Zinc in PDB 8e2q: Crystal Structure of Tadac-1.17 in A Complex with Ssdna

All present enzymatic activity of Crystal Structure of Tadac-1.17 in A Complex with Ssdna:
3.5.4.33;

The structure of Crystal Structure of Tadac-1.17 in A Complex with Ssdna, PDB code: 8e2q was solved by P.R.Feliciano, S.J.Lee, G.Ciaramella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.03 / 2.34
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.93, 85.93, 224.59, 90, 90, 120
R / Rfree (%)	16.9 / 20.5

The binding sites of Zinc atom in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna (pdb code 8e2q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna, PDB code: 8e2q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna


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 Tadac-1.17 in A Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.4 occ:1.00 ND1 A:HIS57 2.0 29.9 1.0 SG A:CYS90 2.0 33.6 1.0 O6 E:UEL9 2.1 45.0 1.0 SG A:CYS87 2.2 36.3 1.0 CE1 A:HIS57 2.9 37.5 1.0 CB A:CYS90 3.0 35.6 1.0 CG A:HIS57 3.1 28.4 1.0 C6 E:UEL9 3.3 38.3 1.0 CB A:CYS87 3.4 31.7 1.0 CB A:HIS57 3.5 34.6 1.0 N A:CYS87 3.7 38.3 1.0 C5 E:UEL9 3.7 33.6 1.0 OE2 A:GLU59 3.8 45.7 1.0 N A:CYS90 3.9 40.9 1.0 CE A:MET89 3.9 32.2 1.0 N1 E:UEL9 4.0 36.2 1.0 CA A:CYS90 4.1 31.2 1.0 NE2 A:HIS57 4.1 29.1 1.0 C2 E:UEL9 4.1 38.0 1.0 CA A:CYS87 4.1 39.4 1.0 CD2 A:HIS57 4.2 25.0 1.0 CD A:GLU59 4.3 38.6 1.0 C4 E:UEL9 4.3 32.7 1.0 OE1 A:GLU59 4.3 38.4 1.0 N3 E:UEL9 4.4 38.8 1.0 N7 E:UEL9 4.5 37.3 1.0 NE2 B:HIS96 4.7 44.2 1.0 C A:CYS87 4.8 40.2 1.0 C A:PRO86 4.8 38.8 1.0 C A:MET89 5.0 31.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna


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 Tadac-1.17 in A Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:38.3 occ:1.00 ND1 B:HIS57 2.0 30.3 1.0 SG B:CYS90 2.0 30.8 1.0 O6 F:UEL9 2.2 39.9 1.0 SG B:CYS87 2.2 34.5 1.0 CE1 B:HIS57 3.0 33.9 1.0 CG B:HIS57 3.1 30.0 1.0 CB B:CYS90 3.2 30.0 1.0 C6 F:UEL9 3.3 36.7 1.0 CB B:HIS57 3.4 35.5 1.0 CB B:CYS87 3.6 32.7 1.0 N B:CYS87 3.7 41.8 1.0 OE2 B:GLU59 3.8 43.4 1.0 N1 F:UEL9 3.9 30.3 1.0 C5 F:UEL9 3.9 30.5 1.0 N B:CYS90 3.9 42.9 1.0 NE2 B:HIS57 4.1 29.8 1.0 CE B:MET89 4.1 37.5 1.0 OE1 B:GLU59 4.1 43.7 1.0 CA B:CYS90 4.2 31.2 1.0 CD2 B:HIS57 4.2 24.9 1.0 CD B:GLU59 4.2 44.0 1.0 CA B:CYS87 4.2 32.1 1.0 C2 F:UEL9 4.2 31.2 1.0 C4 F:UEL9 4.5 30.3 1.0 N3 F:UEL9 4.6 36.3 1.0 N7 F:UEL9 4.6 34.7 1.0 NE2 A:HIS96 4.7 40.2 1.0 C B:PRO86 4.8 35.4 1.0 CB B:MET89 4.8 29.8 1.0 C B:CYS87 4.8 33.3 1.0 CA B:PRO86 4.9 38.5 1.0 CA B:HIS57 4.9 31.0 1.0 O B:CYS87 5.0 43.0 1.0 C B:MET89 5.0 31.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Tadac-1.17 in A Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:42.4 occ:1.00 O6 G:UEL9 2.0 40.4 1.0 ND1 C:HIS57 2.0 36.0 1.0 SG C:CYS90 2.1 35.6 1.0 SG C:CYS87 2.3 43.4 1.0 CE1 C:HIS57 3.0 46.3 1.0 CG C:HIS57 3.1 37.4 1.0 C6 G:UEL9 3.2 45.2 1.0 CB C:CYS90 3.3 35.4 1.0 CB C:CYS87 3.4 36.1 1.0 CB C:HIS57 3.5 35.1 1.0 N C:CYS87 3.6 40.8 1.0 OE2 C:GLU59 3.7 52.7 1.0 C5 G:UEL9 3.7 40.6 1.0 OE1 C:GLU59 4.0 44.4 1.0 N1 G:UEL9 4.0 41.1 1.0 CA C:CYS87 4.1 32.9 1.0 N C:CYS90 4.1 33.8 1.0 CD C:GLU59 4.1 44.6 1.0 NE2 C:HIS57 4.1 35.8 1.0 C2 G:UEL9 4.1 43.4 1.0 CD2 C:HIS57 4.2 38.2 1.0 CE C:MET89 4.2 32.4 1.0 C4 G:UEL9 4.3 43.6 1.0 CA C:CYS90 4.3 30.0 1.0 N7 G:UEL9 4.4 47.9 1.0 N3 G:UEL9 4.4 46.0 1.0 C C:CYS87 4.7 37.8 1.0 C C:PRO86 4.8 41.2 1.0 CE1 D:HIS96 4.9 41.6 1.0 CA C:PRO86 4.9 31.6 1.0 O C:CYS87 5.0 40.3 1.0 CB C:MET89 5.0 33.8 1.0 CA C:HIS57 5.0 37.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Tadac-1.17 in A Complex with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Tadac-1.17 in A Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:41.9 occ:1.00 O6 H:UEL9 2.0 45.6 1.0 ND1 D:HIS57 2.0 36.6 1.0 SG D:CYS90 2.1 37.0 1.0 SG D:CYS87 2.1 39.1 1.0 CE1 D:HIS57 3.0 42.0 1.0 CG D:HIS57 3.1 38.5 1.0 C6 H:UEL9 3.1 43.3 1.0 CB D:CYS90 3.2 36.4 1.0 CB D:HIS57 3.5 37.8 1.0 CB D:CYS87 3.6 43.1 1.0 OE2 D:GLU59 3.6 49.6 1.0 C5 H:UEL9 3.6 38.5 1.0 N D:CYS87 3.7 44.0 1.0 CE D:MET89 3.9 33.5 1.0 N1 H:UEL9 3.9 45.0 1.0 N D:CYS90 4.0 38.6 1.0 NE2 D:HIS57 4.1 30.5 1.0 C2 H:UEL9 4.2 41.8 1.0 CD2 D:HIS57 4.2 40.6 1.0 CA D:CYS87 4.2 39.6 1.0 CD D:GLU59 4.2 48.1 1.0 CA D:CYS90 4.2 32.8 1.0 N7 H:UEL9 4.3 40.9 1.0 OE1 D:GLU59 4.3 47.4 1.0 C4 H:UEL9 4.3 40.3 1.0 N3 H:UEL9 4.5 41.1 1.0 C D:PRO86 4.8 44.4 1.0 CE1 C:HIS96 4.8 40.4 1.0 C D:CYS87 4.9 35.6 1.0 CA D:PRO86 4.9 39.4 1.0 CA D:HIS57 5.0 32.4 1.0

D.K.Lam, P.R.Feliciano, A.Arif, T.Bohnuud, T.P.Fernandez, J.M.Gehrke, P.Grayson, K.D.Lee, M.A.Ortega, C.Sawyer, N.Schwaegerle, L.Peraro, L.Young, S.J.Lee, G.Ciaramella, N.M.Gaudelli. Improved Cytosine Base Editors Generated From Tada Variants Nat.Biotechnol. 2023.
ISSN: ISSN 1087-0156