Zinc in PDB 5ed1: Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene

All present enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene:
3.5.4.37;

The structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene, PDB code: 5ed1 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)	80.39 / 2.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.362, 107.498, 121.097, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 22.3

The binding sites of Zinc atom in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene (pdb code 5ed1). 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) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene, PDB code: 5ed1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene


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) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:50.9 occ:1.00 ND1 A:HIS394 1.9 51.5 1.0 O6 B:8AZ12 2.1 47.6 1.0 SG A:CYS516 2.3 46.0 1.0 SG A:CYS451 2.4 53.9 1.0 CE1 A:HIS394 2.8 45.6 1.0 CG A:HIS394 3.1 41.8 1.0 CB A:CYS516 3.2 54.0 1.0 C6 B:8AZ12 3.2 48.8 1.0 CB A:CYS451 3.4 38.7 1.0 CE A:LYS483 3.5 40.9 1.0 CB A:HIS394 3.6 39.1 1.0 C5 B:8AZ12 3.6 49.2 1.0 N A:CYS451 3.8 32.6 1.0 OE2 A:GLU396 3.8 46.0 1.0 N1 B:8AZ12 3.8 46.0 1.0 NE2 A:HIS394 3.9 42.5 1.0 N A:CYS516 4.0 45.9 1.0 NZ A:LYS483 4.0 45.1 1.0 C2 B:8AZ12 4.1 45.4 1.0 C4 B:8AZ12 4.1 46.7 1.0 CD2 A:HIS394 4.1 38.3 1.0 CA A:CYS451 4.2 37.2 1.0 N7 B:8AZ12 4.2 53.5 1.0 CA A:CYS516 4.2 46.9 1.0 N3 B:8AZ12 4.4 46.5 1.0 CD A:GLU396 4.5 52.1 1.0 C A:PRO450 4.8 41.1 1.0 N9 B:8AZ12 4.8 46.5 1.0 CD A:LYS483 4.9 33.8 1.0 O A:CYS451 4.9 39.6 1.0 OE1 A:GLU396 4.9 46.1 1.0 N8 B:8AZ12 4.9 47.1 1.0 C A:CYS451 4.9 38.5 1.0

Zinc binding site 2 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene


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) Mutant E488Q Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn802 b:46.1 occ:1.00 O D:HOH905 2.0 32.3 1.0 ND1 D:HIS394 2.0 57.7 1.0 SG D:CYS516 2.3 48.9 1.0 SG D:CYS451 2.3 54.5 1.0 CE1 D:HIS394 2.9 54.0 1.0 CG D:HIS394 3.1 47.3 1.0 CB D:CYS516 3.2 38.8 1.0 CB D:CYS451 3.4 27.3 1.0 CB D:HIS394 3.6 44.4 1.0 CE D:LYS483 3.7 57.0 1.0 OE2 D:GLU396 3.7 54.2 1.0 O D:HOH906 3.8 55.5 1.0 N D:CYS451 3.9 35.2 1.0 N D:CYS516 4.0 43.2 1.0 NE2 D:HIS394 4.0 56.3 1.0 NZ D:LYS483 4.1 57.5 1.0 CD D:GLU396 4.2 59.2 1.0 CD2 D:HIS394 4.2 42.2 1.0 CA D:CYS516 4.2 41.6 1.0 CA D:CYS451 4.2 45.7 1.0 OE1 D:GLU396 4.5 65.7 1.0 C D:CYS451 4.9 41.6 1.0 O D:CYS451 5.0 34.2 1.0

M.M.Matthews, J.M.Thomas, Y.Zheng, K.Tran, K.J.Phelps, A.I.Scott, J.Havel, A.J.Fisher, P.A.Beal. Structures of Human ADAR2 Bound to Dsrna Reveal Base-Flipping Mechanism and Basis For Site Selectivity. Nat.Struct.Mol.Biol. V. 23 426 2016.
ISSN: ESSN 1545-9985
PubMed: 27065196
DOI: 10.1038/NSMB.3203