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Magnesium in PDB 7eu0: The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex

Enzymatic activity of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex

All present enzymatic activity of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex:
2.7.7.48; 2.7.7.6;

Other elements in 7eu0:

The structure of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex (pdb code 7eu0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex, PDB code: 7eu0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7eu0

Go back to Magnesium Binding Sites List in 7eu0
Magnesium binding site 1 out of 2 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:21.9
occ:1.00
OD1 A:ASP447 2.1 20.9 1.0
CB A:ASP449 2.1 21.2 1.0
OD2 A:ASP451 2.2 20.9 1.0
OD2 A:ASP449 2.2 21.2 1.0
OP1 O:C11 2.3 76.2 1.0
CG A:ASP449 2.6 21.2 1.0
CG A:ASP447 2.8 20.9 1.0
OD2 A:ASP447 2.9 20.9 1.0
CG A:ASP451 3.0 20.9 1.0
OD1 A:ASP451 3.2 20.9 1.0
CA A:ASP449 3.6 21.2 1.0
P O:C11 3.8 76.2 1.0
OD1 A:ASP449 3.8 21.2 1.0
N A:ASP449 4.2 21.2 1.0
CB A:ASP447 4.2 20.9 1.0
O A:ASP447 4.2 20.9 1.0
C A:ASP449 4.3 21.2 1.0
O A:ASP449 4.3 21.2 1.0
CB A:ASP451 4.4 20.9 1.0
O3' O:A10 4.4 67.0 1.0
C A:ASP447 4.5 20.9 1.0
O5' O:C11 4.6 76.2 1.0
N A:ASP447 4.6 20.9 1.0
CA A:ASP447 4.7 20.9 1.0
OP2 O:C11 4.8 76.2 1.0
C5' O:A10 4.8 67.0 1.0
C A:PHE448 5.0 13.1 1.0

Magnesium binding site 2 out of 2 in 7eu0

Go back to Magnesium Binding Sites List in 7eu0
Magnesium binding site 2 out of 2 in the The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of A. Thaliana Pol IV-RDR2 Backtracked Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg2001

b:44.5
occ:1.00
OD1 M:ASP830 2.1 53.0 1.0
OD1 M:ASP832 2.1 56.9 1.0
OD2 M:ASP834 2.1 58.8 1.0
O3' R:A20 2.2 90.0 1.0
CG M:ASP834 2.9 58.8 1.0
C3' R:A20 3.0 90.0 1.0
CG M:ASP832 3.1 56.9 1.0
CG M:ASP830 3.1 53.0 1.0
C4' R:A20 3.3 90.0 1.0
OD2 M:ASP832 3.5 56.9 1.0
CB M:ASP834 3.5 58.8 1.0
O M:ASP830 3.5 53.0 1.0
N M:ASP830 3.7 53.0 1.0
C M:ASP830 3.8 53.0 1.0
OD2 M:ASP830 3.8 53.0 1.0
OD1 M:ASP834 3.8 58.8 1.0
CA M:ASP830 4.1 53.0 1.0
N M:ASP832 4.1 56.9 1.0
CB M:ASP830 4.1 53.0 1.0
C5' R:A20 4.2 90.0 1.0
CE M:LYS783 4.3 58.6 1.0
C2' R:A20 4.4 90.0 1.0
O4' R:A20 4.4 90.0 1.0
N M:LEU831 4.4 54.5 1.0
NZ M:LYS783 4.4 58.6 1.0
CB M:ASP832 4.4 56.9 1.0
CA M:ASP832 4.7 56.9 1.0
C M:GLY829 4.7 50.9 1.0
CA M:ASP834 4.8 58.8 1.0
C1' R:A20 4.9 90.0 1.0
CA M:LEU831 4.9 54.5 1.0
O2' R:A20 4.9 90.0 1.0
C M:LEU831 4.9 54.5 1.0
N M:ASP834 4.9 58.8 1.0
CA M:GLY829 4.9 50.9 1.0
C M:ASP832 5.0 56.9 1.0

Reference:

K.Huang, X.X.Wu, C.L.Fang, Y.Zhang. Pol IV and RDR2: A Two-Rna-Polymerase Machine That Produces Double-Stranded Rna. Science 2021.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ABJ9184
Page generated: Thu Mar 31 04:06:19 2022

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