Zinc in PDB 6cdd: NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum)

The structure of NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum), PDB code: 6cdd was solved by N.O.Bodnar, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.11 / 2.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.858, 72.221, 193.543, 90.00, 96.71, 90.00
R / Rfree (%)	19.2 / 22.9

The binding sites of Zinc atom in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum) (pdb code 6cdd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum), PDB code: 6cdd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:92.1 occ:1.00 NE2 A:HIS162 2.1 86.3 1.0 SG A:CYS171 2.3 87.3 1.0 SG A:CYS168 2.3 98.1 1.0 SG A:CYS160 2.3 0.3 1.0 HB3 A:CYS160 2.5 0.1 1.0 CB A:CYS160 2.8 0.9 1.0 HB3 A:CYS171 2.9 0.8 1.0 CD2 A:HIS162 3.0 90.0 1.0 H A:CYS168 3.0 1.0 1.0 CE1 A:HIS162 3.1 86.4 1.0 HD2 A:HIS162 3.1 1.0 1.0 CB A:CYS171 3.2 84.0 1.0 HA A:CYS160 3.3 0.6 1.0 HE1 A:HIS162 3.3 0.7 1.0 H A:CYS171 3.4 0.2 1.0 N A:CYS168 3.5 99.2 1.0 CB A:CYS168 3.6 0.3 1.0 HB2 A:TYR170 3.6 0.1 1.0 CA A:CYS160 3.6 0.9 1.0 HB2 A:CYS160 3.7 0.1 1.0 HB3 A:CYS168 3.7 0.8 1.0 N A:CYS171 3.7 94.3 1.0 HA A:MET167 3.9 0.8 1.0 HB2 A:CYS171 3.9 0.8 1.0 H A:TYR170 4.0 0.1 1.0 CA A:CYS168 4.0 94.7 1.0 CA A:CYS171 4.1 84.1 1.0 HA A:ARG156 4.1 0.6 1.0 CG A:HIS162 4.1 92.2 1.0 ND1 A:HIS162 4.2 89.9 1.0 HG2 A:ARG156 4.3 0.1 1.0 O A:CYS168 4.3 88.3 1.0 C A:TYR170 4.3 95.0 1.0 C A:MET167 4.3 96.7 1.0 C A:CYS168 4.3 91.0 1.0 HB2 A:CYS168 4.4 0.8 1.0 H A:ARG161 4.4 0.5 1.0 H A:GLY157 4.4 0.3 1.0 CB A:TYR170 4.5 0.9 1.0 N A:TYR170 4.6 0.9 1.0 CA A:MET167 4.6 95.7 1.0 N A:CYS160 4.6 0.6 1.0 C A:CYS160 4.7 0.1 1.0 HA A:CYS171 4.7 0.9 1.0 CA A:TYR170 4.7 0.8 1.0 H A:CYS160 4.8 0.3 1.0 HD2 A:TYR170 4.8 0.8 1.0 N A:ARG161 4.8 0.1 1.0 HB3 A:TYR170 4.9 0.1 1.0 HA A:CYS168 4.9 0.6 1.0 HD1 A:HIS162 5.0 0.8 1.0 HG3 A:MET167 5.0 0.9 1.0

Zinc binding site 2 out of 4 in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:0.3 occ:1.00 NE2 A:HIS231 2.1 0.5 1.0 SG A:CYS227 2.3 0.3 1.0 SG A:CYS239 2.3 1.0 1.0 SG A:CYS242 2.3 0.2 1.0 H A:CYS239 2.5 0.9 1.0 HB3 A:CYS242 2.9 0.6 1.0 CD2 A:HIS231 3.0 0.5 1.0 HB3 A:CYS239 3.0 0.5 1.0 HD2 A:HIS231 3.1 0.8 1.0 CB A:CYS239 3.1 0.3 1.0 HB3 A:SER229 3.1 0.0 1.0 CE1 A:HIS231 3.1 0.9 1.0 CB A:CYS242 3.2 98.0 1.0 N A:CYS239 3.2 0.2 1.0 H A:CYS242 3.3 0.5 1.0 HE1 A:HIS231 3.4 0.5 1.0 HB2 A:SER229 3.4 0.0 1.0 CB A:CYS227 3.5 0.2 1.0 HB2 A:CYS227 3.6 0.5 1.0 CA A:CYS239 3.6 0.0 1.0 HB3 A:CYS227 3.6 0.5 1.0 CB A:SER229 3.7 0.5 1.0 HG A:SER229 3.7 0.3 1.0 N A:CYS242 3.8 0.1 1.0 HB2 A:CYS242 3.9 0.6 1.0 HA A:ILE238 3.9 0.1 1.0 HB2 A:CYS239 4.0 0.5 1.0 O A:CYS239 4.1 0.4 1.0 C A:CYS239 4.1 95.0 1.0 CA A:CYS242 4.1 94.7 1.0 HB2 A:LYS241 4.1 0.5 1.0 CG A:HIS231 4.1 0.4 1.0 OG A:SER229 4.2 0.2 1.0 ND1 A:HIS231 4.2 0.4 1.0 H A:LYS241 4.3 1.0 1.0 C A:ILE238 4.3 1.0 1.0 HA A:CYS239 4.5 0.6 1.0 CA A:ILE238 4.6 0.8 1.0 H A:SER229 4.6 0.6 1.0 C A:LYS241 4.7 0.8 1.0 HA A:CYS242 4.8 0.7 1.0 HG13 A:ILE238 4.8 0.6 1.0 N A:LYS241 4.8 0.8 1.0 CA A:CYS227 4.9 0.3 1.0 HD1 A:HIS231 5.0 0.3 1.0

Zinc binding site 3 out of 4 in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:0.7 occ:1.00 NE2 B:HIS162 2.1 0.2 1.0 SG B:CYS168 2.3 0.5 1.0 SG B:CYS160 2.3 0.0 1.0 SG B:CYS171 2.3 0.8 1.0 HB3 B:CYS160 2.5 0.3 1.0 CB B:CYS160 2.9 0.4 1.0 CE1 B:HIS162 3.0 0.7 1.0 HB3 B:CYS171 3.1 0.8 1.0 CD2 B:HIS162 3.1 0.0 1.0 H B:CYS168 3.1 0.6 1.0 HE1 B:HIS162 3.2 0.2 1.0 HA B:CYS160 3.2 0.8 1.0 CB B:CYS171 3.3 0.8 1.0 HD2 B:HIS162 3.3 0.7 1.0 H B:CYS171 3.4 0.8 1.0 CB B:CYS168 3.6 0.6 1.0 HB2 B:TYR170 3.6 0.0 1.0 N B:CYS168 3.6 0.3 1.0 CA B:CYS160 3.6 0.2 1.0 HB3 B:CYS168 3.7 0.5 1.0 HB2 B:CYS160 3.7 0.3 1.0 N B:CYS171 3.7 0.0 1.0 HA B:ARG156 3.9 0.4 1.0 HA B:MET167 3.9 0.2 1.0 H B:TYR170 3.9 0.5 1.0 CA B:CYS168 4.0 0.5 1.0 HG2 B:ARG156 4.0 0.4 1.0 HB2 B:CYS171 4.0 0.8 1.0 H B:GLY157 4.1 1.0 1.0 ND1 B:HIS162 4.1 0.2 1.0 CA B:CYS171 4.1 0.1 1.0 CG B:HIS162 4.2 0.6 1.0 C B:TYR170 4.3 0.3 1.0 C B:MET167 4.4 0.9 1.0 O B:CYS168 4.4 1.0 1.0 HB2 B:CYS168 4.4 0.5 1.0 C B:CYS168 4.4 0.5 1.0 CB B:TYR170 4.5 0.3 1.0 H B:ARG161 4.5 0.0 1.0 N B:TYR170 4.6 0.3 1.0 N B:CYS160 4.6 0.3 1.0 CA B:MET167 4.6 0.6 1.0 HD1 B:TYR170 4.6 0.4 1.0 CA B:TYR170 4.7 0.5 1.0 H B:CYS160 4.7 0.2 1.0 C B:CYS160 4.7 0.3 1.0 HB3 B:ARG156 4.8 0.4 1.0 CA B:ARG156 4.8 0.0 1.0 HA B:CYS171 4.8 0.3 1.0 CG B:ARG156 4.9 0.7 1.0 HB3 B:TYR170 4.9 0.0 1.0 N B:ARG161 4.9 0.0 1.0 HD1 B:HIS162 4.9 0.9 1.0 N B:GLY157 4.9 0.1 1.0 HA B:CYS168 4.9 0.8 1.0

Zinc binding site 4 out of 4 in the NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NPL4 Zinc Finger and Mpn Domains (Chaetomium Thermophilum) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:0.3 occ:1.00 NE2 B:HIS231 2.1 0.9 1.0 SG B:CYS242 2.3 0.5 1.0 SG B:CYS227 2.3 0.4 1.0 SG B:CYS239 2.3 0.7 1.0 H B:CYS239 2.6 0.8 1.0 HB3 B:CYS242 2.8 0.9 1.0 CE1 B:HIS231 3.0 0.1 1.0 HB3 B:SER229 3.1 0.4 1.0 CB B:CYS242 3.1 0.5 1.0 CD2 B:HIS231 3.1 0.9 1.0 HE1 B:HIS231 3.2 0.6 1.0 HB3 B:CYS239 3.3 0.7 1.0 CB B:CYS239 3.3 0.1 1.0 HD2 B:HIS231 3.3 0.4 1.0 H B:CYS242 3.3 0.8 1.0 HB2 B:SER229 3.3 0.4 1.0 N B:CYS239 3.4 0.2 1.0 HG B:SER229 3.6 0.3 1.0 CB B:SER229 3.6 0.2 1.0 CB B:CYS227 3.7 0.8 1.0 N B:CYS242 3.8 0.7 1.0 CA B:CYS239 3.8 0.1 1.0 HB2 B:CYS242 3.8 0.9 1.0 HB2 B:CYS227 3.8 0.4 1.0 HB3 B:CYS227 4.0 0.4 1.0 OG B:SER229 4.1 0.1 1.0 CA B:CYS242 4.1 0.6 1.0 HA B:ILE238 4.1 0.2 1.0 HB2 B:LYS241 4.1 0.7 1.0 O B:CYS239 4.1 0.1 1.0 HB2 B:CYS239 4.2 0.7 1.0 ND1 B:HIS231 4.2 0.2 1.0 C B:CYS239 4.2 0.7 1.0 CG B:HIS231 4.2 0.4 1.0 H B:LYS241 4.4 0.3 1.0 C B:ILE238 4.5 0.3 1.0 HG13 B:ILE238 4.6 0.1 1.0 H B:SER229 4.6 0.2 1.0 HA B:CYS242 4.7 0.9 1.0 C B:LYS241 4.7 0.9 1.0 HA B:CYS239 4.7 0.7 1.0 CA B:ILE238 4.8 0.9 1.0 N B:LYS241 4.9 0.6 1.0 HD1 B:HIS231 4.9 0.6 1.0 CA B:SER229 5.0 0.7 1.0

N.O.Bodnar, K.H.Kim, Z.Ji, T.E.Wales, V.Svetlov, E.Nudler, J.R.Engen, T.Walz, T.A.Rapoport. Structure of the CDC48 Atpase with Its Ubiquitin-Binding Cofactor UFD1-NPL4. Nat. Struct. Mol. Biol. V. 25 616 2018.
ISSN: ESSN 1545-9985
PubMed: 29967539
DOI: 10.1038/S41594-018-0085-X