Zinc in PDB 9dnq: Structure of UBR2-Ryf Complex

The structure of Structure of UBR2-Ryf Complex, PDB code: 9dnq was solved by S.Huang, J.Wu, S.Taylor, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	25.187, 50.871, 45.956, 90, 89.98, 90
R / Rfree (%)	13.9 / 15

The binding sites of Zinc atom in the Structure of UBR2-Ryf Complex (pdb code 9dnq). 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 UBR2-Ryf Complex, PDB code: 9dnq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:4.8 occ:1.00 SG A:CYS99 2.3 6.0 1.0 SG A:CYS149 2.3 4.0 1.0 SG A:CYS124 2.3 5.1 1.0 SG A:CYS127 2.4 4.4 1.0 CB A:CYS149 3.2 5.3 1.0 CB A:CYS99 3.2 6.6 1.0 CB A:CYS127 3.3 5.4 1.0 CB A:CYS124 3.5 5.5 1.0 N A:CYS124 3.9 3.6 1.0 O A:HOH397 4.0 17.2 1.0 CB A:CYS151 4.2 4.3 1.0 CA A:CYS124 4.3 5.5 1.0 ZN A:ZN202 4.4 5.1 1.0 CG A:ARG101 4.4 7.8 1.0 O A:HOH374 4.5 12.7 1.0 CE1 A:HIS166 4.5 6.8 1.0 CA A:CYS127 4.5 5.1 1.0 N A:CYS127 4.5 5.0 1.0 CB A:ARG101 4.6 5.9 1.0 CA A:CYS99 4.6 7.8 1.0 CA A:CYS149 4.6 4.6 1.0 C A:CYS124 4.9 4.7 1.0 O A:CYS124 4.9 4.5 1.0 ND1 A:HIS166 4.9 7.4 1.0

Zinc binding site 2 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:5.1 occ:1.00 ND1 A:HIS166 2.1 7.4 1.0 SG A:CYS151 2.3 7.2 1.0 SG A:CYS163 2.3 5.3 1.0 SG A:CYS127 2.4 4.4 1.0 CE1 A:HIS166 3.0 6.8 1.0 CG A:HIS166 3.1 6.9 1.0 CB A:CYS151 3.1 4.3 1.0 CB A:CYS127 3.2 5.4 1.0 CB A:CYS163 3.4 6.0 1.0 CB A:HIS166 3.5 6.4 1.0 CA A:CYS127 3.9 5.1 1.0 N A:CYS163 4.1 5.8 1.0 NE2 A:HIS166 4.1 8.8 1.0 CD2 A:HIS166 4.2 8.0 1.0 N A:HIS166 4.3 6.2 1.0 CA A:CYS163 4.3 5.7 1.0 ZN A:ZN201 4.4 4.8 1.0 CA A:HIS166 4.5 6.1 1.0 CA A:CYS151 4.6 4.5 1.0 O A:HOH397 4.7 17.2 1.0 CB A:CYS99 4.8 6.6 1.0 C A:CYS163 4.8 5.7 1.0 N A:CYS127 4.9 5.0 1.0 C A:CYS127 4.9 5.3 1.0

Zinc binding site 3 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:5.4 occ:1.00 ND1 A:HIS136 2.0 6.7 1.0 ND1 A:HIS133 2.1 6.0 1.0 SG A:CYS112 2.3 5.4 1.0 SG A:CYS115 2.3 6.6 1.0 CE1 A:HIS136 2.9 6.2 1.0 CE1 A:HIS133 3.0 5.1 1.0 CB A:CYS115 3.1 5.2 1.0 CG A:HIS136 3.1 6.0 1.0 CG A:HIS133 3.2 4.7 1.0 CB A:CYS112 3.3 5.5 1.0 CB A:HIS136 3.6 5.9 1.0 CB A:HIS133 3.6 5.8 1.0 CA A:HIS133 3.9 6.1 1.0 N A:CYS115 3.9 5.6 1.0 NE2 A:HIS136 4.1 8.0 1.0 NE2 A:HIS133 4.1 5.5 1.0 CA A:CYS115 4.2 5.4 1.0 CD2 A:HIS136 4.2 6.8 1.0 CD2 A:HIS133 4.2 5.2 1.0 CB A:ASP114 4.3 7.4 1.0 O A:HOH372 4.4 20.2 1.0 C A:ASP114 4.6 6.7 1.0 N A:HIS133 4.7 5.8 1.0 CA A:CYS112 4.7 5.5 1.0 CA A:ASP114 4.9 6.4 1.0 O A:HIS133 5.0 6.3 1.0 C A:HIS133 5.0 5.3 1.0

Zinc binding site 4 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:4.7 occ:1.00 SG B:CYS124 2.3 4.8 1.0 SG B:CYS149 2.3 4.2 1.0 SG B:CYS99 2.4 5.6 1.0 SG B:CYS127 2.4 4.3 1.0 CB B:CYS149 3.2 4.5 1.0 CB B:CYS99 3.2 6.4 1.0 CB B:CYS127 3.4 5.3 1.0 CB B:CYS124 3.4 4.3 1.0 N B:CYS124 3.9 4.3 1.0 O B:HOH307 4.0 16.3 1.0 CA B:CYS124 4.2 4.5 1.0 CB B:CYS151 4.2 4.2 1.0 ZN B:ZN202 4.4 5.1 1.0 O B:HOH399 4.5 14.2 1.0 CG B:ARG101 4.5 7.5 1.0 CE1 B:HIS166 4.5 7.8 1.0 N B:CYS127 4.5 5.2 1.0 CA B:CYS127 4.6 4.9 1.0 CB B:ARG101 4.6 5.9 1.0 CA B:CYS99 4.6 8.0 1.0 CA B:CYS149 4.6 4.2 1.0 C B:CYS124 4.9 4.4 1.0 O B:CYS124 4.9 4.2 1.0 ND1 B:HIS166 5.0 6.9 1.0

Zinc binding site 5 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:5.1 occ:1.00 ND1 B:HIS166 2.1 6.9 1.0 SG B:CYS151 2.3 7.3 1.0 SG B:CYS163 2.3 4.9 1.0 SG B:CYS127 2.4 4.3 1.0 CE1 B:HIS166 3.0 7.8 1.0 CG B:HIS166 3.1 7.0 1.0 CB B:CYS151 3.1 4.2 1.0 CB B:CYS127 3.2 5.3 1.0 CB B:CYS163 3.4 5.8 1.0 CB B:HIS166 3.5 6.7 1.0 CA B:CYS127 3.9 4.9 1.0 N B:CYS163 4.1 5.7 1.0 NE2 B:HIS166 4.1 9.5 1.0 CD2 B:HIS166 4.2 9.5 1.0 CA B:CYS163 4.3 6.2 1.0 N B:HIS166 4.3 6.2 1.0 ZN B:ZN201 4.4 4.7 1.0 CA B:HIS166 4.6 6.5 1.0 CA B:CYS151 4.6 4.2 1.0 O B:HOH375 4.8 21.1 1.0 O B:HOH307 4.8 16.3 1.0 CB B:CYS99 4.8 6.4 1.0 C B:CYS163 4.9 5.3 1.0 N B:CYS127 4.9 5.2 1.0 C B:CYS127 4.9 5.2 1.0 CB B:LYS165 5.0 12.5 1.0

Zinc binding site 6 out of 6 in the Structure of UBR2-Ryf 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 UBR2-Ryf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:5.5 occ:1.00 ND1 B:HIS136 2.1 5.2 1.0 ND1 B:HIS133 2.1 5.0 1.0 SG B:CYS112 2.3 5.5 1.0 SG B:CYS115 2.3 6.1 1.0 CE1 B:HIS136 2.9 6.2 1.0 CE1 B:HIS133 2.9 6.1 1.0 CB B:CYS115 3.1 5.7 1.0 CG B:HIS136 3.2 6.5 1.0 CG B:HIS133 3.2 5.7 1.0 CB B:CYS112 3.3 6.0 1.0 CB B:HIS136 3.6 6.1 1.0 CB B:HIS133 3.6 5.6 1.0 CA B:HIS133 3.9 6.0 1.0 N B:CYS115 4.0 5.4 1.0 NE2 B:HIS136 4.1 7.3 1.0 NE2 B:HIS133 4.1 6.4 1.0 CA B:CYS115 4.2 5.5 1.0 CD2 B:HIS136 4.2 7.1 1.0 CD2 B:HIS133 4.2 6.7 1.0 CB B:ASP114 4.3 8.0 1.0 C B:ASP114 4.6 6.9 1.0 N B:HIS133 4.7 6.0 1.0 CA B:CYS112 4.7 5.5 1.0 CA B:ASP114 4.9 6.6 1.0 O B:HIS133 4.9 6.6 1.0 C B:HIS133 5.0 5.2 1.0 N B:ASP114 5.0 6.1 1.0

S.Huang, J.Wu, S.Taylor, Y.Chen. Structural Flexibility and Selectivity of N-End Rule Ligases To Be Published.