Zinc in PDB 6d06: Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base

All present enzymatic activity of Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base:
3.5.4.37;

The structure of Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base, PDB code: 6d06 was solved by M.M.Matthews, A.J.Fisher, P.A.Beal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.96 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.680, 63.440, 132.060, 90.00, 126.64, 90.00
R / Rfree (%)	19 / 25.5

The binding sites of Zinc atom in the Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base (pdb code 6d06). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base, PDB code: 6d06:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:42.6 occ:1.00 O6 B:8AZ13 2.0 37.9 1.0 ND1 A:HIS394 2.0 40.2 1.0 SG A:CYS451 2.3 44.2 1.0 SG A:CYS516 2.3 41.1 1.0 CE1 A:HIS394 2.9 42.6 1.0 CG A:HIS394 3.1 42.4 1.0 C6 B:8AZ13 3.1 43.6 1.0 CB A:CYS516 3.2 40.0 1.0 CB A:CYS451 3.5 39.1 1.0 CB A:HIS394 3.5 42.0 1.0 C5 B:8AZ13 3.6 48.3 1.0 N1 B:8AZ13 3.6 43.4 1.0 CE A:LYS483 3.7 48.1 1.0 N A:CYS451 3.8 43.0 1.0 NZ A:LYS483 3.9 47.3 1.0 OE2 A:GLU396 3.9 47.5 1.0 C4 B:8AZ13 4.0 50.4 1.0 C2 B:8AZ13 4.0 42.7 1.0 NE2 A:HIS394 4.0 44.2 1.0 N A:CYS516 4.1 40.1 1.0 CD2 A:HIS394 4.1 41.6 1.0 N7 B:8AZ13 4.2 50.6 1.0 CA A:CYS451 4.2 42.0 1.0 CA A:CYS516 4.2 38.9 1.0 N3 B:8AZ13 4.3 46.2 1.0 CD A:GLU396 4.4 47.6 1.0 OE1 A:GLU396 4.5 53.2 1.0 N9 B:8AZ13 4.7 48.5 1.0 N8 B:8AZ13 4.8 54.9 1.0 C A:PRO450 4.9 39.9 1.0 CA A:HIS394 4.9 40.9 1.0

Zinc binding site 2 out of 2 in the Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human ADAR2D E488Y Mutant Complexed with Dsrna Containing An Abasic Site Opposite the Edited Base within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn802 b:58.9 occ:1.00 ND1 D:HIS394 1.9 50.2 1.0 O D:HOH901 2.0 52.2 1.0 SG D:CYS516 2.3 60.5 1.0 SG D:CYS451 2.3 55.3 1.0 CE1 D:HIS394 2.9 50.0 1.0 CG D:HIS394 3.0 48.1 1.0 CB D:CYS516 3.1 59.0 1.0 CB D:CYS451 3.4 58.0 1.0 CB D:HIS394 3.4 53.2 1.0 CE D:LYS483 3.7 71.4 1.0 NZ D:LYS483 3.8 67.4 1.0 OE2 D:GLU396 3.8 48.4 1.0 N D:CYS451 3.9 56.9 1.0 N D:CYS516 3.9 59.8 1.0 NE2 D:HIS394 4.0 51.1 1.0 CD2 D:HIS394 4.0 50.8 1.0 CA D:CYS516 4.1 59.0 1.0 CD D:GLU396 4.1 51.9 1.0 CA D:CYS451 4.2 59.5 1.0 OE1 D:GLU396 4.4 57.9 1.0 CA D:HIS394 4.8 54.5 1.0 CD D:LYS483 4.9 69.8 1.0 CG D:GLU396 4.9 52.8 1.0 O D:CYS451 4.9 54.2 1.0 C D:CYS451 4.9 59.7 1.0

L.R.Monteleone, M.M.Matthews, C.M.Palumbo, J.M.Thomas, Y.Zheng, Y.Chiang, A.J.Fisher, P.A.Beal. A Bump-Hole Approach For Directed Rna Editing. Cell Chem Biol V. 26 269 2019.
ISSN: ESSN 2451-9448
PubMed: 30581135
DOI: 10.1016/J.CHEMBIOL.2018.10.025