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Zinc in PDB 8dau: Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua)

Enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua)

All present enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua):
3.6.4.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua) (pdb code 8dau). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua), PDB code: 8dau:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8dau

Go back to Zinc Binding Sites List in 8dau
Zinc binding site 1 out of 2 in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn601

b:131.8
occ:1.00
 NE2 G:HIS139 2.0 96.6 1.0
SG G:CYS148 2.2 87.8 1.0
SG G:CYS137 2.2 108.4 1.0
SG G:CYS145 2.4 88.1 1.0
CD2 G:HIS139 2.7 96.6 1.0
CB G:CYS137 3.1 108.4 1.0
CE1 G:HIS139 3.2 96.6 1.0
N G:CYS145 3.4 88.1 1.0
CB G:CYS145 3.7 88.1 1.0
CB G:CYS148 3.8 87.8 1.0
CA G:CYS137 3.9 108.4 1.0
CG G:HIS139 4.0 96.6 1.0
CA G:CYS145 4.1 88.1 1.0
ND1 G:HIS139 4.1 96.6 1.0
CA G:MET144 4.1 84.6 1.0
C G:MET144 4.2 84.6 1.0
N G:GLU146 4.5 94.4 1.0
N G:CYS148 4.5 87.8 1.0
O G:GLY143 4.6 85.1 1.0
N G:TYR147 4.7 95.4 1.0
CA G:CYS148 4.8 87.8 1.0
C G:CYS145 4.8 88.1 1.0
N G:CYS137 4.9 108.4 1.0
CB G:MET144 4.9 84.6 1.0
C G:TYR147 4.9 95.4 1.0
C G:CYS137 5.0 108.4 1.0

Zinc binding site 2 out of 2 in 8dau

Go back to Zinc Binding Sites List in 8dau
Zinc binding site 2 out of 2 in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Folded Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 1 (Ua) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn602

b:105.0
occ:1.00
 NE2 G:HIS208 2.1 96.2 1.0
CE1 G:HIS208 2.1 96.2 1.0
SG G:CYS216 2.3 87.5 1.0
SG G:CYS219 2.3 91.0 1.0
SG G:CYS204 2.3 102.0 1.0
CB G:CYS219 2.9 91.0 1.0
N G:CYS216 2.9 87.5 1.0
CB G:CYS216 3.2 87.5 1.0
ND1 G:HIS208 3.4 96.2 1.0
CD2 G:HIS208 3.4 96.2 1.0
CB G:CYS204 3.5 102.0 1.0
CA G:CYS216 3.6 87.5 1.0
C G:ILE215 4.0 84.9 1.0
CG G:HIS208 4.1 96.2 1.0
CA G:ILE215 4.1 84.9 1.0
CA G:CYS219 4.1 91.0 1.0
N G:CYS219 4.2 91.0 1.0
O G:CYS216 4.3 87.5 1.0
C G:CYS216 4.3 87.5 1.0
CB G:ILE215 4.8 84.9 1.0
O G:GLY207 4.8 107.3 1.0
CA G:CYS204 4.9 102.0 1.0
C G:CYS219 4.9 91.0 1.0

Reference:

H.G.Lee, A.A.Lemmon, C.D.Lima. UFD1 Interactions with Sumo Enhance Unfolding of Sumo-Polyubiquitin-Conjugated Substrates By the UFD1/NPL4/CDC48 Complex To Be Published.
Page generated: Fri Aug 22 09:10:59 2025

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