Zinc in PDB 4kbl: Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism

The structure of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism, PDB code: 4kbl was solved by D.M.Duda, J.L.Olszewski, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 3.30
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	147.403, 147.403, 86.821, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.3

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism (pdb code 4kbl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism, PDB code: 4kbl:
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 Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.5 occ:1.00 SG A:CYS367 2.2 0.5 1.0 SG A:CYS347 2.2 0.8 1.0 SG A:CYS344 2.2 0.4 1.0 SG A:CYS362 2.2 0.9 1.0 CB A:CYS362 3.1 0.1 1.0 CB A:CYS344 3.4 0.8 1.0 CB A:CYS347 3.4 0.5 1.0 O A:CYS367 3.7 0.1 1.0 CB A:CYS367 3.7 1.0 1.0 N A:CYS347 3.8 0.3 1.0 CA A:CYS347 4.2 0.0 1.0 ND2 A:ASN364 4.4 0.6 1.0 C A:CYS367 4.4 0.1 1.0 CA A:CYS362 4.6 0.0 1.0 CA A:CYS367 4.6 0.2 1.0 CB A:ASN364 4.7 0.5 1.0 CA A:CYS344 4.7 0.2 1.0 C A:CYS347 4.9 0.7 1.0 CB A:VAL349 4.9 0.3 1.0 C A:LYS346 4.9 0.7 1.0 CB A:LYS346 4.9 0.3 1.0 C A:CYS344 5.0 0.6 1.0 CG A:ASN364 5.0 0.1 1.0 C A:CYS362 5.0 0.7 1.0

Zinc binding site 2 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:0.2 occ:1.00 NE2 A:HIS382 2.0 0.7 1.0 SG A:CYS389 2.2 0.8 1.0 SG A:CYS375 2.2 0.7 1.0 SG A:CYS372 2.2 0.4 1.0 CE1 A:HIS382 2.8 0.4 1.0 CB A:CYS389 2.9 0.7 1.0 CB A:CYS372 3.1 0.8 1.0 CD2 A:HIS382 3.1 0.5 1.0 CB A:CYS375 3.5 0.1 1.0 N A:CYS375 3.8 0.7 1.0 ND1 A:HIS382 4.0 0.2 1.0 CG A:HIS382 4.2 0.9 1.0 CA A:CYS375 4.2 0.8 1.0 CA A:CYS389 4.3 0.7 1.0 CA A:CYS372 4.6 0.8 1.0 OH A:TYR387 4.6 0.7 1.0 CB A:VAL374 4.8 1.0 1.0 C A:VAL374 4.9 0.8 1.0

Zinc binding site 3 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:0.9 occ:1.00 SG A:CYS297 2.1 99.5 1.0 SG A:CYS299 2.2 0.0 1.0 SG A:CYS281 2.2 1.0 1.0 SG A:CYS276 2.2 0.1 1.0 CB A:CYS299 2.5 0.9 1.0 CB A:CYS281 3.0 0.2 1.0 CB A:CYS276 3.2 0.6 1.0 CB A:CYS297 3.5 99.0 1.0 CA A:CYS299 3.7 0.0 1.0 CB A:ALA278 4.4 0.2 1.0 CA A:CYS281 4.5 0.7 1.0 N A:CYS299 4.5 0.5 1.0 CB A:HIS283 4.6 0.3 1.0 CA A:CYS276 4.6 0.9 1.0 O A:CYS297 4.7 0.0 1.0 C A:CYS299 4.7 0.0 1.0 CA A:CYS297 4.8 0.0 1.0 C A:CYS281 4.9 0.6 1.0 C A:CYS276 4.9 0.5 1.0 O A:CYS299 4.9 1.0 1.0 C A:CYS297 5.0 0.5 1.0 CB A:ARG301 5.0 0.3 1.0

Zinc binding site 4 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:0.6 occ:1.00 NE2 A:HIS312 2.0 0.6 1.0 SG A:CYS304 2.2 0.0 1.0 SG A:CYS317 2.2 0.2 1.0 SG A:CYS307 2.2 0.4 1.0 CE1 A:HIS312 2.7 0.7 1.0 CB A:CYS304 3.0 0.1 1.0 CD2 A:HIS312 3.3 0.3 1.0 CB A:CYS307 3.5 0.1 1.0 CB A:CYS317 3.6 0.7 1.0 N A:CYS307 3.8 0.6 1.0 ND1 A:HIS312 3.9 0.9 1.0 CA A:CYS317 4.2 0.6 1.0 CA A:CYS307 4.2 0.5 1.0 CG A:HIS312 4.2 0.9 1.0 CA A:CYS304 4.5 0.2 1.0 CB A:ASN306 4.6 0.8 1.0 C A:ASN306 4.9 0.3 1.0 CB A:ALA292 4.9 0.9 1.0 C A:CYS307 4.9 0.4 1.0 N A:CYS317 5.0 0.8 1.0

Zinc binding site 5 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:0.8 occ:1.00 SG A:CYS211 2.1 0.5 1.0 SG A:CYS208 2.2 0.1 1.0 SG A:CYS189 2.2 0.6 1.0 SG A:CYS186 2.3 0.9 1.0 CB A:CYS211 2.9 0.1 1.0 CB A:CYS189 3.3 0.7 1.0 CB A:CYS186 3.4 0.1 1.0 N A:CYS189 3.5 0.7 1.0 CB A:CYS208 3.6 0.4 1.0 CA A:CYS189 4.0 0.8 1.0 CA A:CYS211 4.2 0.6 1.0 N A:CYS208 4.3 0.6 1.0 CA A:CYS208 4.4 0.9 1.0 N A:CYS211 4.5 0.3 1.0 CB A:ILE188 4.5 0.8 1.0 CE2 A:TYR193 4.6 0.1 1.0 C A:ILE188 4.6 0.1 1.0 O A:CYS208 4.7 0.2 1.0 CA A:CYS186 4.8 0.5 1.0 N A:TYR190 4.8 1.0 1.0 CA A:ILE188 4.9 0.3 1.0 N A:ILE188 4.9 0.0 1.0 C A:CYS208 4.9 0.7 1.0 C A:CYS189 4.9 0.2 1.0

Zinc binding site 6 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:0.8 occ:1.00 ND1 A:HIS205 1.9 0.9 1.0 SG A:CYS203 2.1 0.6 1.0 SG A:CYS236 2.2 0.7 1.0 SG A:CYS231 2.3 0.4 1.0 CE1 A:HIS205 2.6 0.9 1.0 CG A:HIS205 2.9 1.0 1.0 CB A:CYS231 3.3 0.9 1.0 CB A:CYS203 3.4 0.4 1.0 CB A:HIS205 3.5 0.1 1.0 NE2 A:HIS205 3.6 0.6 1.0 CB A:CYS236 3.7 0.4 1.0 CD2 A:HIS205 3.8 0.0 1.0 CB A:ALA233 4.5 0.4 1.0 CG2 A:ILE238 4.6 0.3 1.0 CA A:CYS203 4.7 0.7 1.0 N A:HIS205 4.7 0.7 1.0 CA A:CYS231 4.7 0.1 1.0 CA A:HIS205 4.8 0.5 1.0 C A:CYS203 4.9 0.6 1.0 O A:CYS203 4.9 1.0 1.0 CA A:CYS236 4.9 0.5 1.0

Zinc binding site 7 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.3 occ:1.00 SG B:CYS367 2.1 0.3 1.0 SG B:CYS347 2.2 0.9 1.0 SG B:CYS362 2.3 0.3 1.0 SG B:CYS344 2.3 0.7 1.0 CB B:CYS347 2.7 0.6 1.0 CB B:CYS362 3.3 0.3 1.0 CB B:CYS344 3.4 0.0 1.0 N B:CYS347 3.6 0.2 1.0 CA B:CYS347 3.6 0.6 1.0 O B:CYS367 3.7 0.3 1.0 CB B:CYS367 3.8 0.3 1.0 C B:CYS347 4.2 0.7 1.0 C B:CYS367 4.4 0.2 1.0 CB B:ASN364 4.4 0.8 1.0 N B:HIS348 4.5 0.6 1.0 ND2 B:ASN364 4.6 0.2 1.0 CA B:CYS367 4.7 0.2 1.0 CA B:CYS362 4.7 0.0 1.0 O B:CYS347 4.8 0.7 1.0 C B:LYS346 4.9 0.5 1.0 CA B:CYS344 4.9 0.2 1.0 N B:VAL349 4.9 0.4 1.0 CG B:ASN364 5.0 0.8 1.0

Zinc binding site 8 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:0.5 occ:1.00 NE2 B:HIS382 2.0 0.8 1.0 SG B:CYS389 2.1 0.9 1.0 SG B:CYS372 2.2 97.8 1.0 SG B:CYS375 2.3 0.1 1.0 CE1 B:HIS382 2.8 0.8 1.0 CD2 B:HIS382 3.1 0.8 1.0 CB B:CYS372 3.1 98.0 1.0 CB B:CYS389 3.2 0.8 1.0 CB B:CYS375 3.6 0.9 1.0 N B:CYS375 3.8 0.4 1.0 ND1 B:HIS382 4.0 0.4 1.0 CG B:HIS382 4.1 0.5 1.0 CA B:CYS375 4.2 0.5 1.0 CA B:CYS389 4.4 0.6 1.0 O B:CYS375 4.5 0.9 1.0 CA B:CYS372 4.5 97.8 1.0 C B:CYS375 4.6 0.7 1.0 OH B:TYR387 4.7 0.9 1.0 C B:VAL374 4.9 0.2 1.0 CB B:VAL374 4.9 0.1 1.0 C B:CYS372 4.9 97.8 1.0

Zinc binding site 9 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:0.6 occ:1.00 SG B:CYS297 2.1 99.1 1.0 SG B:CYS281 2.1 0.9 1.0 SG B:CYS299 2.2 0.9 1.0 SG B:CYS276 2.2 0.5 1.0 CB B:CYS299 2.7 0.0 1.0 CB B:CYS281 3.0 0.3 1.0 CB B:CYS276 3.2 0.2 1.0 CB B:CYS297 3.5 98.9 1.0 CA B:CYS299 3.7 0.8 1.0 CB B:ALA278 4.3 0.7 1.0 N B:CYS299 4.4 0.9 1.0 CA B:CYS281 4.4 0.7 1.0 CA B:CYS276 4.6 0.3 1.0 O B:CYS297 4.7 0.9 1.0 CB B:HIS283 4.7 0.3 1.0 CA B:CYS297 4.8 0.5 1.0 C B:CYS297 4.9 0.9 1.0 C B:CYS281 4.9 0.4 1.0 C B:CYS299 4.9 0.9 1.0 C B:CYS276 5.0 0.2 1.0

Zinc binding site 10 out of 12 in the Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:0.2 occ:1.00 NE2 B:HIS312 2.1 0.7 1.0 SG B:CYS304 2.2 0.4 1.0 SG B:CYS317 2.2 0.4 1.0 SG B:CYS307 2.2 0.4 1.0 CE1 B:HIS312 2.6 0.7 1.0 CB B:CYS304 3.0 0.9 1.0 CD2 B:HIS312 3.4 0.7 1.0 CB B:CYS317 3.6 0.2 1.0 CB B:CYS307 3.7 0.7 1.0 ND1 B:HIS312 3.8 0.5 1.0 N B:CYS307 3.9 0.8 1.0 CA B:CYS317 4.2 0.7 1.0 CG B:HIS312 4.2 0.3 1.0 CA B:CYS307 4.3 0.8 1.0 CA B:CYS304 4.5 0.9 1.0 CB B:ASN306 4.6 0.5 1.0 CB B:ALA292 4.6 0.6 1.0 C B:ASN306 4.8 0.6 1.0 C B:CYS307 4.9 0.4 1.0 O B:CYS307 4.9 0.1 1.0 C B:CYS304 4.9 0.9 1.0 CA B:ASN306 5.0 1.0 1.0

D.M.Duda, J.L.Olszewski, J.P.Schuermann, I.Kurinov, D.J.Miller, A.Nourse, A.F.Alpi, B.A.Schulman. Structure of Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism. Structure V. 21 1030 2013.
ISSN: ISSN 0969-2126
PubMed: 23707686
DOI: 10.1016/J.STR.2013.04.019