Zinc in PDB 7od1: Crystal Structure of Rbr Ubiquitin Ligase ARIH2

All present enzymatic activity of Crystal Structure of Rbr Ubiquitin Ligase ARIH2:
2.3.2.31;

The structure of Crystal Structure of Rbr Ubiquitin Ligase ARIH2, PDB code: 7od1 was solved by S.P.Kostrhon, J.R.Prabu, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.65 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.57, 80.54, 92.09, 90, 105.76, 90
R / Rfree (%)	22 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2 (pdb code 7od1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2, PDB code: 7od1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:108.4 occ:0.65 SG A:CYS318 2.3 102.5 1.0 SG A:CYS300 2.3 125.0 1.0 SG A:CYS315 2.3 108.5 1.0 SG A:CYS297 2.3 90.8 1.0 CB A:CYS300 3.0 102.9 1.0 CB A:CYS315 3.1 96.8 1.0 CB A:CYS318 3.2 93.3 1.0 N A:CYS300 3.5 90.8 1.0 CB A:CYS297 3.6 93.7 1.0 N A:CYS318 3.8 97.0 1.0 CA A:CYS300 3.9 95.2 1.0 CA A:CYS318 4.1 76.8 1.0 CG2 A:ILE302 4.2 109.2 1.0 CB A:LYS299 4.2 86.0 1.0 C A:LYS299 4.5 96.4 1.0 CA A:CYS315 4.6 85.6 1.0 CB A:LYS317 4.7 80.1 1.0 CB A:HIS320 4.8 70.7 1.0 C A:CYS318 4.8 90.3 1.0 CA A:LYS299 4.8 93.2 1.0 C A:LYS317 4.9 107.6 1.0 N A:LYS299 4.9 99.7 1.0 CA A:CYS297 5.0 83.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:78.3 occ:0.70 NE2 A:HIS333 2.0 87.8 1.0 SG A:CYS326 2.3 102.1 1.0 SG A:CYS340 2.3 96.5 1.0 SG A:CYS323 2.3 69.1 1.0 CD2 A:HIS333 2.9 82.5 1.0 CB A:CYS340 3.0 55.7 1.0 CE1 A:HIS333 3.0 91.1 1.0 CB A:CYS323 3.3 76.1 1.0 CB A:CYS326 3.5 64.6 1.0 N A:CYS326 3.9 91.7 1.0 CG A:HIS333 4.1 83.8 1.0 ND1 A:HIS333 4.1 82.5 1.0 CA A:CYS340 4.2 74.0 1.0 CA A:CYS326 4.3 72.9 1.0 CB A:MET325 4.4 64.0 1.0 CA A:CYS323 4.8 70.9 1.0 C A:MET325 4.8 75.0 1.0 OH A:TYR338 4.8 74.2 1.0 N A:MET325 5.0 69.8 1.0 CA A:MET325 5.0 58.6 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:75.5 occ:1.00 SG A:CYS233 2.3 62.9 1.0 SG A:CYS228 2.3 60.9 1.0 SG A:CYS252 2.3 64.1 1.0 SG A:CYS249 2.3 57.8 1.0 CB A:CYS249 3.0 56.9 1.0 CB A:CYS233 3.4 65.2 1.0 CB A:CYS252 3.5 55.5 1.0 CB A:CYS228 3.6 67.4 1.0 N A:CYS252 3.8 60.8 1.0 CA A:CYS252 4.2 69.6 1.0 CA A:CYS249 4.4 56.6 1.0 CB A:MET235 4.5 56.3 1.0 CB A:GLU254 4.6 72.0 1.0 CG A:MET235 4.6 62.5 1.0 CA A:GLY230 4.7 59.5 1.0 C A:CYS252 4.7 70.5 1.0 N A:GLY230 4.8 70.2 1.0 CA A:CYS233 4.8 64.5 1.0 CB A:ARG251 4.8 60.1 1.0 C A:ARG251 4.8 57.4 1.0 N A:ASN253 4.8 62.2 1.0 N A:GLU254 4.8 70.2 1.0 C A:CYS249 4.9 64.2 1.0 N A:ARG251 5.0 40.0 1.0 CA A:CYS228 5.0 49.5 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:74.2 occ:0.85 NE2 A:HIS265 2.0 65.4 1.0 SG A:CYS260 2.3 59.4 1.0 SG A:CYS270 2.3 64.5 1.0 SG A:CYS257 2.3 65.5 1.0 CE1 A:HIS265 2.9 53.6 1.0 CD2 A:HIS265 3.1 45.4 1.0 CB A:CYS257 3.3 52.4 1.0 CB A:CYS270 3.4 66.2 1.0 CB A:CYS260 3.4 71.9 1.0 N A:CYS260 3.6 61.7 1.0 CA A:CYS270 3.9 68.0 1.0 ND1 A:HIS265 4.0 48.2 1.0 CA A:CYS260 4.1 65.0 1.0 CG A:HIS265 4.2 49.1 1.0 CB A:LYS259 4.3 71.5 1.0 CB A:ALA244 4.3 69.2 1.0 N A:CYS270 4.4 71.0 1.0 C A:LYS259 4.6 74.2 1.0 CA A:CYS257 4.7 65.6 1.0 N A:LYS259 4.7 66.2 1.0 O A:HOH708 4.7 57.7 1.0 CA A:LYS259 4.8 68.1 1.0 C A:CYS257 4.9 70.9 1.0 CA A:ALA244 5.0 70.8 1.0 C A:CYS260 5.0 64.8 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:89.2 occ:0.79 SG A:CYS164 2.3 84.5 1.0 SG A:CYS139 2.3 81.7 1.0 SG A:CYS161 2.3 71.6 1.0 SG A:CYS142 2.3 97.5 1.0 CB A:CYS139 3.0 86.5 1.0 CB A:CYS164 3.1 70.1 1.0 CB A:CYS142 3.2 78.8 1.0 CB A:CYS161 3.6 89.3 1.0 N A:CYS142 3.8 99.2 1.0 CG2 A:VAL141 4.0 75.1 1.0 N A:CYS161 4.1 70.3 1.0 CA A:CYS142 4.1 78.9 1.0 N A:CYS164 4.2 67.6 1.0 CA A:CYS164 4.2 85.1 1.0 CA A:CYS161 4.3 68.8 1.0 CA A:CYS139 4.4 87.0 1.0 O A:CYS161 4.6 78.7 1.0 C A:CYS161 4.8 79.3 1.0 C A:VAL141 4.8 101.9 1.0 C A:CYS139 4.9 90.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:74.1 occ:0.79 ND1 A:HIS158 2.0 80.5 1.0 SG A:CYS188 2.3 73.0 1.0 SG A:CYS156 2.3 69.1 1.0 SG A:CYS183 2.3 65.9 1.0 CE1 A:HIS158 2.9 80.2 1.0 CG A:HIS158 3.0 84.6 1.0 CB A:CYS183 3.1 71.4 1.0 CB A:CYS188 3.2 62.3 1.0 CB A:CYS156 3.3 71.1 1.0 CB A:HIS158 3.4 63.5 1.0 NE2 A:HIS158 4.0 74.7 1.0 CD2 A:HIS158 4.0 76.4 1.0 CB A:ALA185 4.4 63.0 1.0 CA A:CYS183 4.5 74.0 1.0 CA A:CYS188 4.6 75.6 1.0 N A:HIS158 4.7 78.5 1.0 CA A:HIS158 4.7 73.2 1.0 CA A:CYS156 4.7 76.6 1.0 CB A:LEU190 4.8 66.5 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:78.1 occ:0.68 SG B:CYS300 2.3 107.4 1.0 SG B:CYS318 2.3 91.8 1.0 SG B:CYS315 2.3 84.9 1.0 SG B:CYS297 2.3 84.9 1.0 CB B:CYS315 3.2 81.6 1.0 CB B:CYS297 3.4 84.9 1.0 CB B:CYS300 3.5 79.2 1.0 O B:CYS300 3.5 110.6 1.0 N B:CYS300 3.7 83.4 1.0 CB B:CYS318 3.7 67.8 1.0 CA B:CYS300 3.9 77.1 1.0 O B:CYS318 4.0 98.1 1.0 N B:CYS318 4.0 98.8 1.0 C B:CYS300 4.1 92.9 1.0 CG1 B:ILE302 4.3 90.5 1.0 CA B:CYS318 4.3 86.2 1.0 C B:CYS318 4.6 96.8 1.0 CB B:LYS299 4.7 84.7 1.0 CA B:CYS315 4.7 87.7 1.0 CA B:CYS297 4.8 83.3 1.0 C B:LYS299 4.8 92.0 1.0 CB B:HIS320 4.8 65.8 1.0 CB B:LYS317 5.0 79.4 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:78.5 occ:0.72 NE2 B:HIS333 2.0 69.3 1.0 SG B:CYS326 2.3 67.2 1.0 SG B:CYS323 2.3 58.7 1.0 SG B:CYS340 2.3 70.5 1.0 CE1 B:HIS333 2.9 64.5 1.0 CD2 B:HIS333 3.0 63.2 1.0 CB B:CYS323 3.1 84.6 1.0 CB B:CYS340 3.2 65.2 1.0 CB B:CYS326 3.6 64.8 1.0 ND1 B:HIS333 4.0 53.6 1.0 N B:CYS326 4.0 64.5 1.0 CG B:HIS333 4.0 67.5 1.0 CA B:CYS340 4.4 61.5 1.0 CA B:CYS326 4.4 75.4 1.0 CA B:CYS323 4.6 58.3 1.0 CB B:MET325 4.7 59.5 1.0 OH B:TYR338 4.8 64.7 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:74.3 occ:1.00 SG B:CYS233 2.3 64.0 1.0 SG B:CYS252 2.3 58.8 1.0 SG B:CYS228 2.3 61.3 1.0 SG B:CYS249 2.3 56.4 1.0 CB B:CYS249 3.0 43.8 1.0 CB B:CYS252 3.4 48.5 1.0 CB B:CYS233 3.4 72.2 1.0 CB B:CYS228 3.6 62.7 1.0 N B:CYS252 3.8 61.2 1.0 CA B:CYS252 4.1 54.1 1.0 CA B:CYS249 4.4 58.0 1.0 CB B:MET235 4.5 45.6 1.0 CB B:GLU254 4.5 68.8 1.0 CG B:MET235 4.5 60.5 1.0 O B:HOH711 4.6 67.6 1.0 C B:CYS252 4.6 57.0 1.0 CA B:CYS233 4.8 75.0 1.0 N B:ASN253 4.8 51.5 1.0 CA B:GLY230 4.8 62.4 1.0 N B:GLU254 4.8 66.6 1.0 N B:GLY230 4.9 62.4 1.0 C B:ARG251 4.9 68.0 1.0 CB B:ARG251 4.9 64.2 1.0 C B:CYS249 4.9 48.8 1.0 CA B:CYS228 4.9 57.5 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Rbr Ubiquitin Ligase ARIH2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Rbr Ubiquitin Ligase ARIH2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:59.8 occ:0.90 NE2 B:HIS265 2.0 56.5 1.0 SG B:CYS260 2.3 64.2 1.0 SG B:CYS270 2.3 61.5 1.0 SG B:CYS257 2.3 56.8 1.0 CE1 B:HIS265 2.8 56.4 1.0 CD2 B:HIS265 3.2 43.1 1.0 CB B:CYS257 3.2 48.2 1.0 CB B:CYS260 3.3 57.0 1.0 CB B:CYS270 3.4 63.1 1.0 N B:CYS260 3.7 49.4 1.0 CA B:CYS270 4.0 58.9 1.0 ND1 B:HIS265 4.0 55.2 1.0 CA B:CYS260 4.1 52.6 1.0 CG B:HIS265 4.2 54.1 1.0 CB B:LYS259 4.5 63.9 1.0 N B:CYS270 4.5 59.2 1.0 CB B:ALA244 4.5 73.6 1.0 CA B:CYS257 4.6 46.5 1.0 C B:LYS259 4.8 68.0 1.0 N B:LYS259 4.9 54.7 1.0 C B:CYS257 4.9 58.3 1.0 C B:CYS260 4.9 58.1 1.0 CA B:LYS259 5.0 62.8 1.0

S.P.Kostrhon, J.R.Prabu, B.A.Schulman. Crystal Structure of ARIH2, A Ring-Ibr-Ring Ubiquitin Ligase To Be Published.
DOI: 10.1038/S41589-021-00858-8