Zinc in PDB 5udh: Hhari/ARIH1-UBCH7~Ubiquitin

All present enzymatic activity of Hhari/ARIH1-UBCH7~Ubiquitin:
2.3.2.23;

The structure of Hhari/ARIH1-UBCH7~Ubiquitin, PDB code: 5udh was solved by D.J.Miller, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	141.01 / 3.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.571, 76.788, 147.724, 90.00, 107.33, 90.00
R / Rfree (%)	22.2 / 27.9

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Hhari/ARIH1-UBCH7~Ubiquitin (pdb code 5udh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Hhari/ARIH1-UBCH7~Ubiquitin, PDB code: 5udh:
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 Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.1 occ:1.00 SG A:CYS347 2.3 0.4 1.0 SG A:CYS362 2.3 0.8 1.0 SG A:CYS367 2.4 0.3 1.0 SG A:CYS344 2.4 0.1 1.0 CB A:CYS367 3.3 0.1 1.0 CB A:CYS362 3.4 0.2 1.0 CB A:CYS347 3.4 0.6 1.0 O A:CYS367 3.6 0.8 1.0 CB A:CYS344 3.6 0.2 1.0 N A:CYS347 3.6 0.4 1.0 CA A:CYS347 4.1 0.7 1.0 CB A:LYS346 4.2 90.0 1.0 C A:CYS367 4.3 0.9 1.0 CA A:CYS367 4.4 0.8 1.0 C A:LYS346 4.7 0.8 1.0 CA A:LYS346 4.8 0.3 1.0 CA A:CYS362 4.8 0.7 1.0 N A:LYS346 4.8 0.8 1.0 CB A:ASN364 4.9 0.9 1.0 C A:CYS347 4.9 0.8 1.0 N A:CYS367 5.0 0.2 1.0

Zinc binding site 2 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:0.0 occ:1.00 NE2 A:HIS382 2.1 89.4 1.0 SG A:CYS389 2.3 1.0 1.0 SG A:CYS372 2.3 0.3 1.0 SG A:CYS375 2.4 0.7 1.0 CE1 A:HIS382 2.9 98.5 1.0 CD2 A:HIS382 3.1 0.2 1.0 CB A:CYS372 3.2 0.4 1.0 CB A:CYS389 3.2 0.8 1.0 CB A:CYS375 3.6 0.7 1.0 ND1 A:HIS382 4.1 0.1 1.0 CG A:HIS382 4.2 0.1 1.0 N A:CYS375 4.3 0.4 1.0 CA A:CYS375 4.6 0.2 1.0 CA A:CYS389 4.6 0.2 1.0 CA A:CYS372 4.6 0.2 1.0 OH A:TYR387 4.8 0.3 1.0

Zinc binding site 3 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:98.0 occ:1.00 SG A:CYS297 2.3 77.9 1.0 SG A:CYS276 2.3 76.7 1.0 SG A:CYS281 2.3 93.7 1.0 SG A:CYS299 2.3 0.7 1.0 CB A:CYS281 3.0 0.6 1.0 CB A:CYS297 3.2 88.3 1.0 CB A:CYS299 3.2 0.1 1.0 CB A:CYS276 3.2 86.4 1.0 CB A:ALA278 4.0 0.1 1.0 N A:CYS299 4.1 0.7 1.0 CA A:CYS299 4.2 0.2 1.0 CA A:CYS281 4.5 0.9 1.0 CB A:ARG301 4.5 91.7 1.0 CA A:CYS297 4.6 87.3 1.0 CA A:CYS276 4.7 81.5 1.0 C A:CYS297 4.9 96.0 1.0 C A:CYS281 5.0 0.9 1.0 CB A:HIS283 5.0 97.6 1.0 C A:CYS299 5.0 97.5 1.0

Zinc binding site 4 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:95.0 occ:1.00 NE2 A:HIS312 2.0 85.4 1.0 SG A:CYS317 2.3 83.2 1.0 SG A:CYS304 2.3 75.4 1.0 SG A:CYS307 2.3 87.0 1.0 CE1 A:HIS312 2.9 89.9 1.0 CD2 A:HIS312 3.1 75.5 1.0 CB A:CYS304 3.2 74.5 1.0 CB A:CYS317 3.3 86.5 1.0 CB A:CYS307 3.3 88.6 1.0 CA A:CYS317 3.8 90.5 1.0 ND1 A:HIS312 4.1 88.3 1.0 CG A:HIS312 4.2 76.9 1.0 N A:CYS307 4.2 85.6 1.0 CA A:CYS307 4.4 83.8 1.0 N A:CYS317 4.5 90.4 1.0 CA A:CYS304 4.6 71.5 1.0

Zinc binding site 5 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:96.7 occ:1.00 SG A:CYS208 2.3 93.2 1.0 SG A:CYS186 2.3 98.7 1.0 SG A:CYS189 2.3 87.6 1.0 SG A:CYS211 2.3 81.0 1.0 CB A:CYS186 3.1 0.3 1.0 CB A:CYS189 3.3 91.0 1.0 CB A:CYS211 3.4 77.4 1.0 N A:CYS189 3.4 93.1 1.0 CB A:CYS208 3.4 94.2 1.0 CA A:CYS189 3.9 89.1 1.0 N A:CYS208 4.1 85.3 1.0 CA A:CYS208 4.3 90.6 1.0 CB A:ILE188 4.4 75.5 1.0 C A:ILE188 4.4 85.8 1.0 CA A:CYS211 4.5 79.2 1.0 N A:CYS211 4.5 84.7 1.0 CA A:CYS186 4.5 0.4 1.0 N A:ILE188 4.6 83.4 1.0 O A:CYS208 4.7 86.7 1.0 CA A:ILE188 4.7 78.8 1.0 C A:CYS189 4.8 83.4 1.0 C A:CYS186 4.8 0.8 1.0 N A:TYR190 4.8 85.4 1.0 O A:CYS186 4.9 0.9 1.0 C A:CYS208 4.9 87.8 1.0 CG2 A:ILE188 4.9 71.4 1.0

Zinc binding site 6 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:92.5 occ:1.00 ND1 A:HIS205 2.0 95.5 1.0 SG A:CYS203 2.3 81.6 1.0 SG A:CYS236 2.3 0.6 1.0 SG A:CYS231 2.3 91.9 1.0 CE1 A:HIS205 3.0 95.2 1.0 CG A:HIS205 3.1 95.3 1.0 CB A:CYS203 3.1 88.0 1.0 CB A:CYS231 3.4 85.5 1.0 CB A:HIS205 3.4 97.8 1.0 CB A:CYS236 3.5 0.0 1.0 CB A:ALA233 3.7 87.8 1.0 NE2 A:HIS205 4.1 93.7 1.0 CD2 A:HIS205 4.2 93.0 1.0 CA A:CYS203 4.6 89.7 1.0 N A:HIS205 4.7 91.3 1.0 CA A:HIS205 4.7 93.7 1.0 CA A:CYS236 4.8 0.7 1.0 N A:ALA233 4.9 75.4 1.0 CA A:CYS231 4.9 78.3 1.0 CA A:ALA233 4.9 85.0 1.0 CG1 A:ILE238 5.0 0.5 1.0

Zinc binding site 7 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.7 occ:1.00 SG B:CYS347 2.3 0.9 1.0 SG B:CYS344 2.3 0.5 1.0 SG B:CYS362 2.4 0.7 1.0 SG B:CYS367 2.4 0.5 1.0 CB B:CYS362 3.3 0.0 1.0 CB B:CYS347 3.3 0.2 1.0 CB B:CYS344 3.4 0.7 1.0 CB B:CYS367 3.5 0.7 1.0 N B:CYS347 3.5 0.2 1.0 O B:CYS367 3.9 0.5 1.0 CA B:CYS347 4.0 0.9 1.0 CB B:LYS346 4.1 0.7 1.0 C B:LYS346 4.5 0.5 1.0 C B:CYS367 4.6 0.9 1.0 ND2 B:ASN364 4.6 0.2 1.0 CA B:CYS367 4.7 0.0 1.0 N B:HIS348 4.7 0.0 1.0 C B:CYS347 4.7 0.2 1.0 CA B:LYS346 4.7 0.2 1.0 CA B:CYS362 4.8 0.4 1.0 N B:LYS346 4.8 0.1 1.0 CA B:CYS344 4.9 0.2 1.0

Zinc binding site 8 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:0.7 occ:1.00 NE2 B:HIS382 2.2 0.5 1.0 SG B:CYS389 2.3 0.6 1.0 SG B:CYS372 2.3 0.4 1.0 SG B:CYS375 2.4 0.2 1.0 CE1 B:HIS382 3.1 0.9 1.0 CD2 B:HIS382 3.2 0.7 1.0 CB B:CYS372 3.2 0.6 1.0 CB B:CYS389 3.3 0.1 1.0 CB B:CYS375 3.6 0.9 1.0 ND1 B:HIS382 4.2 0.8 1.0 N B:CYS375 4.2 0.1 1.0 CG B:HIS382 4.3 0.8 1.0 CA B:CYS375 4.5 0.6 1.0 CA B:CYS389 4.6 0.3 1.0 CA B:CYS372 4.6 0.1 1.0 CB B:VAL374 4.9 0.1 1.0

Zinc binding site 9 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:0.1 occ:1.00 SG B:CYS281 2.3 0.4 1.0 SG B:CYS297 2.3 0.1 1.0 SG B:CYS299 2.3 0.5 1.0 SG B:CYS276 2.4 0.5 1.0 CB B:CYS281 3.2 1.0 1.0 CB B:CYS276 3.2 0.2 1.0 CB B:CYS297 3.3 0.8 1.0 CB B:CYS299 3.4 0.4 1.0 CB B:ALA278 3.8 0.8 1.0 ND1 B:HIS283 4.5 0.9 1.0 CB B:ARG301 4.5 0.9 1.0 CB B:HIS283 4.6 0.8 1.0 CA B:CYS299 4.6 0.0 1.0 CA B:CYS281 4.6 0.8 1.0 N B:CYS299 4.6 0.7 1.0 CA B:CYS276 4.7 0.3 1.0 CA B:CYS297 4.7 0.7 1.0 CG B:HIS283 5.0 0.5 1.0 CA B:ALA278 5.0 0.1 1.0

Zinc binding site 10 out of 12 in the Hhari/ARIH1-UBCH7~Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Hhari/ARIH1-UBCH7~Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:0.6 occ:1.00 NE2 B:HIS312 2.1 0.7 1.0 SG B:CYS307 2.3 0.4 1.0 SG B:CYS317 2.3 0.4 1.0 SG B:CYS304 2.3 0.9 1.0 CE1 B:HIS312 3.1 0.0 1.0 CD2 B:HIS312 3.2 0.8 1.0 CB B:CYS304 3.2 0.5 1.0 CB B:CYS307 3.3 0.2 1.0 CB B:CYS317 3.3 0.3 1.0 CA B:CYS317 3.7 0.8 1.0 N B:CYS307 4.2 0.1 1.0 ND1 B:HIS312 4.2 0.2 1.0 CG B:HIS312 4.3 1.0 1.0 CA B:CYS307 4.3 0.2 1.0 N B:CYS317 4.4 0.9 1.0 CA B:CYS304 4.6 0.5 1.0 C B:CYS317 4.8 0.4 1.0 N B:GLY308 4.9 0.9 1.0

K.K.Dove, J.L.Olszewski, L.Martino, D.M.Duda, X.S.Wu, D.J.Miller, K.H.Reiter, K.Rittinger, B.A.Schulman, R.E.Klevit. Structural Studies of Hhari/UBCH7UB Reveal Unique E2UB Conformational Restriction By Rbr RING1. Structure V. 25 890 2017.
ISSN: ISSN 1878-4186
PubMed: 28552575
DOI: 10.1016/J.STR.2017.04.013