Zinc in PDB 3ny3: Structure of the Ubr-Box of UBR2 in Complex with N-Degron

All present enzymatic activity of Structure of the Ubr-Box of UBR2 in Complex with N-Degron:
6.3.2.19;

The structure of Structure of the Ubr-Box of UBR2 in Complex with N-Degron, PDB code: 3ny3 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)	28.09 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.123, 36.940, 29.824, 90.00, 109.60, 90.00
R / Rfree (%)	19 / 21

The binding sites of Zinc atom in the Structure of the Ubr-Box of UBR2 in Complex with N-Degron (pdb code 3ny3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Ubr-Box of UBR2 in Complex with N-Degron, PDB code: 3ny3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of the Ubr-Box of UBR2 in Complex with N-Degron


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 UBR2 in Complex with N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:15.2 occ:1.00 SG A:CYS149 2.3 14.5 1.0 SG A:CYS99 2.3 15.2 1.0 SG A:CYS124 2.4 14.1 1.0 SG A:CYS127 2.4 13.9 1.0 CB A:CYS149 3.1 13.8 1.0 CB A:CYS99 3.2 17.4 1.0 CB A:CYS127 3.4 14.6 1.0 CB A:CYS124 3.5 15.5 1.0 N A:CYS124 4.0 14.5 1.0 CB A:CYS151 4.2 14.9 1.0 CA A:CYS124 4.3 14.6 1.0 N A:CYS127 4.3 14.4 1.0 ZN A:ZN2 4.4 15.2 1.0 CA A:CYS127 4.5 14.5 1.0 CB A:ARG101 4.6 16.9 1.0 CA A:CYS149 4.6 13.7 1.0 CA A:CYS99 4.6 18.3 1.0 CE1 A:HIS166 4.6 14.3 1.0 C A:CYS124 4.9 15.2 1.0 O A:CYS124 4.9 14.2 1.0

Zinc binding site 2 out of 3 in the Structure of the Ubr-Box of UBR2 in Complex with N-Degron


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 UBR2 in Complex with N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:15.2 occ:1.00 ND1 A:HIS166 2.0 16.8 1.0 SG A:CYS127 2.4 13.9 1.0 SG A:CYS151 2.4 15.4 1.0 SG A:CYS163 2.4 14.4 1.0 CE1 A:HIS166 3.0 14.3 1.0 CG A:HIS166 3.1 15.2 1.0 CB A:CYS151 3.2 14.9 1.0 CB A:CYS127 3.2 14.6 1.0 CB A:CYS163 3.5 15.4 1.0 CB A:HIS166 3.5 17.3 1.0 CA A:CYS127 3.9 14.5 1.0 N A:CYS163 4.1 15.9 1.0 NE2 A:HIS166 4.1 16.3 1.0 O A:HOH13 4.2 16.6 1.0 CD2 A:HIS166 4.2 17.0 1.0 CB A:CYS99 4.3 17.4 1.0 N A:HIS166 4.3 17.5 1.0 CA A:CYS163 4.3 15.4 1.0 ZN A:ZN1 4.4 15.2 1.0 CA A:HIS166 4.5 18.0 1.0 CA A:CYS151 4.7 14.2 1.0 N A:CYS127 4.8 14.4 1.0 C A:CYS163 4.9 16.2 1.0 O A:HOH170 5.0 17.9 1.0 O A:CYS163 5.0 16.5 1.0

Zinc binding site 3 out of 3 in the Structure of the Ubr-Box of UBR2 in Complex with N-Degron


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 UBR2 in Complex with N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:17.8 occ:1.00 ND1 A:HIS136 2.1 17.9 1.0 ND1 A:HIS133 2.1 15.3 1.0 SG A:CYS115 2.3 17.1 1.0 SG A:CYS112 2.4 16.7 1.0 CE1 A:HIS133 3.0 15.8 1.0 CE1 A:HIS136 3.0 18.9 1.0 CB A:CYS115 3.1 16.7 1.0 CG A:HIS136 3.2 17.6 1.0 CG A:HIS133 3.2 15.7 1.0 CB A:CYS112 3.3 16.2 1.0 CB A:HIS136 3.5 18.6 1.0 CB A:HIS133 3.7 15.1 1.0 CA A:HIS133 3.9 15.1 1.0 N A:CYS115 3.9 17.3 1.0 CA A:CYS115 4.1 16.7 1.0 NE2 A:HIS136 4.1 18.2 1.0 NE2 A:HIS133 4.1 16.0 1.0 CD2 A:HIS136 4.2 19.3 1.0 CB A:ASP114 4.3 18.5 1.0 CD2 A:HIS133 4.3 15.4 1.0 N A:HIS133 4.6 15.2 1.0 C A:ASP114 4.6 18.4 1.0 CA A:CYS112 4.7 16.0 1.0 CG1 A:ILE132 4.7 16.9 1.0 CD1 A:ILE132 4.8 18.4 1.0 CA A:ASP114 4.9 18.5 1.0 C A:HIS133 5.0 15.6 1.0 O A:HIS133 5.0 15.7 1.0 N A:ASP114 5.0 17.8 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