Zinc in PDB 6ww3: Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail

All present enzymatic activity of Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail:
2.3.2.26;

The structure of Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail, PDB code: 6ww3 was solved by J.Liu, K.R.Vann, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.43 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.882, 47.262, 55.476, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.7

The binding sites of Zinc atom in the Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail (pdb code 6ww3). 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 HERC2 Zz Domain in Complex with SUMO1 Tail, PDB code: 6ww3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail


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 HERC2 Zz Domain in Complex with SUMO1 Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2801 b:11.9 occ:1.00 SG A:CYS2735 2.2 8.6 1.0 SG A:CYS2711 2.3 8.1 1.0 SG A:CYS2708 2.3 9.2 1.0 SG A:CYS2732 2.4 12.6 1.0 CB A:CYS2735 3.1 9.7 1.0 CB A:CYS2711 3.3 13.3 1.0 CB A:CYS2708 3.4 7.3 1.0 CB A:CYS2732 3.5 9.3 1.0 N A:CYS2711 3.6 11.7 1.0 N A:CYS2732 3.9 6.4 1.0 CA A:CYS2711 4.0 11.7 1.0 N A:CYS2735 4.2 10.7 1.0 CA A:CYS2732 4.2 6.2 1.0 CA A:CYS2735 4.3 12.7 1.0 C A:GLY2710 4.4 12.9 1.0 O A:HOH2950 4.5 21.1 1.0 CA A:GLY2710 4.6 9.8 1.0 N A:GLY2710 4.7 8.3 1.0 CB A:MET2713 4.7 8.3 1.0 CA A:CYS2708 4.8 6.8 1.0 C A:CYS2711 4.8 12.1 1.0 C A:CYS2732 4.8 8.7 1.0 CE A:MET2713 4.9 10.8 1.0 O A:CYS2732 4.9 10.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail


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 HERC2 Zz Domain in Complex with SUMO1 Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2802 b:9.2 occ:1.00 NE2 A:HIS2741 2.1 6.9 1.0 ND1 A:HIS2745 2.2 9.9 1.0 SG A:CYS2726 2.3 8.3 1.0 SG A:CYS2723 2.3 6.4 1.0 CD2 A:HIS2741 3.1 9.0 1.0 CE1 A:HIS2741 3.1 8.8 1.0 CE1 A:HIS2745 3.1 9.1 1.0 CG A:HIS2745 3.2 10.4 1.0 CB A:CYS2723 3.3 5.7 1.0 CB A:CYS2726 3.4 7.3 1.0 CB A:HIS2745 3.5 11.7 1.0 N A:CYS2726 3.6 6.8 1.0 CA A:CYS2726 4.1 9.6 1.0 ND1 A:HIS2741 4.2 6.8 1.0 CG A:HIS2741 4.2 7.4 1.0 NE2 A:HIS2745 4.3 8.9 1.0 CD2 A:HIS2745 4.3 10.0 1.0 CB A:ASN2725 4.6 9.0 1.0 C A:ASN2725 4.7 10.8 1.0 CA A:CYS2723 4.7 7.8 1.0 CZ A:PHE2747 4.7 7.6 1.0 CB A:PHE2729 4.9 6.6 1.0 N A:ASN2725 4.9 10.4 1.0 CG A:PHE2729 5.0 9.3 1.0 CD1 A:PHE2729 5.0 7.5 1.0 CA A:ASN2725 5.0 8.9 1.0 CA A:HIS2745 5.0 13.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail


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 HERC2 Zz Domain in Complex with SUMO1 Tail within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2801 b:10.9 occ:1.00 NE2 B:HIS2741 2.0 10.4 1.0 ND1 B:HIS2745 2.2 9.5 1.0 SG B:CYS2723 2.3 6.8 1.0 SG B:CYS2726 2.3 7.7 1.0 CE1 B:HIS2741 3.0 9.1 1.0 CD2 B:HIS2741 3.0 9.8 1.0 CE1 B:HIS2745 3.1 11.2 1.0 CG B:HIS2745 3.2 9.5 1.0 CB B:CYS2723 3.3 8.4 1.0 CB B:CYS2726 3.4 8.5 1.0 CB B:HIS2745 3.6 9.3 1.0 N B:CYS2726 3.7 14.0 1.0 ND1 B:HIS2741 4.1 9.0 1.0 CA B:CYS2726 4.1 11.8 1.0 CG B:HIS2741 4.1 10.8 1.0 NE2 B:HIS2745 4.3 10.7 1.0 CD2 B:HIS2745 4.3 10.6 1.0 CA B:CYS2723 4.7 9.5 1.0 C B:ASN2725 4.8 11.2 1.0 CB B:ASN2725 4.8 11.8 1.0 CZ B:PHE2747 4.8 10.5 1.0 CB B:PHE2729 4.9 10.6 1.0 CG B:PHE2729 4.9 10.8 1.0 CD1 B:PHE2729 4.9 9.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of HERC2 Zz Domain in Complex with SUMO1 Tail


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 HERC2 Zz Domain in Complex with SUMO1 Tail within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2802 b:14.6 occ:1.00 SG B:CYS2708 2.3 9.8 1.0 SG B:CYS2732 2.3 14.6 1.0 SG B:CYS2735 2.4 15.2 1.0 SG B:CYS2711 2.4 13.5 1.0 CB B:CYS2735 3.1 13.5 1.0 CB B:CYS2711 3.2 15.8 1.0 CB B:CYS2708 3.4 10.2 1.0 CB B:CYS2732 3.4 11.7 1.0 N B:CYS2711 3.6 14.9 1.0 N B:CYS2732 3.8 11.5 1.0 CA B:CYS2711 4.0 16.9 1.0 O B:HOH2954 4.1 18.3 1.0 N B:CYS2735 4.2 13.7 1.0 CA B:CYS2732 4.2 9.6 1.0 CA B:CYS2735 4.3 16.6 1.0 C B:GLY2710 4.3 18.7 1.0 CA B:GLY2710 4.5 12.3 1.0 N B:GLY2710 4.7 12.5 1.0 CB B:MET2713 4.7 10.3 1.0 C B:CYS2711 4.8 13.1 1.0 CA B:CYS2708 4.8 13.5 1.0 C B:CYS2732 4.8 10.3 1.0 O B:HOH2957 4.9 23.7 1.0 O B:CYS2732 4.9 12.5 1.0 C B:PHE2731 5.0 12.1 1.0 CE B:MET2713 5.0 11.1 1.0

J.Liu, Z.Xue, Y.Zhang, K.R.Vann, X.Shi, T.G.Kutateladze. Structural Insight Into Binding of the Zz Domain of HERC2 to Histone H3 and SUMO1. Structure V. 28 1225 2020.
ISSN: ISSN 0969-2126
PubMed: 32726574
DOI: 10.1016/J.STR.2020.07.003