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

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 8daw

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


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

b:144.2
occ:1.00
 NE2 G:HIS139 2.0 88.0 1.0
SG G:CYS148 2.1 80.0 1.0
SG G:CYS137 2.2 98.8 1.0
SG G:CYS145 2.3 77.9 1.0
CD2 G:HIS139 2.8 88.0 1.0
CB G:CYS137 3.1 98.8 1.0
CE1 G:HIS139 3.2 88.0 1.0
N G:CYS145 3.3 77.9 1.0
CB G:CYS145 3.6 77.9 1.0
CB G:CYS148 3.7 80.0 1.0
CA G:CYS137 3.9 98.8 1.0
CG G:HIS139 4.0 88.0 1.0
CA G:CYS145 4.0 77.9 1.0
CA G:MET144 4.1 74.5 1.0
C G:MET144 4.1 74.5 1.0
ND1 G:HIS139 4.1 88.0 1.0
N G:GLU146 4.4 84.9 1.0
N G:CYS148 4.5 80.0 1.0
O G:GLY143 4.7 67.7 1.0
N G:TYR147 4.7 85.1 1.0
CA G:CYS148 4.7 80.0 1.0
C G:CYS145 4.8 77.9 1.0
N G:CYS137 4.8 98.8 1.0
CB G:MET144 4.8 74.5 1.0
C G:TYR147 5.0 85.1 1.0

Zinc binding site 2 out of 2 in 8daw

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


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

b:103.3
occ:1.00
 NE2 G:HIS208 2.0 89.9 1.0
CE1 G:HIS208 2.1 89.9 1.0
SG G:CYS219 2.3 79.1 1.0
SG G:CYS216 2.3 75.8 1.0
SG G:CYS204 2.3 103.5 1.0
CB G:CYS219 2.9 79.1 1.0
N G:CYS216 3.0 75.8 1.0
CB G:CYS216 3.3 75.8 1.0
ND1 G:HIS208 3.4 89.9 1.0
CD2 G:HIS208 3.4 89.9 1.0
CB G:CYS204 3.6 103.5 1.0
CA G:CYS216 3.7 75.8 1.0
C G:ILE215 4.0 70.8 1.0
CG G:HIS208 4.1 89.9 1.0
CA G:CYS219 4.1 79.1 1.0
CA G:ILE215 4.1 70.8 1.0
N G:CYS219 4.1 79.1 1.0
C G:CYS216 4.5 75.8 1.0
O G:CYS216 4.7 75.8 1.0
O G:GLY207 4.8 110.7 1.0
CB G:ILE215 4.8 70.8 1.0
C G:CYS219 4.9 79.1 1.0
CA G:CYS204 5.0 103.5 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: Wed Oct 30 19:08:49 2024

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