Zinc in PDB 5edv: Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex

All present enzymatic activity of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex:
2.3.2.23; 2.3.2.24;

The structure of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex, PDB code: 5edv was solved by B.C.Lechtenberg, P.D.Mace, R.Sanishvili, S.J.Riedl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 3.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.820, 75.740, 120.960, 90.00, 95.56, 90.00
R / Rfree (%)	24.9 / 30.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex (pdb code 5edv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex, PDB code: 5edv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:0.6 occ:1.00 SG A:CYS702 2.3 0.9 1.0 SG A:CYS722 2.3 0.3 1.0 SG A:CYS725 2.4 0.9 1.0 SG A:CYS699 2.4 0.3 1.0 CB A:CYS722 3.4 0.1 1.0 CB A:CYS699 3.4 0.2 1.0 CB A:CYS702 3.4 0.0 1.0 CB A:CYS725 3.5 0.8 1.0 CG2 A:VAL701 3.7 0.6 1.0 N A:CYS722 3.7 0.8 1.0 N A:CYS702 3.9 0.2 1.0 CA A:CYS722 4.1 0.9 1.0 CA A:CYS702 4.2 0.5 1.0 O A:CYS722 4.4 0.1 1.0 CA A:CYS725 4.6 0.9 1.0 C A:CYS722 4.6 0.6 1.0 C A:VAL701 4.7 0.1 1.0 N A:CYS725 4.8 0.3 1.0 C A:CYS702 4.8 0.7 1.0 CA A:CYS699 4.8 0.2 1.0 C A:ILE721 4.9 0.6 1.0 CG2 A:ILE721 4.9 0.9 1.0 CB A:VAL701 5.0 0.5 1.0

Zinc binding site 2 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:0.9 occ:1.00 SG A:CYS719 2.3 0.1 1.0 SG A:CYS744 2.3 0.7 1.0 SG A:CYS717 2.3 0.7 1.0 SG A:CYS747 2.3 0.5 1.0 CB A:CYS717 3.0 0.5 1.0 CB A:CYS719 3.4 0.6 1.0 CB A:CYS744 3.5 0.2 1.0 CB A:CYS747 3.5 0.9 1.0 N A:CYS747 3.7 0.5 1.0 N A:CYS719 3.9 0.5 1.0 CA A:CYS747 4.2 0.1 1.0 CA A:CYS719 4.3 0.4 1.0 CA A:CYS717 4.4 0.3 1.0 N A:GLU718 4.4 0.2 1.0 CB A:ALA746 4.5 0.7 1.0 C A:CYS717 4.7 0.1 1.0 C A:ALA746 4.7 0.4 1.0 CA A:CYS744 4.9 0.6 1.0 C A:GLU718 5.0 0.4 1.0 CA A:ALA746 5.0 0.6 1.0

Zinc binding site 3 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:0.9 occ:1.00 SG A:CYS820 2.3 0.9 1.0 SG A:CYS817 2.3 0.4 1.0 SG A:CYS799 2.3 1.0 1.0 SG A:CYS802 2.3 0.7 1.0 CB A:CYS817 3.2 0.9 1.0 CB A:CYS799 3.3 0.7 1.0 CB A:CYS802 3.3 0.4 1.0 CB A:CYS820 3.3 0.0 1.0 N A:CYS820 3.6 0.9 1.0 N A:CYS802 3.9 0.6 1.0 CA A:CYS820 4.0 0.2 1.0 CA A:CYS802 4.1 0.6 1.0 CB A:GLN819 4.5 0.1 1.0 CB A:PHE804 4.6 0.6 1.0 CA A:CYS817 4.6 0.3 1.0 C A:GLN819 4.7 0.4 1.0 C A:CYS820 4.7 0.2 1.0 CA A:CYS799 4.7 0.1 1.0 C A:CYS802 4.8 0.7 1.0 N A:GLN819 4.8 0.8 1.0 N A:HIS821 4.8 0.1 1.0 CA A:GLN819 4.8 0.2 1.0 C A:CYS817 5.0 0.4 1.0 C A:GLN801 5.0 0.9 1.0

Zinc binding site 4 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:0.7 occ:1.00 NE2 A:HIS836 2.1 0.9 1.0 SG A:CYS828 2.3 0.6 1.0 SG A:CYS825 2.3 0.1 1.0 SG A:CYS841 2.3 0.4 1.0 CE1 A:HIS836 2.8 0.6 1.0 CD2 A:HIS836 3.3 0.3 1.0 CB A:CYS825 3.3 0.3 1.0 CB A:CYS828 3.3 0.8 1.0 CB A:CYS841 3.4 0.8 1.0 N A:CYS828 3.6 1.0 1.0 CA A:CYS841 3.8 0.7 1.0 ND1 A:HIS836 4.0 0.4 1.0 CA A:CYS828 4.0 0.8 1.0 CG A:HIS836 4.2 0.9 1.0 CB A:ARG827 4.4 0.3 1.0 N A:CYS841 4.6 0.9 1.0 C A:ARG827 4.7 0.6 1.0 CA A:CYS825 4.7 0.1 1.0 CA A:ARG827 4.9 0.5 1.0 C A:CYS841 4.9 0.4 1.0

Zinc binding site 5 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:0.5 occ:1.00 SG A:CYS871 2.3 0.4 1.0 SG A:CYS890 2.3 0.6 1.0 SG A:CYS874 2.3 0.0 1.0 SG A:CYS893 2.3 0.5 1.0 CB A:CYS890 3.3 0.2 1.0 CB A:CYS893 3.3 0.5 1.0 CB A:CYS874 3.3 1.0 1.0 CB A:CYS871 3.4 0.3 1.0 N A:CYS874 3.8 0.3 1.0 N A:CYS893 3.9 0.9 1.0 CA A:CYS893 4.1 0.1 1.0 CA A:CYS874 4.1 0.9 1.0 CB A:LYS873 4.5 0.4 1.0 CB A:HIS895 4.5 0.3 1.0 CB A:GLN892 4.7 0.0 1.0 C A:CYS893 4.7 0.1 1.0 CA A:CYS890 4.7 0.2 1.0 CA A:CYS871 4.8 1.0 1.0 C A:LYS873 4.9 0.2 1.0 C A:CYS874 4.9 1.0 1.0 CG A:LYS873 4.9 0.5 1.0 C A:GLN892 5.0 0.1 1.0 N A:HIS895 5.0 0.1 1.0 N A:ARG894 5.0 1.0 1.0

Zinc binding site 6 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2006 b:0.1 occ:1.00 ND1 A:HIS926 2.1 0.2 1.0 SG A:CYS901 2.3 0.5 1.0 SG A:CYS898 2.3 0.1 1.0 SG A:CYS930 2.3 0.5 1.0 CE1 A:HIS926 2.9 0.9 1.0 CG A:HIS926 3.1 0.6 1.0 CB A:CYS898 3.3 1.0 1.0 CB A:CYS930 3.4 0.9 1.0 CB A:CYS901 3.5 0.9 1.0 CB A:HIS926 3.6 0.0 1.0 N A:CYS901 4.0 0.8 1.0 NE2 A:HIS926 4.0 0.5 1.0 CB A:PHE932 4.1 0.4 1.0 CD1 A:PHE932 4.1 0.4 1.0 CD2 A:HIS926 4.1 0.4 1.0 CA A:HIS926 4.2 0.2 1.0 CG A:PHE932 4.3 0.8 1.0 CA A:CYS901 4.4 0.7 1.0 CD A:PRO927 4.6 0.9 1.0 CA A:CYS898 4.8 0.8 1.0 O A:HIS925 4.9 0.7 1.0 CA A:CYS930 4.9 0.8 1.0 CE1 A:PHE932 4.9 0.8 1.0

Zinc binding site 7 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2007 b:0.6 occ:1.00 NE2 A:HIS923 2.1 0.1 1.0 NE2 A:HIS925 2.1 0.1 1.0 SG A:CYS911 2.3 0.4 1.0 SG A:CYS916 2.3 0.2 1.0 CD2 A:HIS923 2.9 0.3 1.0 CD2 A:HIS925 2.9 0.1 1.0 CE1 A:HIS925 2.9 0.6 1.0 CE1 A:HIS923 3.2 0.6 1.0 CB A:CYS911 3.4 0.5 1.0 CB A:CYS916 3.4 0.5 1.0 ND1 A:HIS925 3.9 0.9 1.0 CG A:HIS925 3.9 0.5 1.0 CG A:HIS923 4.1 0.2 1.0 ND1 A:HIS923 4.2 0.8 1.0 CA A:CYS916 4.4 0.4 1.0 CG A:GLU913 4.7 0.6 1.0 CA A:CYS911 4.8 0.9 1.0 OE2 A:GLU913 4.8 0.1 1.0 CD2 A:TYR906 4.9 0.9 1.0

Zinc binding site 8 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2008 b:0.9 occ:1.00 ND1 A:HIS1001 2.1 0.2 1.0 CE1 A:HIS1001 2.3 0.4 1.0 SG A:CYS986 2.3 0.7 1.0 SG A:CYS998 2.3 0.3 1.0 SG A:CYS969 2.4 0.9 1.0 CG A:HIS1001 3.0 0.5 1.0 NE2 A:HIS1001 3.2 0.2 1.0 CB A:CYS986 3.2 0.8 1.0 CB A:CYS969 3.4 0.9 1.0 CB A:CYS998 3.4 0.8 1.0 CD2 A:HIS1001 3.5 0.2 1.0 CB A:HIS1001 3.9 0.4 1.0 N A:CYS998 4.1 0.5 1.0 CA A:CYS998 4.4 0.0 1.0 CB A:LYS988 4.4 0.1 1.0 CD A:LYS988 4.5 0.1 1.0 CA A:CYS986 4.7 0.8 1.0 CA A:CYS969 4.8 0.1 1.0 CB A:VAL971 4.8 0.5 1.0 CG2 A:VAL971 4.9 0.0 1.0 CG A:LYS988 4.9 0.6 1.0 N A:HIS1001 5.0 0.5 1.0

Zinc binding site 9 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:0.6 occ:1.00 SG B:CYS702 2.3 0.1 1.0 SG B:CYS699 2.3 0.8 1.0 SG B:CYS725 2.3 0.7 1.0 SG B:CYS722 2.3 1.0 1.0 CB B:CYS699 3.4 0.1 1.0 CB B:CYS722 3.4 0.2 1.0 CB B:CYS702 3.4 0.6 1.0 CB B:CYS725 3.5 0.5 1.0 CG2 B:VAL701 3.7 0.2 1.0 N B:CYS722 3.7 0.8 1.0 N B:CYS702 3.9 0.1 1.0 CA B:CYS722 4.1 0.9 1.0 CA B:CYS702 4.2 0.9 1.0 O B:CYS722 4.4 0.4 1.0 CA B:CYS725 4.6 0.7 1.0 C B:CYS722 4.6 0.5 1.0 N B:CYS725 4.7 0.2 1.0 C B:VAL701 4.8 0.4 1.0 CA B:CYS699 4.8 0.9 1.0 C B:CYS702 4.8 0.6 1.0 C B:ILE721 4.9 0.9 1.0 CG2 B:ILE721 4.9 0.1 1.0 CB B:VAL701 5.0 0.1 1.0

Zinc binding site 10 out of 16 in the Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Hoip-Rbr/UBCH5B~Ubiquitin Transfer Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:0.6 occ:1.00 SG B:CYS747 2.3 1.0 1.0 SG B:CYS744 2.4 0.2 1.0 SG B:CYS719 2.4 0.5 1.0 SG B:CYS717 2.4 0.9 1.0 CB B:CYS744 3.3 0.4 1.0 CB B:CYS747 3.5 0.3 1.0 CB B:CYS719 3.5 0.6 1.0 CB B:CYS717 3.6 0.9 1.0 N B:CYS719 3.9 0.2 1.0 O B:CYS717 4.0 0.8 1.0 C B:CYS717 4.1 0.4 1.0 N B:CYS747 4.1 0.3 1.0 C B:GLU718 4.2 0.4 1.0 CA B:CYS719 4.4 0.4 1.0 O B:GLU718 4.5 0.1 1.0 N B:GLU718 4.5 0.6 1.0 CA B:CYS747 4.5 0.2 1.0 CA B:CYS717 4.5 0.7 1.0 CB B:LEU714 4.5 0.5 1.0 CA B:GLU718 4.7 0.8 1.0 CA B:CYS744 4.8 0.5 1.0 CB B:ALA746 4.8 0.9 1.0 CD2 B:LEU714 4.9 0.7 1.0

B.C.Lechtenberg, A.Rajput, R.Sanishvili, M.K.Dobaczewska, C.F.Ware, P.D.Mace, S.J.Riedl. Structure of A Hoip/E2~Ubiquitin Complex Reveals Rbr E3 Ligase Mechanism and Regulation. Nature V. 529 546 2016.
ISSN: ESSN 1476-4687
PubMed: 26789245
DOI: 10.1038/NATURE16511