Zinc in PDB 9dnp: Structure of UBR2-Rff Complex

The structure of Structure of UBR2-Rff Complex, PDB code: 9dnp 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)	37.81 / 1.22
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.538, 56.987, 115.606, 90, 90, 90
R / Rfree (%)	18.6 / 20.1

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

Zinc binding site 1 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:14.4 occ:1.00 SG A:CYS99 2.3 14.8 1.0 SG A:CYS149 2.3 14.3 1.0 SG A:CYS124 2.3 14.1 1.0 SG A:CYS127 2.4 14.3 1.0 CB A:CYS149 3.2 14.6 1.0 CB A:CYS99 3.3 18.2 1.0 CB A:CYS127 3.3 14.6 1.0 CB A:CYS124 3.5 13.6 1.0 N A:CYS124 3.9 14.3 1.0 CB A:CYS151 4.2 14.0 1.0 O A:HOH367 4.3 25.7 1.0 CA A:CYS124 4.3 15.0 1.0 ZN A:ZN202 4.4 15.8 1.0 N A:CYS127 4.4 14.7 1.0 CA A:CYS127 4.5 15.2 1.0 CG A:ARG101 4.6 18.6 1.0 CA A:CYS149 4.6 15.3 1.0 CA A:CYS99 4.7 19.8 1.0 CE1 A:HIS166 4.7 17.0 1.0 NE A:ARG101 4.9 19.4 1.0 C A:CYS124 4.9 14.6 1.0

Zinc binding site 2 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:15.8 occ:1.00 ND1 A:HIS166 2.1 16.8 1.0 SG A:CYS151 2.3 17.6 1.0 SG A:CYS163 2.3 16.8 1.0 SG A:CYS127 2.3 14.3 1.0 CE1 A:HIS166 3.0 17.0 1.0 CG A:HIS166 3.1 17.8 1.0 CB A:CYS151 3.2 14.0 1.0 CB A:CYS127 3.2 14.6 1.0 CB A:CYS163 3.4 18.6 1.0 CB A:HIS166 3.5 19.1 1.0 CA A:CYS127 3.9 15.2 1.0 N A:CYS163 4.1 18.7 1.0 NE2 A:HIS166 4.1 18.5 1.0 CD2 A:HIS166 4.2 19.0 1.0 CB A:CYS99 4.3 18.2 1.0 CA A:CYS163 4.3 19.2 1.0 ZN A:ZN201 4.4 14.4 1.0 N A:HIS166 4.4 20.2 1.0 CA A:HIS166 4.6 19.8 1.0 CA A:CYS151 4.6 15.0 1.0 N A:CYS127 4.9 14.7 1.0 O A:HOH329 4.9 18.7 1.0 C A:CYS163 4.9 20.5 1.0 C A:CYS127 5.0 15.4 1.0

Zinc binding site 3 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:21.2 occ:1.00 ND1 A:HIS136 2.1 20.1 1.0 ND1 A:HIS133 2.1 20.0 1.0 SG A:CYS115 2.3 22.4 1.0 SG A:CYS112 2.3 21.8 1.0 CE1 A:HIS136 2.9 25.5 1.0 CE1 A:HIS133 3.0 21.2 1.0 CB A:CYS115 3.1 19.7 1.0 CG A:HIS133 3.2 20.4 1.0 CG A:HIS136 3.2 22.9 1.0 CB A:CYS112 3.4 20.3 1.0 CB A:HIS133 3.6 21.1 1.0 CB A:HIS136 3.6 22.6 1.0 CA A:HIS133 3.9 20.4 1.0 N A:CYS115 4.0 21.1 1.0 NE2 A:HIS136 4.1 25.2 1.0 NE2 A:HIS133 4.1 19.8 1.0 CA A:CYS115 4.2 21.2 1.0 CD2 A:HIS136 4.2 24.6 1.0 CD2 A:HIS133 4.2 20.0 1.0 CB A:ASP114 4.3 27.5 1.0 C A:ASP114 4.6 24.9 1.0 N A:HIS133 4.7 20.9 1.0 CA A:CYS112 4.8 20.8 1.0 CA A:ASP114 4.9 26.5 1.0 CG1 A:ILE132 4.9 23.7 1.0 N A:ASP114 4.9 24.7 1.0 CD1 A:ILE132 5.0 26.8 1.0

Zinc binding site 4 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.0 occ:1.00 SG B:CYS99 2.3 15.3 1.0 SG B:CYS149 2.3 14.6 1.0 SG B:CYS124 2.3 14.8 1.0 SG B:CYS127 2.4 14.4 1.0 CB B:CYS149 3.2 16.1 1.0 CB B:CYS99 3.2 16.5 1.0 CB B:CYS127 3.3 14.2 1.0 CB B:CYS124 3.5 15.2 1.0 N B:CYS124 3.9 14.3 1.0 O B:HOH318 4.1 27.1 1.0 CB B:CYS151 4.2 14.1 1.0 CA B:CYS124 4.3 13.0 1.0 O B:HOH370 4.3 24.4 1.0 ZN B:ZN202 4.4 16.2 1.0 N B:CYS127 4.4 15.5 1.0 CA B:CYS127 4.5 14.2 1.0 CA B:CYS149 4.6 14.4 1.0 CA B:CYS99 4.7 19.6 1.0 CE1 B:HIS166 4.8 18.4 1.0 CB B:ARG101 4.8 24.7 1.0 C B:CYS124 4.9 15.0 1.0 O B:CYS124 5.0 14.3 1.0

Zinc binding site 5 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:16.2 occ:1.00 ND1 B:HIS166 2.0 17.1 1.0 SG B:CYS151 2.3 16.7 1.0 SG B:CYS163 2.3 16.5 1.0 SG B:CYS127 2.4 14.4 1.0 CE1 B:HIS166 2.9 18.4 1.0 CG B:HIS166 3.1 18.1 1.0 CB B:CYS151 3.2 14.1 1.0 CB B:CYS127 3.3 14.2 1.0 CB B:CYS163 3.4 18.9 1.0 CB B:HIS166 3.6 19.8 1.0 CA B:CYS127 4.0 14.2 1.0 NE2 B:HIS166 4.0 20.2 1.0 N B:CYS163 4.1 18.5 1.0 O B:HOH333 4.2 21.1 1.0 CD2 B:HIS166 4.2 21.0 1.0 CA B:CYS163 4.3 19.3 1.0 CB B:CYS99 4.3 16.5 1.0 ZN B:ZN201 4.4 15.0 1.0 N B:HIS166 4.5 19.8 1.0 CA B:CYS151 4.7 15.0 1.0 CA B:HIS166 4.7 20.2 1.0 C B:CYS163 4.9 19.6 1.0 N B:CYS127 4.9 15.5 1.0 O B:HOH329 5.0 17.9 1.0

Zinc binding site 6 out of 6 in the Structure of UBR2-Rff 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-Rff Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:18.2 occ:1.00 ND1 B:HIS136 2.1 18.5 1.0 ND1 B:HIS133 2.1 17.3 1.0 SG B:CYS112 2.3 18.2 1.0 SG B:CYS115 2.3 19.1 1.0 CE1 B:HIS136 2.9 21.9 1.0 CE1 B:HIS133 3.0 17.7 1.0 CG B:HIS136 3.2 20.6 1.0 CB B:CYS115 3.2 18.2 1.0 CG B:HIS133 3.2 18.9 1.0 CB B:CYS112 3.4 18.3 1.0 CB B:HIS136 3.6 20.3 1.0 CB B:HIS133 3.6 18.6 1.0 CA B:HIS133 3.8 19.7 1.0 N B:CYS115 3.9 18.1 1.0 NE2 B:HIS136 4.1 22.3 1.0 NE2 B:HIS133 4.1 18.7 1.0 CA B:CYS115 4.1 20.3 1.0 CD2 B:HIS136 4.2 22.1 1.0 CD2 B:HIS133 4.3 19.0 1.0 CB B:ASP114 4.3 23.4 1.0 N B:HIS133 4.6 19.2 1.0 C B:ASP114 4.6 23.0 1.0 CA B:CYS112 4.8 19.0 1.0 CG1 B:ILE132 4.9 21.3 1.0 CA B:ASP114 4.9 21.5 1.0 CD1 B:ILE132 5.0 23.9 1.0 C B:HIS133 5.0 18.8 1.0 N B:ASP114 5.0 21.4 1.0

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