Zinc in PDB 6jwi: Yeast NPL4 in Complex with LYS48-Linked Diubiquitin

The structure of Yeast NPL4 in Complex with LYS48-Linked Diubiquitin, PDB code: 6jwi was solved by Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.351, 103.103, 99.620, 90.00, 100.40, 90.00
R / Rfree (%)	19.1 / 22.6

The binding sites of Zinc atom in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin (pdb code 6jwi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin, PDB code: 6jwi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast NPL4 in Complex with LYS48-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:45.6 occ:1.00 NE2 A:HIS139 2.0 37.8 1.0 SG A:CYS148 2.3 38.5 1.0 SG A:CYS145 2.3 51.8 1.0 SG A:CYS137 2.4 40.3 1.0 CE1 A:HIS139 2.7 37.5 1.0 CD2 A:HIS139 3.2 47.4 1.0 CB A:CYS137 3.3 37.6 1.0 CB A:CYS148 3.3 40.9 1.0 CB A:CYS145 3.3 44.6 1.0 N A:CYS145 3.5 39.1 1.0 CA A:CYS145 3.9 39.2 1.0 ND1 A:HIS139 3.9 38.6 1.0 N A:CYS148 3.9 36.1 1.0 CA A:CYS137 4.0 50.8 1.0 C A:MET144 4.1 42.8 1.0 CG A:HIS139 4.2 39.6 1.0 CA A:CYS148 4.2 37.4 1.0 C A:CYS145 4.4 39.8 1.0 O A:CYS145 4.6 43.1 1.0 CA A:MET144 4.6 42.1 1.0 O A:MET144 4.7 44.9 1.0 C A:TYR147 4.7 42.3 1.0 N A:TYR147 4.8 45.1 1.0 CB A:TYR147 4.9 42.5 1.0 N A:CYS137 4.9 54.9 1.0

Zinc binding site 2 out of 4 in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast NPL4 in Complex with LYS48-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:83.5 occ:1.00 NE2 A:HIS208 2.2 90.6 1.0 SG A:CYS216 2.3 72.7 1.0 SG A:CYS204 2.3 96.3 1.0 SG A:CYS219 2.4 84.1 1.0 CE1 A:HIS208 3.0 91.0 1.0 CB A:CYS204 3.2 99.2 1.0 CD2 A:HIS208 3.3 92.8 1.0 CB A:CYS219 3.4 82.3 1.0 CB A:CYS216 3.5 80.2 1.0 N A:CYS216 3.6 96.1 1.0 N A:CYS219 4.0 85.4 1.0 CA A:CYS216 4.0 92.8 1.0 ND1 A:HIS208 4.2 92.6 1.0 O A:CYS216 4.2 93.9 1.0 C A:ILE215 4.3 96.6 1.0 C A:CYS216 4.3 96.8 1.0 CA A:CYS219 4.3 82.9 1.0 CG A:HIS208 4.3 93.7 1.0 CA A:CYS204 4.6 0.3 1.0 CB A:ASN206 4.6 0.0 1.0 CB A:LYS218 4.7 0.9 1.0 CA A:ILE215 4.7 89.1 1.0 O A:CYS204 4.7 0.8 1.0 N A:LYS218 4.8 0.2 1.0 C A:LYS218 4.8 91.6 1.0 C A:CYS204 4.8 0.7 1.0 O A:ILE215 5.0 0.5 1.0

Zinc binding site 3 out of 4 in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast NPL4 in Complex with LYS48-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:73.7 occ:1.00 NE2 E:HIS208 2.1 81.6 1.0 SG E:CYS216 2.3 77.3 1.0 SG E:CYS204 2.3 82.9 1.0 SG E:CYS219 2.3 72.3 1.0 CE1 E:HIS208 3.0 83.0 1.0 CB E:CYS204 3.0 81.5 1.0 CD2 E:HIS208 3.2 84.7 1.0 CB E:CYS219 3.3 72.5 1.0 CB E:CYS216 3.6 82.7 1.0 N E:CYS216 3.7 89.2 1.0 N E:CYS219 3.9 78.6 1.0 CA E:CYS216 4.1 86.1 1.0 ND1 E:HIS208 4.1 84.6 1.0 CA E:CYS219 4.2 73.5 1.0 CG E:HIS208 4.2 86.5 1.0 CA E:CYS204 4.3 91.6 1.0 C E:ILE215 4.4 93.8 1.0 O E:CYS204 4.4 96.5 1.0 O E:CYS216 4.5 93.2 1.0 C E:CYS216 4.5 90.0 1.0 C E:CYS204 4.5 97.7 1.0 CB E:ASN206 4.5 0.0 1.0 CB E:LYS218 4.7 0.1 1.0 C E:LYS218 4.8 81.5 1.0 N E:ASN206 4.8 0.2 1.0 CA E:ILE215 4.8 89.6 1.0 N E:LYS218 4.8 83.7 1.0

Zinc binding site 4 out of 4 in the Yeast NPL4 in Complex with LYS48-Linked Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast NPL4 in Complex with LYS48-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn602 b:48.3 occ:1.00 NE2 E:HIS139 2.1 35.8 1.0 SG E:CYS148 2.3 38.0 1.0 SG E:CYS145 2.3 45.9 1.0 SG E:CYS137 2.3 47.1 1.0 CE1 E:HIS139 2.8 35.7 1.0 CB E:CYS137 3.2 35.8 1.0 CD2 E:HIS139 3.3 41.2 1.0 CB E:CYS148 3.3 34.3 1.0 CB E:CYS145 3.4 40.3 1.0 N E:CYS145 3.5 34.5 1.0 CA E:CYS137 3.9 48.2 1.0 CA E:CYS145 3.9 34.2 1.0 N E:CYS148 4.0 36.0 1.0 ND1 E:HIS139 4.0 36.8 1.0 C E:MET144 4.1 36.6 1.0 CA E:CYS148 4.2 30.8 1.0 CG E:HIS139 4.2 37.6 1.0 C E:CYS145 4.5 39.0 1.0 CA E:MET144 4.6 36.9 1.0 O E:CYS145 4.6 40.6 1.0 C E:TYR147 4.7 42.1 1.0 N E:TYR147 4.8 48.9 1.0 CB E:TYR147 4.8 47.5 1.0 O E:MET144 4.8 35.4 1.0 N E:CYS137 4.9 55.2 1.0 C E:CYS137 4.9 46.6 1.0

Y.Sato, H.Tsuchiya, A.Yamagata, K.Okatsu, K.Tanaka, Y.Saeki, S.Fukai. Structural Insights Into Ubiquitin Recognition and UFD1 Interaction of NPL4. Nat Commun V. 10 5708 2019.
ISSN: ESSN 2041-1723
PubMed: 31836717
DOI: 10.1038/S41467-019-13697-Y