Zinc in PDB 5jg6: APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C

The structure of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C, PDB code: 5jg6 was solved by N.G.Brown, W.Zhang, S.Yu, D.J.Miller, S.S.Sidhu, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.33 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.066, 35.193, 72.768, 90.00, 120.42, 90.00
R / Rfree (%)	18.5 / 22

The binding sites of Zinc atom in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C (pdb code 5jg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C, PDB code: 5jg6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:23.6 occ:1.00 ND1 A:HIS56 2.0 20.8 1.0 SG A:CYS59 2.2 24.9 1.0 SG A:CYS23 2.3 21.2 1.0 SG A:CYS26 2.4 25.7 1.0 CB A:CYS23 2.9 35.1 1.0 CE1 A:HIS56 3.0 23.2 1.0 CG A:HIS56 3.1 17.2 1.0 CB A:CYS26 3.2 23.5 1.0 CB A:CYS59 3.4 18.1 1.0 CB A:HIS56 3.4 16.5 1.0 N A:CYS26 3.7 28.3 1.0 N A:HIS56 4.0 17.7 1.0 CA A:CYS26 4.1 26.3 1.0 NE2 A:HIS56 4.1 24.3 1.0 CD2 A:HIS56 4.2 17.3 1.0 CB A:CYS34 4.3 22.3 1.0 CA A:HIS56 4.3 17.4 1.0 CA A:CYS23 4.4 36.7 1.0 CB A:ILE25 4.7 25.1 1.0 CA A:CYS34 4.7 25.6 1.0 CD A:PRO35 4.7 42.0 1.0 CA A:CYS59 4.7 19.8 1.0 C A:ILE25 4.8 34.4 1.0 C A:CYS23 4.8 35.6 1.0 C A:CYS26 4.9 28.0 1.0 O A:CYS23 4.9 28.5 1.0 O A:HIS56 5.0 17.4 1.0

Zinc binding site 2 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:29.4 occ:1.00 ND1 A:HIS58 2.0 23.4 1.0 SG A:CYS44 2.3 26.3 1.0 SG A:CYS34 2.3 27.8 1.0 SG A:CYS37 2.4 34.5 1.0 CE1 A:HIS58 2.9 23.9 1.0 CG A:HIS58 3.1 21.8 1.0 CB A:CYS44 3.3 24.1 1.0 CB A:CYS34 3.3 22.3 1.0 CB A:CYS37 3.4 38.7 1.0 CB A:HIS58 3.6 20.6 1.0 N A:CYS34 3.7 30.0 1.0 O A:HOH211 3.9 18.6 1.0 CA A:CYS44 4.0 33.2 1.0 CA A:CYS34 4.0 25.6 1.0 NE2 A:HIS58 4.0 19.8 1.0 N A:CYS37 4.1 40.9 1.0 CD2 A:HIS58 4.2 20.6 1.0 CA A:CYS37 4.3 43.4 1.0 C A:CYS34 4.6 37.0 1.0 O A:CYS34 4.6 35.5 1.0 C A:CYS33 4.9 32.6 1.0 O A:ASP43 4.9 43.1 1.0 O A:HOH212 5.0 34.1 1.0 CA A:HIS58 5.0 22.0 1.0

Zinc binding site 3 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:24.2 occ:1.00 ND1 A:HIS53 2.0 30.6 1.0 SG A:CYS51 2.3 22.8 1.0 SG A:CYS76 2.3 23.3 1.0 SG A:CYS73 2.4 20.3 1.0 CE1 A:HIS53 2.9 37.4 1.0 CG A:HIS53 3.0 33.1 1.0 CB A:CYS73 3.0 16.4 1.0 CB A:CYS51 3.2 26.0 1.0 CB A:CYS76 3.4 20.9 1.0 CB A:HIS53 3.4 25.6 1.0 N A:CYS76 3.8 28.5 1.0 NE2 A:HIS53 4.0 41.7 1.0 CD2 A:HIS53 4.1 40.8 1.0 CA A:CYS76 4.2 27.8 1.0 O A:CYS51 4.4 26.7 1.0 CB A:MET75 4.4 31.4 1.0 N A:HIS53 4.4 24.7 1.0 CA A:CYS51 4.5 26.9 1.0 CA A:CYS73 4.5 22.0 1.0 C A:CYS51 4.6 27.4 1.0 CA A:HIS53 4.6 23.2 1.0 C A:MET75 4.9 34.8 1.0 C A:CYS76 4.9 29.4 1.0 CZ3 A:TRP80 5.0 18.8 1.0

Zinc binding site 4 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:17.6 occ:1.00 ND1 D:HIS56 2.1 14.8 1.0 SG D:CYS59 2.3 19.4 1.0 SG D:CYS26 2.3 17.9 1.0 SG D:CYS23 2.4 19.4 1.0 CB D:CYS23 2.9 16.8 1.0 CE1 D:HIS56 3.1 15.3 1.0 CG D:HIS56 3.2 15.5 1.0 CB D:CYS26 3.2 19.5 1.0 CB D:CYS59 3.3 15.0 1.0 CB D:HIS56 3.5 16.9 1.0 N D:CYS26 3.7 18.1 1.0 N D:HIS56 4.1 15.8 1.0 CA D:CYS26 4.1 15.9 1.0 NE2 D:HIS56 4.2 17.9 1.0 CD2 D:HIS56 4.3 15.4 1.0 CB D:CYS34 4.3 15.4 1.0 CA D:HIS56 4.4 13.6 1.0 CA D:CYS23 4.4 16.5 1.0 CA D:CYS59 4.7 13.5 1.0 CB D:ILE25 4.7 24.8 1.0 CA D:CYS34 4.8 16.2 1.0 C D:ILE25 4.8 22.6 1.0 C D:CYS26 4.9 21.6 1.0 C D:CYS23 4.9 21.5 1.0 CD D:PRO35 4.9 23.6 1.0 O D:HIS56 5.0 13.9 1.0

Zinc binding site 5 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:23.1 occ:1.00 ND1 D:HIS53 2.0 26.8 1.0 SG D:CYS73 2.3 20.4 1.0 SG D:CYS76 2.3 24.9 1.0 SG D:CYS51 2.3 19.5 1.0 CE1 D:HIS53 2.9 36.4 1.0 CB D:CYS73 2.9 17.3 1.0 CG D:HIS53 3.1 21.1 1.0 CB D:CYS51 3.2 20.9 1.0 CB D:CYS76 3.5 30.6 1.0 CB D:HIS53 3.6 13.4 1.0 N D:CYS76 3.8 30.6 1.0 NE2 D:HIS53 4.0 40.5 1.0 CD2 D:HIS53 4.1 32.8 1.0 CA D:CYS76 4.2 29.1 1.0 O D:CYS51 4.4 33.3 1.0 CA D:CYS73 4.4 15.0 1.0 CA D:CYS51 4.5 25.6 1.0 N D:HIS53 4.5 16.7 1.0 C D:CYS51 4.6 27.5 1.0 CB D:MET75 4.6 31.6 1.0 CA D:HIS53 4.7 18.3 1.0 C D:CYS76 4.8 25.6 1.0 N D:ARG77 4.8 20.6 1.0 C D:MET75 4.9 34.0 1.0 OE1 D:GLN78 4.9 48.2 1.0 CZ3 D:TRP80 5.0 19.0 1.0 N D:MET75 5.0 23.6 1.0 C D:CYS73 5.0 20.8 1.0

Zinc binding site 6 out of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:21.4 occ:1.00 ND1 D:HIS58 2.0 19.8 1.0 SG D:CYS34 2.3 20.1 1.0 SG D:CYS37 2.3 23.7 1.0 SG D:CYS44 2.3 19.9 1.0 CE1 D:HIS58 2.9 20.4 1.0 CG D:HIS58 3.2 22.1 1.0 CB D:CYS34 3.3 15.4 1.0 CB D:CYS44 3.3 15.6 1.0 CB D:CYS37 3.3 27.1 1.0 CB D:HIS58 3.6 13.7 1.0 N D:CYS34 3.9 16.5 1.0 O D:HOH218 3.9 43.4 1.0 O D:HOH212 3.9 20.2 1.0 NE2 D:HIS58 4.1 22.5 1.0 N D:CYS37 4.1 24.7 1.0 CA D:CYS44 4.1 20.8 1.0 CA D:CYS34 4.1 16.2 1.0 CD2 D:HIS58 4.2 24.1 1.0 CA D:CYS37 4.3 30.9 1.0 C D:CYS34 4.6 24.0 1.0 O D:CYS34 4.6 20.3 1.0 O D:ASP43 4.9 21.9 1.0 C D:ASP36 5.0 32.1 1.0 CA D:HIS58 5.0 16.8 1.0

N.G.Brown, R.Vanderlinden, E.R.Watson, F.Weissmann, A.Ordureau, K.P.Wu, W.Zhang, S.Yu, P.Y.Mercredi, J.S.Harrison, I.F.Davidson, R.Qiao, Y.Lu, P.Dube, M.R.Brunner, C.R.Grace, D.J.Miller, D.Haselbach, M.A.Jarvis, M.Yamaguchi, D.Yanishevski, G.Petzold, S.S.Sidhu, B.Kuhlman, M.W.Kirschner, J.W.Harper, J.M.Peters, H.Stark, B.A.Schulman. Dual Ring E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation By Apc/C. Cell V. 165 1440 2016.
ISSN: ISSN 1097-4172
PubMed: 27259151
DOI: 10.1016/J.CELL.2016.05.037