Zinc in PDB 8e4x: Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site

All present enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site:
3.5.4.37;

The structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site, PDB code: 8e4x was solved by A.J.Fisher, H.G.Mendoza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.27 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.914, 63.236, 142.646, 90, 118.07, 90
R / Rfree (%)	19.5 / 23.9

The binding sites of Zinc atom in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site (pdb code 8e4x). 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 Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site, PDB code: 8e4x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:74.8 occ:1.00 O6 C:8AZ13 2.0 82.5 1.0 ND1 A:HIS394 2.0 79.1 1.0 SG A:CYS516 2.3 118.1 1.0 SG A:CYS451 2.4 109.4 1.0 CE1 A:HIS394 2.9 82.1 1.0 C6 C:8AZ13 3.0 83.4 1.0 CG A:HIS394 3.1 81.6 1.0 CB A:CYS516 3.2 82.6 1.0 CB A:CYS451 3.3 77.0 1.0 N1 C:8AZ13 3.3 81.1 1.0 C5 C:8AZ13 3.4 76.7 1.0 CB A:HIS394 3.5 76.6 1.0 CE A:LYS483 3.6 74.3 1.0 OE2 A:GLU396 3.7 80.4 1.0 N A:CYS451 3.7 74.4 1.0 NZ A:LYS483 3.8 71.8 1.0 C2 C:8AZ13 3.9 76.8 1.0 C4 C:8AZ13 4.0 74.5 1.0 NE2 A:HIS394 4.0 77.9 1.0 N A:CYS516 4.1 69.3 1.0 N7 C:8AZ13 4.1 75.6 1.0 CD2 A:HIS394 4.1 76.3 1.0 CA A:CYS451 4.1 72.2 1.0 CD A:GLU396 4.2 77.3 1.0 CA A:CYS516 4.2 73.4 1.0 N3 C:8AZ13 4.3 74.7 1.0 OE1 A:GLU396 4.4 76.7 1.0 C A:PRO450 4.8 76.8 1.0 N9 C:8AZ13 4.9 77.8 1.0 N8 C:8AZ13 4.9 81.3 1.0 CA A:HIS394 4.9 77.7 1.0

Zinc binding site 2 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Adenosine Deaminase Acting on Dsrna (ADAR2-R2D) Bound to Dsrna Containing A G:3-Deaza Da Pair Adjacent to the Target Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:90.0 occ:1.00 O B:HOH901 1.9 78.7 1.0 SG B:CYS516 2.1 82.7 1.0 ND1 B:HIS394 2.1 83.7 1.0 SG B:CYS451 2.2 84.9 1.0 CE1 B:HIS394 3.0 84.5 1.0 CB B:CYS516 3.2 86.2 1.0 CG B:HIS394 3.3 81.8 1.0 CB B:CYS451 3.5 80.3 1.0 OE2 B:GLU396 3.7 81.4 1.0 CB B:HIS394 3.7 81.2 1.0 N B:CYS516 3.9 82.8 1.0 N B:CYS451 4.0 80.4 1.0 NZ B:LYS483 4.1 80.9 1.0 NE2 B:HIS394 4.1 83.5 1.0 CA B:CYS516 4.1 84.4 1.0 CD B:LYS483 4.3 85.5 1.0 CD2 B:HIS394 4.3 84.5 1.0 CE B:LYS483 4.3 86.0 1.0 OE1 B:GLU396 4.3 82.5 1.0 CA B:CYS451 4.3 79.0 1.0 CD B:GLU396 4.3 81.9 1.0 NH2 B:ARG455 4.9 85.8 1.0

E.E.Doherty, A.Karki, X.E.Wilcox, H.G.Mendoza, A.Manjunath, V.J.Matos, A.J.Fisher, P.A.Beal. Adar Activation By Inducing A Syn Conformation at Guanosine Adjacent to An Editing Site. Nucleic Acids Res. V. 50 10857 2022.
ISSN: ESSN 1362-4962
PubMed: 36243986
DOI: 10.1093/NAR/GKAC897