Magnesium in PDB 5lop: Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP

The structure of Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP, PDB code: 5lop was solved by C.Charenton, V.Taverniti, C.Gaudon-Plesse, R.Back, B.Seraphin, M.Graille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 3.50
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	219.810, 219.810, 74.190, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 26.6

The binding sites of Magnesium atom in the Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP (pdb code 5lop). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP, PDB code: 5lop:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:0.6 occ:1.00 O3B A:M7G303 2.0 0.7 1.0 O A:HOH404 2.1 0.3 1.0 O A:ARG132 2.2 0.9 1.0 O2B A:M7G303 2.7 0.2 1.0 O A:HOH407 2.8 1.0 1.0 OE2 A:GLU152 2.8 0.4 1.0 PB A:M7G303 2.9 0.2 1.0 C A:ARG132 3.4 0.5 1.0 MG A:MG302 3.4 0.1 1.0 CD A:GLU152 3.8 0.8 1.0 CA A:GLY133 3.9 0.9 1.0 O1B A:M7G303 3.9 0.8 1.0 CD A:ARG132 4.0 0.2 1.0 O3A A:M7G303 4.0 0.6 1.0 OE1 A:GLU152 4.0 0.7 1.0 N A:GLY133 4.1 0.6 1.0 CG A:ARG132 4.4 0.9 1.0 CA A:ARG132 4.5 0.4 1.0 OE1 A:GLU148 4.5 0.1 1.0 NH1 A:ARG132 4.5 0.1 1.0 N A:ARG132 4.6 0.6 1.0 O A:HOH405 4.6 0.2 1.0

Magnesium binding site 2 out of 3 in the Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:0.1 occ:1.00 O A:HOH402 1.9 0.2 1.0 OE2 A:GLU152 1.9 0.4 1.0 O2B A:M7G303 1.9 0.2 1.0 OE1 A:GLU148 2.3 0.1 1.0 OE2 A:GLU197 2.7 0.3 1.0 CD A:GLU152 3.0 0.8 1.0 PB A:M7G303 3.1 0.2 1.0 O A:HOH401 3.1 0.7 1.0 CG A:GLU152 3.3 0.3 1.0 O1B A:M7G303 3.3 0.8 1.0 MG A:MG301 3.4 0.6 1.0 CD A:GLU148 3.4 0.1 1.0 CD A:GLU197 3.5 0.3 1.0 O3B A:M7G303 3.8 0.7 1.0 O A:ARG132 3.8 0.9 1.0 OE2 A:GLU148 3.9 0.2 1.0 OE1 A:GLU197 4.0 0.6 1.0 OE1 A:GLU152 4.1 0.7 1.0 O A:HOH404 4.2 0.3 1.0 O3A A:M7G303 4.3 0.6 1.0 OE1 A:GLU151 4.4 0.5 1.0 CG A:GLU197 4.5 0.2 1.0 O2A A:M7G303 4.5 0.1 1.0 CA A:GLY133 4.7 0.9 1.0 CG A:GLU148 4.7 0.8 1.0 C A:ARG132 4.7 0.5 1.0 O A:GLU148 4.7 0.2 1.0 CB A:GLU152 4.8 0.1 1.0

Magnesium binding site 3 out of 3 in the Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Active Form of /K. Lactis/ DCP1-DCP2-EDC3 Decapping Complex Bound to M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:0.8 occ:1.00 O A:HOH403 2.2 0.8 1.0 O A:HOH406 2.8 0.7 1.0 NH2 A:ARG147 2.9 0.3 1.0 O A:HOH401 3.0 0.7 1.0 OE2 A:GLU148 3.0 0.2 1.0 O1B A:M7G303 3.2 0.8 1.0 NH1 A:ARG147 3.6 0.1 1.0 O2A A:M7G303 3.6 0.1 1.0 CZ A:ARG147 3.6 0.2 1.0 O A:LYS134 4.1 0.1 1.0 CD A:GLU148 4.2 0.1 1.0 O1A A:M7G303 4.3 0.2 1.0 PA A:M7G303 4.4 0.0 1.0 PB A:M7G303 4.5 0.2 1.0 CD A:LYS134 4.6 0.6 1.0 CB A:LYS134 4.6 0.9 1.0 O3A A:M7G303 4.7 0.6 1.0 OE1 A:GLU148 4.8 0.1 1.0 N A:LYS134 4.8 0.7 1.0 NE A:ARG147 4.9 0.6 1.0

C.Charenton, V.Taverniti, C.Gaudon-Plesse, R.Back, B.Seraphin, M.Graille. Structure of the Active Form of DCP1-DCP2 Decapping Enzyme Bound to M(7)Gdp and Its EDC3 Activator. Nat.Struct.Mol.Biol. V. 23 982 2016.
ISSN: ESSN 1545-9985
PubMed: 27694841
DOI: 10.1038/NSMB.3300