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Zinc in PDB 5hp3: Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site

Enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site

All present enzymatic activity of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site:
3.5.4.37;

Protein crystallography data

The structure of Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site, PDB code: 5hp3 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) 36.33 / 3.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.510, 107.210, 120.620, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site (pdb code 5hp3). 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) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site, PDB code: 5hp3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5hp3

Go back to Zinc Binding Sites List in 5hp3
Zinc binding site 1 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction 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) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:47.4
occ:1.00
 O6 B:8AZ12 1.9 52.3 1.0
ND1 A:HIS394 2.1 36.5 1.0
SG A:CYS451 2.3 47.0 1.0
SG A:CYS516 2.3 45.3 1.0
CE1 A:HIS394 3.0 39.1 1.0
CG A:HIS394 3.1 30.6 1.0
C6 B:8AZ12 3.2 54.2 1.0
CB A:CYS516 3.2 60.5 1.0
CB A:HIS394 3.4 33.0 1.0
CB A:CYS451 3.5 49.9 1.0
C5 B:8AZ12 3.6 58.0 1.0
OE2 A:GLU396 3.7 41.8 1.0
CE A:LYS483 3.7 43.1 1.0
N A:CYS451 3.7 43.1 1.0
N1 B:8AZ12 3.8 51.3 1.0
NZ A:LYS483 3.8 44.3 1.0
C4 B:8AZ12 4.1 49.2 1.0
C2 B:8AZ12 4.1 45.8 1.0
N A:CYS516 4.1 46.0 1.0
NE2 A:HIS394 4.1 39.0 1.0
CA A:CYS451 4.2 46.4 1.0
CD2 A:HIS394 4.2 39.8 1.0
N7 B:8AZ12 4.2 57.3 1.0
CA A:CYS516 4.3 49.6 1.0
N3 B:8AZ12 4.4 39.9 1.0
CD A:GLU396 4.5 53.0 1.0
N9 B:8AZ12 4.8 50.2 1.0
C A:PRO450 4.8 45.7 1.0
OE1 A:GLU396 4.9 65.8 1.0
N8 B:8AZ12 4.9 58.6 1.0
CA A:HIS394 4.9 37.2 1.0
C A:CYS451 5.0 48.5 1.0
O A:CYS451 5.0 55.7 1.0

Zinc binding site 2 out of 2 in 5hp3

Go back to Zinc Binding Sites List in 5hp3
Zinc binding site 2 out of 2 in the Human Adenosine Deaminase Acting on Dsrna (ADAR2) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction 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) Bound to Dsrna Sequence Derived From S. Cerevisiae BDF2 Gene with Ac Mismatch at Reaction Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:50.7
occ:1.00
 ND1 D:HIS394 2.1 51.9 1.0
O D:HOH901 2.1 50.2 1.0
SG D:CYS451 2.2 50.4 1.0
SG D:CYS516 2.3 58.0 1.0
CE1 D:HIS394 3.0 49.7 1.0
CG D:HIS394 3.1 49.8 1.0
CB D:CYS516 3.2 47.6 1.0
CB D:CYS451 3.3 45.0 1.0
OE2 D:GLU396 3.4 51.6 1.0
CB D:HIS394 3.5 42.4 1.0
N D:CYS451 3.6 45.3 1.0
CE D:LYS483 3.9 68.9 1.0
CA D:CYS451 4.0 51.5 1.0
CD D:GLU396 4.1 53.7 1.0
NE2 D:HIS394 4.1 54.6 1.0
N D:CYS516 4.2 46.0 1.0
CD2 D:HIS394 4.2 54.6 1.0
NZ D:LYS483 4.3 73.3 1.0
CA D:CYS516 4.3 44.3 1.0
OE1 D:GLU396 4.7 58.7 1.0
C D:PRO450 4.7 50.9 1.0
NH2 D:ARG455 4.8 46.1 1.0
C D:CYS451 4.8 53.1 1.0
CG D:GLU396 4.9 49.6 1.0
CA D:HIS394 4.9 39.8 1.0
O D:CYS451 5.0 56.6 1.0

Reference:

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
Page generated: Sun Oct 27 17:37:52 2024

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