Zinc in PDB 6chs: CDC48-NPL4 Complex in the Presence of Atp-Gamma-S

The structure of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Zinc atom in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S (pdb code 6chs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S, PDB code: 6chs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:92.3 occ:1.00 NE2 A:HIS162 2.1 91.2 1.0 SG A:CYS168 2.3 93.0 1.0 SG A:CYS160 2.3 0.3 1.0 SG A:CYS171 2.3 87.5 1.0 CB A:CYS168 2.8 98.4 1.0 CD2 A:HIS162 2.9 92.7 1.0 N A:CYS168 3.1 94.7 1.0 CB A:CYS160 3.2 91.4 1.0 CA A:CYS160 3.3 1.0 1.0 CE1 A:HIS162 3.3 93.1 1.0 CB A:CYS171 3.3 86.2 1.0 CA A:CYS168 3.5 90.5 1.0 C A:MET167 3.8 94.7 1.0 N A:CYS160 4.0 0.5 1.0 N A:CYS171 4.1 0.9 1.0 CG A:HIS162 4.1 93.3 1.0 CA A:MET167 4.1 89.7 1.0 ND1 A:HIS162 4.3 92.6 1.0 C A:CYS168 4.3 92.3 1.0 CA A:CYS171 4.3 91.8 1.0 C A:CYS160 4.5 0.6 1.0 O A:MET159 4.5 0.6 1.0 N A:GLY157 4.5 88.4 1.0 C A:MET159 4.5 0.6 1.0 O A:MET167 4.6 0.9 1.0 C A:TYR170 4.6 89.9 1.0 N A:ARG161 4.6 95.5 1.0 O A:CYS168 4.7 87.8 1.0 N A:TYR170 4.8 0.7 1.0 CA A:ARG156 5.0 0.0 1.0

Zinc binding site 2 out of 2 in the CDC48-NPL4 Complex in the Presence of Atp-Gamma-S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDC48-NPL4 Complex in the Presence of Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:0.1 occ:1.00 NE2 A:HIS231 2.1 0.7 1.0 SG A:CYS242 2.3 96.0 1.0 SG A:CYS227 2.3 0.6 1.0 SG A:CYS239 2.3 0.0 1.0 N A:CYS242 2.5 0.1 1.0 CB A:CYS242 2.5 94.5 1.0 CE1 A:HIS231 2.7 0.3 1.0 CA A:CYS242 3.0 96.1 1.0 C A:LYS241 3.0 0.9 1.0 CD2 A:HIS231 3.3 0.1 1.0 N A:LYS241 3.4 0.9 1.0 CA A:LYS241 3.5 0.8 1.0 N A:CYS239 3.5 0.7 1.0 CB A:LYS241 3.7 0.9 1.0 CB A:CYS239 3.7 0.6 1.0 CB A:CYS227 3.7 0.4 1.0 C A:CYS239 3.7 96.5 1.0 O A:CYS239 3.8 0.0 1.0 O A:LYS241 3.8 0.2 1.0 CA A:CYS239 3.8 0.8 1.0 ND1 A:HIS231 3.9 0.3 1.0 CG A:HIS231 4.2 0.3 1.0 C A:THR240 4.2 0.5 1.0 C A:CYS242 4.2 0.7 1.0 N A:THR240 4.3 0.5 1.0 C A:ILE238 4.5 0.5 1.0 CB A:SER229 4.6 0.3 1.0 N A:GLN243 4.7 0.5 1.0 CA A:THR240 4.9 0.3 1.0 O A:THR240 4.9 0.3 1.0 CA A:CYS227 4.9 0.7 1.0 CG A:LYS241 4.9 0.2 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