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Zinc in PDB 9d5j: Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand

Enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand

All present enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand:
3.5.4.37;

Protein crystallography data

The structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand, PDB code: 9d5j was solved by A.J.Fisher, J.Cheng, A.Manjunath, K.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.60 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.694, 63.13, 141.778, 90, 118.23, 90
R / Rfree (%) 18.8 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand (pdb code 9d5j). 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-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand, PDB code: 9d5j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9d5j

Go back to Zinc Binding Sites List in 9d5j
Zinc binding site 1 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand


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-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:42.1
occ:1.00
 ND1 A:HIS394 2.1 43.1 1.0
O6 C:8AZ13 2.2 35.6 1.0
SG A:CYS516 2.3 37.3 1.0
SG A:CYS451 2.4 37.9 1.0
CB A:CYS516 3.0 38.6 1.0
N1 C:8AZ13 3.0 42.4 1.0
CG A:HIS394 3.0 38.5 1.0
CE1 A:HIS394 3.1 44.6 1.0
C6 C:8AZ13 3.1 38.6 1.0
CB A:HIS394 3.4 39.7 1.0
OE2 A:GLU396 3.5 39.3 1.0
NZ A:LYS483 3.5 35.2 1.0
CB A:CYS451 3.6 46.8 1.0
N A:CYS451 3.7 39.3 1.0
C5 C:8AZ13 3.9 40.2 1.0
C2 C:8AZ13 4.0 39.6 1.0
N A:CYS516 4.0 31.8 1.0
CA A:CYS516 4.1 28.4 1.0
NE2 A:HIS394 4.2 41.1 1.0
CD2 A:HIS394 4.2 38.9 1.0
CA A:CYS451 4.3 40.0 1.0
CD A:GLU396 4.3 33.7 1.0
C4 C:8AZ13 4.3 37.9 1.0
N3 C:8AZ13 4.4 37.8 1.0
CE A:LYS483 4.4 30.3 1.0
N7 C:8AZ13 4.6 42.5 1.0
CD A:LYS483 4.6 31.7 1.0
OE1 A:GLU396 4.7 33.1 1.0
C A:PRO450 4.8 35.6 1.0
CA A:HIS394 4.8 37.0 1.0
CA A:PRO450 4.9 36.4 1.0

Zinc binding site 2 out of 2 in 9d5j

Go back to Zinc Binding Sites List in 9d5j
Zinc binding site 2 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand


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-Rd) Bound to Dsrna Containing Deoxyinosine at the -1 Position of the Guide Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:55.1
occ:1.00
 O B:HOH901 2.0 51.5 1.0
ND1 B:HIS394 2.1 51.2 1.0
SG B:CYS516 2.2 50.7 1.0
SG B:CYS451 2.3 39.2 1.0
CE1 B:HIS394 2.9 53.7 1.0
CB B:CYS516 3.1 41.9 1.0
CG B:HIS394 3.1 48.5 1.0
NZ B:LYS483 3.5 53.1 1.0
CB B:HIS394 3.6 47.2 1.0
CB B:CYS451 3.7 48.3 1.0
N B:CYS451 4.1 52.9 1.0
OE2 B:GLU396 4.1 48.9 1.0
NE2 B:HIS394 4.1 49.3 1.0
N B:CYS516 4.2 49.8 1.0
CA B:CYS516 4.2 46.8 1.0
CD2 B:HIS394 4.2 52.7 1.0
CD B:GLU396 4.3 45.6 1.0
CE B:LYS483 4.3 52.1 1.0
OE1 B:GLU396 4.4 43.7 1.0
CA B:CYS451 4.5 47.5 1.0
CD B:LYS483 4.9 51.5 1.0
CA B:HIS394 5.0 45.3 1.0

Reference:

A.Manjunath, J.Cheng, K.B.Campbell, C.S.Jacobsen, H.G.Mendoza, L.Bierbaum, V.Jauregui-Matos, E.E.Doherty, A.J.Fisher, P.A.Beal. Nucleoside Analogs in Adar Guide Strands Enable Editing at 5'-G A Sites. Biomolecules V. 14 2024.
ISSN: ESSN 2218-273X
PubMed: 39456162
DOI: 10.3390/BIOM14101229
Page generated: Fri Aug 22 17:03:36 2025

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