0 1.0 SG A:CYS154 2.4 21.6 1.0 SG A:CYS131 2.5 29.1 1.0 CB A:CYS128 3.1 18.1 1.0 CB A:CYS154 3.3 19.9 1.0 CB A:CYS131 3.4 19.3 1.0 CB A:CYS151 3.5 15.8 1.0 N A:CYS131 3.6 24.4 1.0 N A:CYS151 3.8 16.6 1.0 O A:HOH346 4.0 33.5 1.0 CA A:CYS131 4.1 24.5 1.0 N A:CYS154 4.1 16.3 1.0 CA A:CYS151 4.2 16.2 1.0 CA A:CYS154 4.3 17.1 1.0 O A:HOH308 4.5 22.0 1.0 C A:GLY130 4.5 30.0 1.0 CA A:CYS128 4.6 23.0 1.0 CA A:GLY130 4.6 26.3 1.0 O A:CYS151 4.7 11.9 1.0 C A:CYS151 4.8 15.6 1.0 N A:GLY130 4.8 21.3 1.0 C A:CYS131 4.8 22.6 1.0 C A:LEU150 5.0 15.4 1.0 N A:GLY133 5.0 18.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:16.2 occ:1.00 NE2 A:HIS160 2.1 17.0 1.0 ND1 A:HIS163 2.2 19.7 1.0 SG A:CYS145 2.3 18.0 1.0 SG A:CYS142 2.3 12.8 1.0 CE1 A:HIS160 3.1 20.2 1.0 CD2 A:HIS160 3.1 11.2 1.0 CG A:HIS163 3.1 14.4 1.0 CE1 A:HIS163 3.2 15.8 1.0 CB A:CYS145 3.2 18.7 1.0 CB A:CYS142 3.4 14.8 1.0 CB A:HIS163 3.4 11.2 1.0 N A:CYS145 3.6 15.3 1.0 CA A:CYS145 4.0 21.6 1.0 ND1 A:HIS160 4.2 14.2 1.0 CG A:HIS160 4.2 10.8 1.0 NE2 A:HIS163 4.3 15.8 1.0 CD2 A:HIS163 4.3 17.4 1.0 CB A:VAL144 4.4 16.0 1.0 C A:VAL144 4.6 19.5 1.0 CB A:TYR148 4.7 13.0 1.0 CA A:CYS142 4.8 15.3 1.0 CG A:TYR148 4.8 18.6 1.0 N A:VAL144 4.9 16.5 1.0 CA A:VAL144 4.9 16.0 1.0 CD2 A:TYR148 4.9 15.2 1.0 CA A:HIS163 4.9 11.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.0 occ:1.00 SG B:CYS151 2.2 14.9 1.0 SG B:CYS128 2.2 18.0 1.0 SG B:CYS154 2.4 21.3 1.0 SG B:CYS131 2.5 25.6 1.0 CB B:CYS128 3.1 15.9 1.0 CB B:CYS154 3.1 18.1 1.0 CB B:CYS151 3.4 23.3 1.0 CB B:CYS131 3.5 19.3 1.0 N B:CYS131 3.5 27.7 1.0 N B:CYS151 3.8 15.1 1.0 CA B:CYS131 4.1 19.1 1.0 N B:CYS154 4.2 13.8 1.0 CA B:CYS151 4.2 16.5 1.0 CA B:CYS154 4.2 17.8 1.0 C B:GLY130 4.4 29.9 1.0 CA B:GLY130 4.4 20.3 1.0 O B:HOH322 4.5 23.6 1.0 CG2 B:VAL153 4.5 32.6 1.0 CA B:CYS128 4.5 17.8 1.0 O B:CYS151 4.6 11.7 1.0 N B:GLY130 4.7 19.4 1.0 C B:CYS151 4.7 14.9 1.0 C B:CYS131 4.9 24.9 1.0 C B:LEU150 5.0 12.6 1.0 C B:CYS128 5.0 21.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P62 Zz Domain in Complex with Arg-Glu Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:15.7 occ:1.00 NE2 B:HIS160 2.1 14.2 1.0 ND1 B:HIS163 2.2 18.5 1.0 SG B:CYS142 2.3 10.7 1.0 SG B:CYS145 2.3 17.3 1.0 CE1 B:HIS160 3.0 21.0 1.0 CD2 B:HIS160 3.1 12.1 1.0 CE1 B:HIS163 3.2 13.5 1.0 CG B:HIS163 3.2 18.6 1.0 CB B:CYS142 3.3 9.3 1.0 CB B:CYS145 3.4 13.7 1.0 CB B:HIS163 3.5 9.7 1.0 N B:CYS145 3.7 15.5 1.0 CA B:CYS145 4.1 18.3 1.0 ND1 B:HIS160 4.1 13.7 1.0 CG B:HIS160 4.2 11.3 1.0 NE2 B:HIS163 4.3 16.7 1.0 CD2 B:HIS163 4.3 14.2 1.0 CB B:VAL144 4.4 21.9 1.0 O B:HOH365 4.5 41.2 1.0 CB B:TYR148 4.7 13.3 1.0 C B:VAL144 4.7 20.1 1.0 CA B:CYS142 4.7 14.8 1.0 CG B:TYR148 4.8 17.6 1.0 CD2 B:TYR148 4.9 14.0 1.0 N B:VAL144 4.9 11.9 1.0 CA B:VAL144 4.9 16.3 1.0 CA B:HIS163 5.0 14.3 1.0

Y.Zhang, S.R.Mun, J.F.Linares, J.Ahn, C.G.Towers, C.H.Ji, B.E.Fitzwalter, M.R.Holden, W.Mi, X.Shi, J.Moscat, A.Thorburn, M.T.Diaz-Meco, Y.T.Kwon, T.G.Kutateladze. Zz-Dependent Regulation of P62/SQSTM1 in Autophagy. Nat Commun V. 9 4373 2018.
ISSN: ESSN 2041-1723
PubMed: 30349045
DOI: 10.1038/S41467-018-06878-8