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Magnesium in PDB 6y3z: Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3)

Enzymatic activity of Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3)

All present enzymatic activity of Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3):
3.6.1.62; 6.3.2.25;

Protein crystallography data

The structure of Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3), PDB code: 6y3z was solved by M.Graille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 3.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.210, 90.600, 194.240, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 32.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3) (pdb code 6y3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3), PDB code: 6y3z:

Magnesium binding site 1 out of 1 in 6y3z

Go back to Magnesium Binding Sites List in 6y3z
Magnesium binding site 1 out of 1 in the Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the PBY1 Atp-Grasp Enzyme Bound to the S. Cerevisiae Mrna Decapping Complex (DCP1-DCP2-EDC3) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg801

b:1.0
occ:1.00
 OD2 P:ASP446 2.2 0.9 1.0
OD1 P:ASP446 2.3 0.8 1.0
CG P:ASP446 2.4 0.9 1.0
OE1 P:GLU451 2.5 0.8 1.0
OE2 P:GLU451 2.6 0.3 1.0
OE1 P:GLU459 2.8 0.5 1.0
CD P:GLU451 2.9 0.8 1.0
OD1 P:ASP448 3.1 0.0 1.0
O P:ASP446 3.1 0.8 1.0
OE2 P:GLU459 3.1 0.4 1.0
CD P:GLU459 3.4 0.1 1.0
CB P:ASP446 3.7 0.2 1.0
C P:ASP446 3.8 0.2 1.0
CE A:LYS192 3.8 1.0 1.0
NZ A:LYS192 4.3 0.7 1.0
CG P:ASP448 4.3 0.9 1.0
CA P:ASP446 4.4 0.1 1.0
CG P:GLU451 4.4 0.2 1.0
N P:ASP448 4.5 0.8 1.0
N P:LEU447 4.6 0.7 1.0
CB P:ALA456 4.8 0.8 1.0
CA P:LEU447 4.8 0.3 1.0
CG P:GLU459 4.9 0.4 1.0

Reference:

C.Charenton, C.Gaudon-Plesse, R.Back, N.Ulryck, L.Cosson, B.Seraphin, M.Graille. PBY1 Is A Direct Partner of the DCP2 Decapping Enzyme Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA337
Page generated: Wed Oct 2 00:08:53 2024

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