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

Protein crystallography data

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

Zinc Binding Sites:

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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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 5jg6

Go back to Zinc Binding Sites List in 5jg6
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

Reference:

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
Page generated: Sun Oct 27 18:55:10 2024

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