Zinc in PDB 6o3p: Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions:
3.6.1.22;

The structure of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions, PDB code: 6o3p was solved by L.Tong, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.67 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.207, 58.550, 61.707, 102.40, 115.19, 104.66
R / Rfree (%)	18 / 21.9

The structure of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions (pdb code 6o3p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions, PDB code: 6o3p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:33.7 occ:1.00 SG A:CYS302 2.3 33.0 1.0 SG A:CYS287 2.3 35.0 1.0 SG A:CYS307 2.3 34.5 1.0 SG A:CYS284 2.4 29.9 1.0 CB A:CYS284 3.1 28.9 1.0 CB A:CYS307 3.1 36.3 1.0 CB A:CYS302 3.2 31.6 1.0 CB A:CYS287 3.4 32.1 1.0 OG A:SER309 3.8 35.5 1.0 N A:CYS287 3.8 35.1 1.0 NH1 A:ARG304 3.8 81.1 1.0 CA A:CYS287 4.1 34.5 1.0 CA A:CYS307 4.5 38.9 1.0 CA A:CYS302 4.5 31.7 1.0 CA A:CYS284 4.6 28.7 1.0 CB A:SER289 4.7 36.8 1.0 CB A:SER309 4.7 32.8 1.0 C A:CYS287 4.7 34.3 1.0 C A:THR286 4.7 35.6 1.0 N A:GLY288 4.7 32.3 1.0 N A:SER289 4.8 33.3 1.0 CB A:THR286 4.8 28.4 1.0 CB A:ARG304 4.8 35.7 1.0 O A:HOH735 5.0 36.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:36.5 occ:1.00 SG B:CYS307 2.3 35.2 1.0 SG B:CYS302 2.3 36.0 1.0 SG B:CYS284 2.4 31.6 1.0 SG B:CYS287 2.4 35.3 1.0 CB B:CYS284 3.1 32.7 1.0 CB B:CYS302 3.1 29.2 1.0 CB B:CYS307 3.2 35.8 1.0 CB B:CYS287 3.4 38.5 1.0 OG B:SER309 3.8 32.0 1.0 N B:CYS287 3.9 31.1 1.0 CA B:CYS287 4.2 35.5 1.0 CA B:CYS307 4.6 38.3 1.0 CA B:CYS284 4.6 29.0 1.0 CA B:CYS302 4.6 32.3 1.0 CB B:SER309 4.7 33.8 1.0 CB B:ARG304 4.7 39.7 1.0 CB B:SER289 4.7 33.4 1.0 CB B:THR286 4.7 30.1 1.0 C B:THR286 4.7 34.1 1.0 C B:CYS287 4.7 30.7 1.0 N B:GLY288 4.8 32.8 1.0 N B:SER289 4.8 31.9 1.0 OG B:SER289 5.0 40.2 1.0

E.Grudzien-Nogalska, Y.Wu, X.Jiao, H.Cui, M.K.Mateyak, R.P.Hart, L.Tong, M.Kiledjian. Structural and Mechanistic Basis of Mammalian NUDT12 Rna Denadding. Nat.Chem.Biol. V. 15 575 2019.
ISSN: ESSN 1552-4469
PubMed: 31101919
DOI: 10.1038/S41589-019-0293-7