Zinc in PDB 4kc9: 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: 4kc9 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)	36.47 / 3.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	96.126, 96.126, 151.329, 90.00, 90.00, 120.00
R / Rfree (%)	27 / 30.2

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 4kc9). 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 Hhari, A Ring-Ibr-Ring Ubiquitin Ligase: Autoinhibition of An Ariadne-Family E3 and Insights Into Ligation Mechanism, PDB code: 4kc9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 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:99.4 occ:1.00 SG A:CYS347 2.0 0.6 1.0 SG A:CYS367 2.1 99.3 1.0 SG A:CYS362 2.3 0.1 1.0 SG A:CYS344 2.4 0.9 1.0 CB A:CYS362 3.2 97.4 1.0 CB A:CYS344 3.3 74.5 1.0 CB A:CYS347 3.4 1.0 1.0 CB A:CYS367 3.8 1.0 1.0 N A:CYS347 3.8 0.8 1.0 CA A:CYS347 4.1 0.1 1.0 O A:CYS367 4.5 0.8 1.0 O A:ALA369 4.5 67.5 1.0 CA A:CYS362 4.6 91.2 1.0 CB A:LYS346 4.7 0.5 1.0 C A:CYS347 4.7 0.9 1.0 CA A:CYS367 4.7 0.1 1.0 N A:HIS348 4.7 0.4 1.0 CA A:CYS344 4.8 83.6 1.0 CB A:VAL349 4.8 0.5 1.0 O A:CYS362 4.8 92.3 1.0 C A:CYS367 4.8 0.2 1.0 C A:CYS362 4.9 95.0 1.0 C A:LYS346 4.9 0.8 1.0 N A:VAL349 4.9 96.2 1.0 CB A:ASN364 5.0 0.9 1.0 N A:CYS367 5.0 0.2 1.0

Zinc binding site 2 out of 6 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:81.9 occ:1.00 NE2 A:HIS382 2.0 61.2 1.0 SG A:CYS375 2.2 51.7 1.0 SG A:CYS389 2.3 0.2 1.0 SG A:CYS372 2.3 77.8 1.0 CE1 A:HIS382 3.0 40.6 1.0 CB A:CYS372 3.0 57.5 1.0 CD2 A:HIS382 3.1 55.2 1.0 CB A:CYS389 3.7 98.5 1.0 CB A:CYS375 3.7 88.1 1.0 O A:CYS375 4.0 98.7 1.0 N A:CYS375 4.0 83.2 1.0 ND1 A:HIS382 4.1 52.4 1.0 CG A:HIS382 4.2 50.7 1.0 CA A:CYS375 4.3 88.0 1.0 CA A:CYS372 4.5 52.4 1.0 CA A:CYS389 4.6 99.6 1.0 C A:CYS375 4.6 89.9 1.0 OH A:TYR387 4.8 90.0 1.0 C A:CYS372 5.0 44.6 1.0

Zinc binding site 3 out of 6 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:65.0 occ:1.00 SG A:CYS281 2.0 97.6 1.0 SG A:CYS276 2.1 0.2 1.0 SG A:CYS297 2.1 31.5 1.0 SG A:CYS299 2.3 0.3 1.0 CB A:CYS281 2.7 86.8 1.0 CB A:CYS299 2.7 64.5 1.0 CB A:CYS276 3.1 94.9 1.0 CB A:CYS297 3.6 20.4 1.0 CA A:CYS299 3.9 69.4 1.0 CA A:CYS281 4.1 89.3 1.0 CB A:ALA278 4.4 0.4 1.0 CA A:CYS276 4.6 94.5 1.0 N A:CYS299 4.6 68.1 1.0 CB A:HIS283 4.7 41.1 1.0 C A:CYS281 4.8 82.9 1.0 O A:CYS297 4.8 75.2 1.0 CA A:CYS297 4.9 71.5 1.0

Zinc binding site 4 out of 6 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:0.9 occ:1.00 SG A:CYS307 2.0 42.5 1.0 NE2 A:HIS312 2.1 0.5 1.0 SG A:CYS317 2.2 100.0 1.0 SG A:CYS304 2.3 49.9 1.0 CE1 A:HIS312 2.4 0.7 1.0 CB A:CYS304 2.9 92.1 1.0 CB A:CYS307 3.3 98.8 1.0 CD2 A:HIS312 3.4 0.7 1.0 CB A:CYS317 3.6 84.7 1.0 ND1 A:HIS312 3.7 0.8 1.0 N A:CYS307 4.2 0.3 1.0 CA A:CYS317 4.2 84.0 1.0 CG A:HIS312 4.2 0.1 1.0 CA A:CYS307 4.3 97.8 1.0 CA A:CYS304 4.4 82.8 1.0 N A:CYS317 4.6 80.4 1.0 C A:CYS304 4.9 66.0 1.0 O A:CYS304 5.0 43.3 1.0 C A:CYS307 5.0 93.0 1.0

Zinc binding site 5 out of 6 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:90.6 occ:1.00 SG A:CYS211 2.0 30.6 1.0 SG A:CYS208 2.1 54.0 1.0 SG A:CYS189 2.2 0.4 1.0 SG A:CYS186 2.4 47.6 1.0 CB A:CYS208 3.0 66.3 1.0 CB A:CYS186 3.4 82.6 1.0 O A:CYS189 3.5 96.8 1.0 CB A:CYS211 3.5 39.8 1.0 N A:CYS189 3.6 61.9 1.0 CB A:CYS189 3.6 59.6 1.0 N A:CYS208 3.9 68.2 1.0 CA A:CYS189 4.0 68.0 1.0 CA A:CYS208 4.1 62.9 1.0 C A:CYS189 4.2 84.7 1.0 CE2 A:TYR193 4.4 59.2 1.0 OH A:TYR193 4.6 70.7 1.0 CB A:ILE188 4.6 52.2 1.0 CA A:CYS211 4.6 35.0 1.0 C A:ILE188 4.7 53.4 1.0 N A:CYS211 4.7 18.9 1.0 CZ A:TYR193 4.8 64.6 1.0 N A:ILE188 4.8 59.4 1.0 CA A:CYS186 4.9 81.9 1.0 CG2 A:ILE188 4.9 45.5 1.0 CA A:ILE188 4.9 56.7 1.0

Zinc binding site 6 out of 6 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:0.9 occ:1.00 SG A:CYS236 2.0 0.5 1.0 ND1 A:HIS205 2.0 0.6 1.0 SG A:CYS203 2.1 99.9 1.0 SG A:CYS231 2.3 0.9 1.0 CB A:CYS236 2.7 0.6 1.0 CB A:CYS203 2.8 79.1 1.0 CE1 A:HIS205 2.9 0.6 1.0 CG A:HIS205 3.1 0.7 1.0 CB A:CYS231 3.7 94.0 1.0 CB A:HIS205 3.7 94.0 1.0 NE2 A:HIS205 4.1 0.7 1.0 CA A:CYS236 4.1 0.3 1.0 O A:CYS236 4.1 0.3 1.0 CA A:CYS203 4.2 80.8 1.0 CD2 A:HIS205 4.2 0.2 1.0 C A:CYS203 4.4 77.6 1.0 C A:CYS236 4.5 0.2 1.0 O A:CYS203 4.6 88.5 1.0 N A:HIS205 4.6 94.1 1.0 CA A:HIS205 4.8 90.5 1.0 CB A:ALA233 4.9 0.6 1.0 CG2 A:ILE238 4.9 53.3 1.0 CA A:CYS231 5.0 82.6 1.0 N A:GLY204 5.0 67.7 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