Magnesium in PDB 5n2v: Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme

The structure of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme, PDB code: 5n2v was solved by I.Holdermann, R.Sprangers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.29 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.841, 76.522, 89.526, 90.00, 102.83, 90.00
R / Rfree (%)	23.9 / 28.7

The binding sites of Magnesium atom in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme (pdb code 5n2v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme, PDB code: 5n2v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:29.9 occ:1.00 O2A B:8NK304 2.4 31.5 1.0 OE2 B:GLU146 2.7 44.9 1.0 O3B B:8NK304 3.0 29.3 1.0 OE2 B:GLU143 3.4 38.1 1.0 MG B:MG302 3.6 27.2 1.0 CD B:GLU146 3.6 58.1 1.0 PA B:8NK304 3.7 34.3 1.0 OE1 B:GLU146 3.9 42.7 1.0 PB B:8NK304 4.0 44.3 1.0 OE1 B:GLU192 4.0 37.8 1.0 O3A B:8NK304 4.1 37.7 1.0 O1A B:8NK304 4.1 58.7 1.0 O2B B:8NK304 4.2 33.9 1.0 CD B:GLU143 4.3 29.8 1.0 OE2 B:GLU192 4.4 51.8 1.0 OE1 B:GLU143 4.4 31.7 1.0 NH2 B:ARG142 4.4 66.8 1.0 NH1 B:ARG142 4.5 48.9 1.0 CD B:GLU192 4.6 44.3 1.0 O5' B:8NK304 4.9 38.0 1.0 CZ B:ARG142 4.9 56.1 1.0

Magnesium binding site 2 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:27.2 occ:1.00 O2B B:8NK304 2.0 33.9 1.0 OE2 B:GLU192 2.1 51.8 1.0 OE1 B:GLU143 2.2 31.7 1.0 OE2 B:GLU147 2.4 31.5 1.0 CD B:GLU192 3.0 44.3 1.0 CD B:GLU143 3.1 29.8 1.0 PB B:8NK304 3.2 44.3 1.0 CD B:GLU147 3.3 41.1 1.0 CG B:GLU147 3.3 30.4 1.0 OE2 B:GLU146 3.4 44.9 1.0 OE1 B:GLU192 3.4 37.8 1.0 OE2 B:GLU143 3.4 38.1 1.0 O3B B:8NK304 3.4 29.3 1.0 MG B:MG301 3.6 29.9 1.0 O3A B:8NK304 3.8 37.7 1.0 CD B:GLU146 3.9 58.1 1.0 MG B:MG303 3.9 18.1 1.0 O2A B:8NK304 4.1 31.5 1.0 O B:LYS127 4.2 25.6 1.0 CG B:GLU192 4.3 28.2 1.0 OE1 B:GLU146 4.4 42.7 1.0 OE1 B:GLU147 4.5 42.5 1.0 CG B:GLU146 4.5 46.7 1.0 O1B B:8NK304 4.5 26.9 1.0 CG B:GLU143 4.5 30.6 1.0 CA B:GLY128 4.6 41.0 1.0 PA B:8NK304 4.7 34.3 1.0 CB B:GLU146 4.7 30.6 1.0 CB B:GLU143 4.8 26.0 1.0 CB B:GLU147 4.8 35.7 1.0 O B:GLU143 4.9 25.7 1.0

Magnesium binding site 3 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:18.1 occ:1.00 O B:LYS127 2.2 25.6 1.0 OE2 B:GLU147 2.4 31.5 1.0 O2B B:8NK304 2.5 33.9 1.0 CD B:GLU147 3.4 41.1 1.0 O1B B:8NK304 3.4 26.9 1.0 PB B:8NK304 3.4 44.3 1.0 C B:LYS127 3.4 24.9 1.0 OE2 B:GLU192 3.5 51.8 1.0 OE1 B:GLU147 3.6 42.5 1.0 MG B:MG302 3.9 27.2 1.0 O3A B:8NK304 3.9 37.7 1.0 CA B:GLY128 4.1 41.0 1.0 N B:GLY128 4.2 41.7 1.0 N B:LYS127 4.4 33.0 1.0 CG B:LYS127 4.5 20.6 1.0 CA B:LYS127 4.5 27.9 1.0 OE1 B:GLU143 4.6 31.7 1.0 CD B:GLU192 4.6 44.3 1.0 CG B:GLU147 4.7 30.4 1.0 O3B B:8NK304 4.8 29.3 1.0 CG B:GLU192 4.9 28.2 1.0

Magnesium binding site 4 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:18.5 occ:1.00 O E:LYS127 2.1 31.5 1.0 OE2 E:GLU147 2.1 37.6 1.0 O3B E:8NK304 2.6 20.0 1.0 O2B E:8NK304 3.0 24.8 1.0 CD E:GLU147 3.1 47.8 1.0 PB E:8NK304 3.2 36.5 1.0 C E:LYS127 3.3 28.3 1.0 OE2 E:GLU192 3.4 53.2 1.0 OE1 E:GLU147 3.5 39.2 1.0 CA E:GLY128 3.8 26.5 1.0 MG E:MG302 3.9 17.4 1.0 O3A E:8NK304 3.9 38.2 1.0 N E:GLY128 4.0 27.6 1.0 OE1 E:GLU143 4.3 34.9 1.0 N E:LYS127 4.4 36.2 1.0 CA E:LYS127 4.4 31.3 1.0 CD E:GLU192 4.5 49.5 1.0 CG E:GLU147 4.5 40.1 1.0 CG E:LYS127 4.6 25.8 1.0 O1B E:8NK304 4.6 24.2 1.0 CG E:GLU192 4.8 40.0 1.0

Magnesium binding site 5 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:17.4 occ:1.00 OE2 E:GLU192 2.0 53.2 1.0 O3B E:8NK304 2.0 20.0 1.0 OE1 E:GLU143 2.4 34.9 1.0 OE2 E:GLU147 2.9 37.6 1.0 CD E:GLU192 2.9 49.5 1.0 MG E:MG303 3.1 19.2 1.0 OE1 E:GLU192 3.2 39.6 1.0 CD E:GLU143 3.2 24.9 1.0 PB E:8NK304 3.3 36.5 1.0 OE2 E:GLU143 3.4 28.6 1.0 OE2 E:GLU146 3.4 45.9 1.0 CG E:GLU147 3.7 40.1 1.0 CD E:GLU147 3.7 47.8 1.0 O1B E:8NK304 3.8 24.2 1.0 O3A E:8NK304 3.9 38.2 1.0 O1A E:8NK304 3.9 39.1 1.0 MG E:MG301 3.9 18.5 1.0 CD E:GLU146 4.0 60.0 1.0 CG E:GLU192 4.3 40.0 1.0 O2B E:8NK304 4.5 24.8 1.0 PA E:8NK304 4.6 38.7 1.0 OE1 E:GLU146 4.6 37.2 1.0 CG E:GLU146 4.6 54.7 1.0 O E:LYS127 4.7 31.5 1.0 CG E:GLU143 4.7 28.9 1.0 CA E:GLY128 4.7 26.5 1.0 CG2 E:THR189 4.8 32.2 1.0 OE1 E:GLU147 4.9 39.2 1.0 CB E:GLU146 4.9 41.9 1.0

Magnesium binding site 6 out of 6 in the Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:19.2 occ:1.00 O1A E:8NK304 2.1 39.1 1.0 O1B E:8NK304 2.7 24.2 1.0 MG E:MG302 3.1 17.4 1.0 OE2 E:GLU143 3.2 28.6 1.0 PA E:8NK304 3.3 38.7 1.0 PB E:8NK304 3.3 36.5 1.0 O3B E:8NK304 3.4 20.0 1.0 O3A E:8NK304 3.5 38.2 1.0 OE2 E:GLU146 3.6 45.9 1.0 O2A E:8NK304 3.9 57.2 1.0 CD E:GLU143 4.1 24.9 1.0 OE1 E:GLU143 4.1 34.9 1.0 OE2 E:GLU192 4.2 53.2 1.0 OE1 E:GLU192 4.3 39.6 1.0 NH2 E:ARG142 4.3 52.8 1.0 CD E:GLU146 4.5 60.0 1.0 O5' E:8NK304 4.6 27.1 1.0 CD E:GLU192 4.6 49.5 1.0 OE1 E:GLU146 4.7 37.2 1.0 O2B E:8NK304 4.8 24.8 1.0 NH1 E:ARG142 4.9 53.2 1.0

J.P.Wurm, I.Holdermann, J.H.Overbeck, P.H.O.Mayer, R.Sprangers. Changes in Conformational Equilibria Regulate the Activity of the DCP2 Decapping Enzyme. Proc. Natl. Acad. Sci. V. 114 6034 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533364
DOI: 10.1073/PNAS.1704496114