Zinc in PDB 8ei5: Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide

All present enzymatic activity of Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide:
2.3.2.26;

The structure of Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide, PDB code: 8ei5 was solved by K.Li, O.S.Tokareva, T.M.Thomson, G.L.Verdine, J.H.Mcgee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	120.66, 63.1, 122.26, 90, 96.78, 90
R / Rfree (%)	21.3 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide (pdb code 8ei5). 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 the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide, PDB code: 8ei5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide


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 the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:89.5 occ:1.00 O A:THR799 2.5 26.0 1.0 O A:THR837 2.7 28.2 1.0 OD1 A:ASN840 2.9 25.3 1.0 C A:THR799 3.5 22.2 1.0 CE2 A:TYR587 3.7 32.2 1.0 C A:THR837 3.8 22.9 1.0 CG A:ASN840 3.9 22.6 1.0 O A:ILE813 3.9 27.0 1.0 CA A:THR799 3.9 23.9 1.0 C1 A:GOL903 4.1 45.0 1.0 OH A:TYR587 4.3 30.4 1.0 CB A:THR799 4.3 27.0 1.0 ND2 A:ASN840 4.3 25.3 1.0 O A:HOH1097 4.3 29.0 1.0 CZ A:TYR587 4.5 29.6 1.0 CB A:THR837 4.5 23.7 1.0 CA A:THR837 4.6 24.6 1.0 CD2 A:TYR587 4.6 28.6 1.0 N A:GLY800 4.7 24.0 1.0 N A:CYS838 4.7 24.1 1.0 CA A:CYS838 4.8 26.0 1.0 O1 A:GOL903 4.8 47.5 1.0 OG1 A:THR837 5.0 37.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide


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 the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:84.6 occ:1.00 O B:THR799 2.5 24.2 1.0 O B:THR837 2.5 26.7 1.0 OD1 B:ASN840 2.7 24.0 1.0 C B:THR799 3.5 25.9 1.0 C B:THR837 3.7 28.9 1.0 CG B:ASN840 3.7 16.5 1.0 CA B:THR799 3.8 30.2 1.0 CE1 B:TYR587 3.9 26.6 1.0 O B:ILE813 4.1 24.1 1.0 ND2 B:ASN840 4.1 19.8 1.0 CB B:THR799 4.2 29.6 1.0 OH B:TYR587 4.3 25.4 1.0 CB B:THR837 4.3 28.4 1.0 CA B:THR837 4.3 25.5 1.0 CZ B:TYR587 4.6 29.4 1.0 N B:GLY800 4.6 25.3 1.0 N B:CYS838 4.6 25.1 1.0 CA B:CYS838 4.8 28.2 1.0 N B:ASN840 4.8 22.8 1.0 OG1 B:THR837 4.8 25.7 1.0 CB B:ASN840 4.9 25.9 1.0 CD1 B:TYR587 4.9 26.5 1.0 C B:CYS838 5.0 30.6 1.0 CA B:ASN840 5.0 26.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide


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 the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn901 b:91.2 occ:1.00 O C:THR799 2.4 23.6 1.0 O C:THR837 2.5 24.9 1.0 C C:THR837 3.2 26.9 1.0 C C:THR799 3.3 25.5 1.0 CB C:THR837 3.5 25.8 1.0 OD1 C:ASN840 3.6 32.5 1.0 O2 C:EDO902 3.7 33.0 1.0 OG1 C:THR837 3.7 27.3 1.0 CA C:THR837 3.8 28.4 1.0 OH C:TYR587 3.8 31.8 1.0 CE1 C:TYR587 3.9 26.0 1.0 O1 C:EDO902 3.9 29.2 1.0 CA C:THR799 4.0 30.4 1.0 N C:CYS838 4.0 30.7 1.0 N C:GLY800 4.2 28.4 1.0 CA C:CYS838 4.3 31.7 1.0 CZ C:TYR587 4.3 22.6 1.0 CA C:GLY800 4.5 25.3 1.0 C2 C:EDO902 4.5 32.7 1.0 CG C:ASN840 4.6 28.4 1.0 CB C:THR799 4.7 26.7 1.0 C1 C:EDO902 4.8 35.7 1.0 C C:CYS838 4.9 31.7 1.0 CG2 C:THR837 4.9 23.4 1.0 O C:VAL798 4.9 24.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide


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 the WWP2 Hect Domain in Complex with H301, A Helicon Polypeptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:100.8 occ:1.00 O D:THR799 2.3 36.1 1.0 O D:THR837 2.6 39.4 1.0 O D:HOH1030 2.6 28.7 1.0 OD1 D:ASN840 2.8 37.2 1.0 C D:THR799 3.3 34.4 1.0 C D:THR837 3.5 33.8 1.0 CA D:THR799 3.7 36.4 1.0 CG D:ASN840 4.0 32.8 1.0 O1 D:EDO904 4.0 37.5 1.0 CB D:THR837 4.0 27.6 1.0 CA D:THR837 4.1 27.5 1.0 CE2 D:TYR587 4.2 29.9 1.0 O2 D:EDO904 4.2 30.5 1.0 CB D:THR799 4.2 32.5 1.0 N D:GLY800 4.4 31.0 1.0 O D:ILE813 4.4 22.1 1.0 N D:CYS838 4.5 37.1 1.0 OG1 D:THR837 4.5 35.8 1.0 ND2 D:ASN840 4.6 25.0 1.0 OH D:TYR587 4.7 35.1 1.0 CA D:CYS838 4.7 30.6 1.0 CA D:GLY800 4.7 26.5 1.0 C1 D:EDO904 4.9 39.4 1.0 N D:ASN840 4.9 33.4 1.0 O D:VAL798 4.9 32.3 1.0 CZ D:TYR587 4.9 28.6 1.0 C2 D:EDO904 5.0 36.4 1.0 C D:CYS838 5.0 36.0 1.0

K.Li, T.L.Travaline, J.-M.Swiecicki, O.S.Tokareva, T.M.Thomson, G.L.Verdine, J.H.Mcgee. Recognition and Reprogramming of E3 Ubiquitin Ligase Surfaces By Alpha-Helical Peptides Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-42395-Z