Zinc in PDB 8dav: Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)

Enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc)

All present enzymatic activity of Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc):
3.6.4.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Saccharomyces Cerevisiae UFD1/NPL4/CDC48 Complex Bound to Two Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) (pdb code 8dav). 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 Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc), PDB code: 8dav:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8dav

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


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 Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn601

b:95.8
occ:1.00
 NE2 G:HIS139 2.0 63.5 1.0
SG G:CYS148 2.1 56.0 1.0
SG G:CYS137 2.2 78.0 1.0
SG G:CYS145 2.3 58.4 1.0
CD2 G:HIS139 2.8 63.5 1.0
CB G:CYS137 3.1 78.0 1.0
CE1 G:HIS139 3.1 63.5 1.0
N G:CYS145 3.3 58.4 1.0
CB G:CYS145 3.6 58.4 1.0
CB G:CYS148 3.7 56.0 1.0
CA G:CYS137 3.9 78.0 1.0
CG G:HIS139 4.0 63.5 1.0
CA G:CYS145 4.1 58.4 1.0
ND1 G:HIS139 4.1 63.5 1.0
CA G:MET144 4.2 52.2 1.0
C G:MET144 4.2 52.2 1.0
N G:CYS148 4.5 56.0 1.0
N G:GLU146 4.5 63.4 1.0
O G:GLY143 4.6 53.0 1.0
N G:TYR147 4.8 66.8 1.0
CA G:CYS148 4.8 56.0 1.0
N G:CYS137 4.8 78.0 1.0
C G:CYS145 4.8 58.4 1.0
CB G:MET144 4.9 52.2 1.0
C G:TYR147 5.0 66.8 1.0

Zinc binding site 2 out of 2 in 8dav

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


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 Ubiquitin Moieties and One Unfolded Ubiquitin in Presence of Sumo- Ubiquitin(K48POLYUB)-Meos and Atp, State 2 (Uc) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn602

b:89.7
occ:1.00
 NE2 G:HIS208 2.0 73.0 1.0
CE1 G:HIS208 2.1 73.0 1.0
SG G:CYS219 2.3 66.4 1.0
SG G:CYS216 2.3 61.1 1.0
SG G:CYS204 2.3 86.3 1.0
CB G:CYS219 3.0 66.4 1.0
N G:CYS216 3.1 61.1 1.0
CB G:CYS216 3.3 61.1 1.0
ND1 G:HIS208 3.4 73.0 1.0
CD2 G:HIS208 3.4 73.0 1.0
CA G:CYS216 3.7 61.1 1.0
CB G:CYS204 3.7 86.3 1.0
CG G:HIS208 4.0 73.0 1.0
C G:ILE215 4.1 56.1 1.0
CA G:CYS219 4.1 66.4 1.0
N G:CYS219 4.1 66.4 1.0
CA G:ILE215 4.2 56.1 1.0
C G:CYS216 4.4 61.1 1.0
O G:CYS216 4.6 61.1 1.0
O G:GLY207 4.8 84.7 1.0
CB G:ILE215 4.9 56.1 1.0
C G:CYS219 4.9 66.4 1.0
CG G:LYS218 5.0 76.5 1.0
CB G:ASN206 5.0 78.8 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: Sat Apr 8 08:10:19 2023

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