Zinc in PDB 3ny1: Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase

All present enzymatic activity of Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase:
6.3.2.19;

The structure of Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase, PDB code: 3ny1 was solved by E.Matta-Camacho, G.Kozlov, F.Li, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.10 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.702, 49.262, 43.831, 90.00, 100.51, 90.00
R / Rfree (%)	19.4 / 24.8

The binding sites of Zinc atom in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase (pdb code 3ny1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase, PDB code: 3ny1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:13.3 occ:1.00 SG A:CYS99 2.3 17.8 1.0 SG A:CYS127 2.4 9.9 1.0 SG A:CYS149 2.4 16.6 1.0 SG A:CYS124 2.4 13.8 1.0 CB A:CYS99 3.1 19.3 1.0 CB A:CYS127 3.2 12.9 1.0 CB A:CYS149 3.3 15.0 1.0 CB A:CYS124 3.6 14.9 1.0 N A:CYS124 4.0 15.3 1.0 CB A:CYS151 4.1 14.8 1.0 ZN A:ZN5 4.2 17.0 1.0 CA A:CYS124 4.3 15.1 1.0 N A:CYS127 4.4 13.9 1.0 CA A:CYS127 4.4 13.0 1.0 CA A:CYS99 4.5 19.9 1.0 CE1 A:HIS166 4.6 14.6 1.0 CA A:CYS149 4.7 15.0 1.0 O A:CYS124 4.9 14.8 1.0 CG A:ARG101 5.0 24.1 1.0 C A:CYS124 5.0 15.2 1.0 ND1 A:HIS166 5.0 16.0 1.0

Zinc binding site 2 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:17.0 occ:1.00 ND1 A:HIS166 2.1 16.0 1.0 SG A:CYS127 2.2 9.9 1.0 SG A:CYS163 2.3 16.0 1.0 SG A:CYS151 2.3 18.0 1.0 CE1 A:HIS166 3.0 14.6 1.0 CB A:CYS151 3.2 14.8 1.0 CB A:CYS127 3.2 12.9 1.0 CG A:HIS166 3.2 16.1 1.0 CB A:CYS163 3.4 15.0 1.0 CB A:HIS166 3.6 17.2 1.0 CA A:CYS127 4.0 13.0 1.0 N A:CYS163 4.0 15.1 1.0 NE2 A:HIS166 4.2 15.3 1.0 ZN A:ZN4 4.2 13.3 1.0 CA A:CYS163 4.3 15.5 1.0 CD2 A:HIS166 4.3 16.1 1.0 N A:HIS166 4.3 17.0 1.0 CB A:CYS99 4.5 19.3 1.0 CA A:HIS166 4.6 17.3 1.0 CA A:CYS151 4.6 14.5 1.0 SG A:CYS99 5.0 17.8 1.0

Zinc binding site 3 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn6 b:6.8 occ:1.00 ND1 A:HIS136 2.0 8.8 1.0 ND1 A:HIS133 2.1 10.4 1.0 SG A:CYS112 2.2 11.8 1.0 SG A:CYS115 2.2 14.2 1.0 CE1 A:HIS136 2.9 10.3 1.0 CE1 A:HIS133 3.0 9.6 1.0 CG A:HIS136 3.1 10.8 1.0 CG A:HIS133 3.2 11.7 1.0 CB A:CYS115 3.2 12.1 1.0 CB A:CYS112 3.4 13.6 1.0 CB A:HIS136 3.5 11.9 1.0 CB A:HIS133 3.6 12.9 1.0 CA A:HIS133 3.9 12.9 1.0 N A:CYS115 3.9 12.3 1.0 NE2 A:HIS136 4.1 9.6 1.0 NE2 A:HIS133 4.1 10.5 1.0 CA A:CYS115 4.2 12.0 1.0 CD2 A:HIS136 4.2 9.2 1.0 CB A:ASP114 4.2 12.7 1.0 CD2 A:HIS133 4.3 10.4 1.0 N A:HIS133 4.6 13.6 1.0 C A:ASP114 4.6 12.9 1.0 CA A:ASP114 4.8 12.7 1.0 CA A:CYS112 4.8 13.3 1.0 N A:ASP114 4.9 13.1 1.0 CG2 A:VAL132 5.0 13.4 1.0 C A:HIS133 5.0 13.1 1.0

Zinc binding site 4 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:10.6 occ:1.00 SG B:CYS149 2.2 11.2 1.0 SG B:CYS124 2.3 12.8 1.0 SG B:CYS99 2.3 17.3 1.0 SG B:CYS127 2.4 13.3 1.0 CB B:CYS149 3.1 13.2 1.0 CB B:CYS127 3.2 13.2 1.0 CB B:CYS99 3.4 19.2 1.0 CB B:CYS124 3.5 12.5 1.0 N B:CYS124 4.0 12.3 1.0 CB B:CYS151 4.1 13.4 1.0 CA B:CYS124 4.3 12.5 1.0 N B:CYS127 4.4 12.6 1.0 ZN B:ZN2 4.4 10.2 1.0 CA B:CYS127 4.4 12.9 1.0 CG B:ARG101 4.5 22.9 1.0 CA B:CYS149 4.6 13.2 1.0 CE1 B:HIS166 4.7 17.3 1.0 O B:CYS124 4.8 13.0 1.0 CA B:CYS99 4.8 19.6 1.0 C B:CYS124 4.8 13.0 1.0

Zinc binding site 5 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:10.2 occ:1.00 ND1 B:HIS166 2.1 18.2 1.0 SG B:CYS151 2.2 14.8 1.0 SG B:CYS127 2.2 13.3 1.0 SG B:CYS163 2.3 12.5 1.0 CE1 B:HIS166 3.0 17.3 1.0 CG B:HIS166 3.2 17.3 1.0 CB B:CYS151 3.2 13.4 1.0 CB B:CYS127 3.3 13.2 1.0 CB B:CYS163 3.4 12.6 1.0 CB B:HIS166 3.6 17.9 1.0 CA B:CYS127 4.0 12.9 1.0 N B:CYS163 4.0 11.9 1.0 NE2 B:HIS166 4.1 17.4 1.0 CD2 B:HIS166 4.3 16.7 1.0 CA B:CYS163 4.3 12.6 1.0 N B:HIS166 4.3 17.2 1.0 ZN B:ZN1 4.4 10.6 1.0 CB B:CYS99 4.5 19.2 1.0 CA B:HIS166 4.6 18.0 1.0 CA B:CYS151 4.6 13.7 1.0 C B:CYS163 4.9 13.3 1.0 O B:CYS163 4.9 13.3 1.0 N B:CYS127 4.9 12.6 1.0 SG B:CYS99 5.0 17.3 1.0

Zinc binding site 6 out of 6 in the Structure of the Ubr-Box of the UBR1 Ubiquitin Ligase


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 Ubr-Box of the UBR1 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:7.6 occ:1.00 ND1 B:HIS136 2.1 12.3 1.0 ND1 B:HIS133 2.1 14.1 1.0 SG B:CYS115 2.2 10.6 1.0 SG B:CYS112 2.3 11.3 1.0 CE1 B:HIS136 3.0 12.4 1.0 CE1 B:HIS133 3.0 15.0 1.0 CG B:HIS136 3.2 13.0 1.0 CG B:HIS133 3.2 13.3 1.0 CB B:CYS115 3.2 10.4 1.0 CB B:CYS112 3.3 12.7 1.0 CB B:HIS136 3.5 14.8 1.0 CB B:HIS133 3.6 12.5 1.0 CA B:HIS133 3.8 12.9 1.0 N B:CYS115 3.9 10.6 1.0 NE2 B:HIS136 4.1 12.1 1.0 NE2 B:HIS133 4.1 12.7 1.0 CA B:CYS115 4.2 10.7 1.0 CB B:ASP114 4.2 10.1 1.0 CD2 B:HIS136 4.2 12.2 1.0 CD2 B:HIS133 4.2 12.6 1.0 C B:ASP114 4.6 10.7 1.0 N B:HIS133 4.6 12.6 1.0 CA B:CYS112 4.7 12.4 1.0 CA B:ASP114 4.8 10.7 1.0 C B:HIS133 4.9 13.4 1.0 O B:HIS133 5.0 13.8 1.0 N B:ASP114 5.0 11.2 1.0

E.Matta-Camacho, G.Kozlov, F.F.Li, K.Gehring. Structural Basis of Substrate Recognition and Specificity in the N-End Rule Pathway. Nat.Struct.Mol.Biol. V. 17 1182 2010.
ISSN: ISSN 1545-9993
PubMed: 20835242
DOI: 10.1038/NSMB.1894