Zinc in PDB 6jwh: Yeast NPL4 Zinc Finger, Mpn and Ctd Domains

The structure of Yeast NPL4 Zinc Finger, Mpn and Ctd Domains, PDB code: 6jwh 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)	47.87 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.971, 82.936, 92.123, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.3

The binding sites of Zinc atom in the Yeast NPL4 Zinc Finger, Mpn and Ctd Domains (pdb code 6jwh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Yeast NPL4 Zinc Finger, Mpn and Ctd Domains, PDB code: 6jwh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Yeast NPL4 Zinc Finger, Mpn and Ctd Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast NPL4 Zinc Finger, Mpn and Ctd Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:66.3 occ:1.00 NE2 A:HIS139 2.1 55.7 1.0 SG A:CYS137 2.3 62.0 1.0 SG A:CYS148 2.3 45.9 1.0 SG A:CYS145 2.3 52.0 1.0 CE1 A:HIS139 2.9 52.3 1.0 CB A:CYS148 3.1 44.1 1.0 CB A:CYS137 3.2 61.8 1.0 CD2 A:HIS139 3.2 54.6 1.0 CB A:CYS145 3.4 55.8 1.0 N A:CYS145 3.5 52.8 1.0 N A:CYS148 3.8 51.2 1.0 CA A:CYS145 3.9 54.7 1.0 CA A:CYS137 4.0 65.7 1.0 CA A:CYS148 4.1 50.6 1.0 ND1 A:HIS139 4.1 57.7 1.0 C A:MET144 4.1 56.0 1.0 CG A:HIS139 4.2 56.3 1.0 C A:CYS145 4.3 51.7 1.0 O A:CYS145 4.3 49.5 1.0 CA A:MET144 4.4 55.8 1.0 CB A:TYR147 4.5 56.0 1.0 C A:TYR147 4.6 51.3 1.0 N A:TYR147 4.6 51.5 1.0 CA A:TYR147 4.8 50.1 1.0 CG A:LYS133 4.8 71.1 1.0 O A:MET144 4.9 52.7 1.0 C A:CYS148 4.9 50.0 1.0 N A:CYS137 5.0 76.5 1.0 C A:CYS137 5.0 71.6 1.0 N A:MET144 5.0 55.5 1.0

Zinc binding site 2 out of 2 in the Yeast NPL4 Zinc Finger, Mpn and Ctd Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast NPL4 Zinc Finger, Mpn and Ctd Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:45.4 occ:1.00 NE2 A:HIS208 2.1 34.5 1.0 SG A:CYS219 2.3 34.5 1.0 SG A:CYS216 2.3 37.4 1.0 SG A:CYS204 2.4 34.3 1.0 CE1 A:HIS208 3.0 33.6 1.0 CB A:CYS204 3.2 42.8 1.0 CD2 A:HIS208 3.2 37.3 1.0 CB A:CYS219 3.2 35.0 1.0 CB A:CYS216 3.4 36.9 1.0 N A:CYS216 3.5 41.3 1.0 N A:CYS219 3.7 35.3 1.0 CA A:CYS216 3.9 39.4 1.0 CA A:CYS219 4.1 33.1 1.0 ND1 A:HIS208 4.1 35.1 1.0 C A:ILE215 4.2 32.7 1.0 CB A:ASN206 4.2 36.2 1.0 CG A:HIS208 4.3 37.2 1.0 C A:CYS216 4.4 31.3 1.0 CA A:CYS204 4.5 33.8 1.0 O A:CYS216 4.5 31.3 1.0 N A:ASN206 4.5 38.0 1.0 C A:CYS204 4.6 40.2 1.0 CA A:ILE215 4.6 34.8 1.0 O A:CYS204 4.6 41.8 1.0 O A:HOH922 4.6 47.9 1.0 C A:LYS218 4.7 40.8 1.0 O A:ASN206 4.8 44.6 1.0 CB A:LYS218 4.8 41.1 1.0 O A:ILE215 4.9 35.7 1.0 CA A:ASN206 4.9 40.6 1.0 O A:HOH1078 4.9 58.6 1.0 N A:LYS218 4.9 42.1 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