Zinc in PDB 5iw4: Crystal Structure of E. Coli Nudc in Complex with Nad

All present enzymatic activity of Crystal Structure of E. Coli Nudc in Complex with Nad:
3.6.1.22;

The structure of Crystal Structure of E. Coli Nudc in Complex with Nad, PDB code: 5iw4 was solved by S.Li, J.Du, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.932, 99.369, 113.655, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.8

The binding sites of Zinc atom in the Crystal Structure of E. Coli Nudc in Complex with Nad (pdb code 5iw4). 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 E. Coli Nudc in Complex with Nad, PDB code: 5iw4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of E. Coli Nudc in Complex with Nad


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 E. Coli Nudc in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:56.9 occ:1.00 SG A:CYS119 2.3 49.8 1.0 SG A:CYS116 2.3 56.5 1.0 SG A:CYS101 2.4 71.3 1.0 SG A:CYS98 2.4 61.5 1.0 CB A:CYS98 3.1 39.4 1.0 CB A:CYS116 3.3 45.1 1.0 CB A:CYS119 3.4 49.1 1.0 CB A:CYS101 3.5 46.8 1.0 N A:CYS101 3.7 42.7 1.0 N A:CYS119 3.9 56.7 1.0 CA A:CYS101 4.1 44.8 1.0 CA A:CYS119 4.1 50.6 1.0 CB A:TYR100 4.4 47.7 1.0 CA A:CYS98 4.6 39.4 1.0 C A:CYS101 4.7 44.5 1.0 C A:CYS119 4.7 54.6 1.0 CA A:CYS116 4.7 45.2 1.0 N A:GLY102 4.7 43.1 1.0 C A:TYR100 4.8 50.1 1.0 CB A:HIS118 4.9 64.9 1.0 N A:HIS103 4.9 54.0 1.0 O A:CYS119 4.9 53.6 1.0 CB A:HIS103 5.0 47.0 1.0 CB A:GLU121 5.0 47.1 1.0 CA A:TYR100 5.0 43.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of E. Coli Nudc in Complex with Nad


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 E. Coli Nudc in Complex with Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:49.5 occ:1.00 SG B:CYS119 2.1 57.2 1.0 SG B:CYS101 2.2 40.3 1.0 SG B:CYS98 2.4 47.5 1.0 SG B:CYS116 2.6 43.4 1.0 CB B:CYS98 3.3 31.6 1.0 CB B:CYS101 3.3 44.1 1.0 CB B:CYS116 3.4 40.2 1.0 N B:CYS101 3.7 41.6 1.0 CB B:CYS119 3.8 49.9 1.0 CB B:TYR100 4.1 37.6 1.0 N B:CYS119 4.1 46.4 1.0 CA B:CYS101 4.1 41.4 1.0 CA B:CYS119 4.5 46.3 1.0 O B:CYS119 4.5 56.0 1.0 C B:TYR100 4.7 42.1 1.0 CB B:HIS118 4.7 52.2 1.0 CA B:CYS98 4.7 28.6 1.0 CA B:TYR100 4.8 35.3 1.0 N B:GLY102 4.8 41.0 1.0 C B:CYS119 4.9 49.7 1.0 CA B:CYS116 4.9 45.0 1.0 ND1 B:HIS118 4.9 62.6 1.0 N B:TYR100 4.9 33.4 1.0 C B:CYS101 4.9 38.4 1.0

K.Hofer, S.Li, F.Abele, J.Frindert, J.Schlotthauer, J.Grawenhoff, J.Du, D.J.Patel, A.Jaschke. Structure and Function of the Bacterial Decapping Enzyme Nudc Nat.Chem.Biol. V. 12 730 2016.
ISSN: ESSN 1552-4469
PubMed: 27428510
DOI: 10.1038/NCHEMBIO.2132