Zinc in PDB 6jwj: NPL4 in Complex with UFD1

The structure of NPL4 in Complex with UFD1, PDB code: 6jwj 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)	47.55 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.005, 82.546, 94.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The binding sites of Zinc atom in the NPL4 in Complex with UFD1 (pdb code 6jwj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the NPL4 in Complex with UFD1, PDB code: 6jwj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the NPL4 in Complex with UFD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NPL4 in Complex with UFD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:45.1 occ:1.00 NE2 A:HIS139 2.1 50.7 1.0 SG A:CYS148 2.3 41.7 1.0 SG A:CYS137 2.3 45.0 1.0 SG A:CYS145 2.3 51.3 1.0 CD2 A:HIS139 3.0 53.1 1.0 CE1 A:HIS139 3.1 54.8 1.0 CB A:CYS148 3.2 40.4 1.0 CB A:CYS137 3.2 57.5 1.0 CB A:CYS145 3.4 56.8 1.0 N A:CYS145 3.4 48.1 1.0 N A:CYS148 3.7 49.6 1.0 CA A:CYS145 3.9 54.5 1.0 CA A:CYS148 4.1 48.8 1.0 CG A:LYS133 4.1 66.3 1.0 CG A:HIS139 4.2 52.7 1.0 ND1 A:HIS139 4.2 52.7 1.0 C A:MET144 4.2 49.6 1.0 CA A:CYS137 4.3 55.0 1.0 C A:CYS145 4.3 55.3 1.0 O A:CYS145 4.3 49.6 1.0 C A:TYR147 4.4 51.4 1.0 CB A:TYR147 4.5 54.2 1.0 CA A:MET144 4.5 51.3 1.0 N A:TYR147 4.7 56.0 1.0 CA A:TYR147 4.8 48.9 1.0 CD A:LYS133 4.8 66.7 1.0 C A:CYS148 5.0 47.1 1.0

Zinc binding site 2 out of 2 in the NPL4 in Complex with UFD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NPL4 in Complex with UFD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:27.4 occ:1.00 NE2 A:HIS208 2.0 28.0 1.0 SG A:CYS219 2.2 26.1 1.0 SG A:CYS204 2.3 26.4 1.0 SG A:CYS216 2.3 29.3 1.0 CE1 A:HIS208 2.9 28.0 1.0 CD2 A:HIS208 3.2 29.3 1.0 CB A:CYS219 3.2 23.6 1.0 CB A:CYS204 3.2 27.8 1.0 CB A:CYS216 3.3 27.5 1.0 N A:CYS216 3.6 29.6 1.0 N A:CYS219 3.9 30.1 1.0 CA A:CYS216 3.9 33.9 1.0 ND1 A:HIS208 4.1 29.2 1.0 CB A:ASN206 4.2 31.7 1.0 CA A:CYS219 4.2 30.9 1.0 CG A:HIS208 4.2 31.5 1.0 C A:ILE215 4.3 27.5 1.0 O A:CYS216 4.3 26.8 1.0 C A:CYS216 4.3 25.6 1.0 N A:ASN206 4.5 30.5 1.0 CA A:CYS204 4.5 30.0 1.0 O A:HOH924 4.6 38.0 1.0 C A:CYS204 4.6 31.0 1.0 O A:CYS204 4.6 34.3 1.0 CA A:ILE215 4.7 29.9 1.0 C A:LYS218 4.7 31.5 1.0 O A:ASN206 4.7 40.3 1.0 CB A:LYS218 4.8 31.8 1.0 CA A:ASN206 4.8 30.2 1.0 N A:LYS218 4.9 33.6 1.0 O A:ILE215 5.0 32.7 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