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Zinc in PDB 7kfn: Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base

Enzymatic activity of Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base

All present enzymatic activity of Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base:
3.5.4.37;

Protein crystallography data

The structure of Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base, PDB code: 7kfn was solved by X.E.Wilcox, 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) 68.99 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.024, 63.612, 132.149, 90, 126.77, 90
R / Rfree (%) 17.1 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base (pdb code 7kfn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base, PDB code: 7kfn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7kfn

Go back to Zinc Binding Sites List in 7kfn
Zinc binding site 1 out of 2 in the Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z 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 Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:37.1
occ:1.00
 O6 B:8AZ13 1.9 34.3 1.0
ND1 A:HIS394 1.9 36.4 1.0
SG A:CYS451 2.2 38.2 1.0
SG A:CYS516 2.3 32.4 1.0
CE1 A:HIS394 2.8 33.5 1.0
CG A:HIS394 3.0 32.7 1.0
C6 B:8AZ13 3.1 38.0 1.0
CB A:CYS516 3.2 34.1 1.0
CB A:HIS394 3.4 32.8 1.0
CB A:CYS451 3.5 31.8 1.0
N1 B:8AZ13 3.6 38.4 1.0
C5 B:8AZ13 3.7 36.8 1.0
CE A:LYS483 3.7 49.6 1.0
OE2 A:GLU396 3.8 34.0 1.0
N A:CYS451 3.8 31.3 1.0
NE2 A:HIS394 3.9 30.3 1.0
CD2 A:HIS394 4.0 35.0 1.0
N A:CYS516 4.1 32.5 1.0
C2 B:8AZ13 4.1 39.6 1.0
NZ A:LYS483 4.1 45.8 1.0
C4 B:8AZ13 4.2 38.2 1.0
CA A:CYS516 4.2 33.3 1.0
CA A:CYS451 4.2 32.6 1.0
N7 B:8AZ13 4.3 39.0 1.0
CD A:GLU396 4.3 36.5 1.0
N3 B:8AZ13 4.4 37.3 1.0
OE1 A:GLU396 4.6 35.8 1.0
CA A:HIS394 4.8 34.8 1.0
C A:PRO450 4.9 30.5 1.0
N9 B:8AZ13 4.9 40.2 1.0
N8 B:8AZ13 5.0 39.5 1.0

Zinc binding site 2 out of 2 in 7kfn

Go back to Zinc Binding Sites List in 7kfn
Zinc binding site 2 out of 2 in the Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z 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 Structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Containing A 2'-Deoxy Benner'S Base Z Opposite the Edited Base within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:41.8
occ:1.00
 ND1 D:HIS394 2.1 34.1 1.0
O D:HOH902 2.2 29.8 1.0
SG D:CYS516 2.3 39.1 1.0
SG D:CYS451 2.4 42.4 1.0
CE1 D:HIS394 3.0 35.4 1.0
CG D:HIS394 3.1 37.3 1.0
CB D:CYS516 3.2 38.7 1.0
CB D:CYS451 3.3 44.1 1.0
CB D:HIS394 3.5 37.0 1.0
CE D:LYS483 3.6 48.1 1.0
N D:CYS451 3.8 39.0 1.0
OE2 D:GLU396 3.8 42.3 1.0
CD D:GLU396 4.1 38.5 1.0
N D:CYS516 4.1 38.0 1.0
NE2 D:HIS394 4.1 34.8 1.0
CA D:CYS451 4.1 39.1 1.0
OE1 D:GLU396 4.1 35.9 1.0
CD2 D:HIS394 4.2 36.3 1.0
NZ D:LYS483 4.2 52.1 1.0
CA D:CYS516 4.2 37.5 1.0
O D:CYS451 4.8 40.5 1.0
CG D:GLU396 4.9 40.9 1.0
C D:CYS451 4.9 40.2 1.0
C D:PRO450 4.9 40.3 1.0
CA D:HIS394 4.9 36.8 1.0
CD D:LYS483 5.0 51.9 1.0

Reference:

E.E.Doherty, X.E.Wilcox, L.Van Sint Fiet, C.Kemmel, J.J.Turunen, B.Klein, D.J.Tantillo, A.J.Fisher, P.A.Beal. Rational Design of Rna Editing Guide Strands: Cytidine Analogs at the Orphan Position. J.Am.Chem.Soc. V. 143 6865 2021.
ISSN: ESSN 1520-5126
PubMed: 33939417
DOI: 10.1021/JACS.0C13319
Page generated: Tue Oct 29 22:12:57 2024

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