Magnesium in PDB 4kg3: Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation)

The structure of Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation), PDB code: 4kg3 was solved by R.A.Aglietti, S.N.Floor, J.D.Gross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.50 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.789, 49.270, 84.022, 90.00, 91.37, 90.00
R / Rfree (%)	17.7 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation) (pdb code 4kg3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation), PDB code: 4kg3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation)


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 Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.4 occ:1.00 OE1 A:GLU149 2.0 19.3 1.0 O A:HOH513 2.1 22.8 1.0 O A:HOH406 2.1 20.4 1.0 O A:HOH412 2.1 25.1 1.0 O A:HOH408 2.1 22.0 1.0 O A:HOH401 2.1 20.9 1.0 CD A:GLU149 3.0 26.9 1.0 OE2 A:GLU149 3.3 28.3 1.0 OE1 A:GLU152 3.8 23.7 1.0 OE2 A:GLU198 4.0 23.2 1.0 CA A:GLY134 4.2 19.7 1.0 O A:HOH458 4.2 38.5 1.0 OE1 A:GLU198 4.3 27.0 1.0 CG A:GLU149 4.3 20.1 1.0 O A:ARG133 4.4 18.7 1.0 O A:HOH450 4.5 36.1 1.0 O A:HOH510 4.5 52.8 1.0 CD A:GLU198 4.5 26.4 1.0 NE2 A:GLN153 4.7 20.1 1.0 CB A:GLU149 4.8 16.5 1.0 CD A:GLU152 4.8 28.8 1.0 N A:LYS135 4.8 24.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:19.3 occ:1.00 O C:HOH532 2.0 21.9 1.0 O C:HOH404 2.0 19.7 1.0 OE1 B:GLU149 2.1 23.3 1.0 O B:HOH406 2.1 24.1 1.0 O C:HOH402 2.1 18.3 1.0 O B:HOH403 2.1 17.2 1.0 CD B:GLU149 3.1 26.6 1.0 OE2 B:GLU149 3.4 30.4 1.0 OE1 B:GLU152 3.8 24.2 1.0 OE2 B:GLU198 4.0 23.7 1.0 CA B:GLY134 4.2 18.5 1.0 O B:HOH471 4.2 39.9 1.0 OE1 B:GLU198 4.2 26.1 1.0 O C:GLU244 4.2 28.9 1.0 O C:ASP245 4.2 29.1 1.0 O C:ASN243 4.3 28.9 1.0 O B:ARG133 4.4 19.6 1.0 CG B:GLU149 4.4 19.0 1.0 CD B:GLU198 4.5 29.7 1.0 C C:GLU244 4.5 26.1 1.0 O B:HOH473 4.7 41.4 1.0 NE2 B:GLN153 4.7 15.7 1.0 CB B:GLU149 4.8 18.4 1.0 CD B:GLU152 4.8 29.6 1.0 N B:LYS135 4.8 25.7 1.0 C C:ASP245 4.9 37.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Saccharomyces Cerevisiae DCP2 Nudix Domain in Complex with Mg (E153Q Mutation) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:33.0 occ:1.00 O C:HOH419 2.0 33.4 1.0 O C:HOH533 2.1 28.6 1.0 O C:HOH434 2.1 27.1 1.0 O C:HOH416 2.1 30.0 1.0 O C:HOH486 2.1 35.4 1.0 OE1 C:GLU149 2.1 27.3 1.0 CD C:GLU149 3.0 33.6 1.0 OE2 C:GLU149 3.2 40.6 1.0 OE1 C:GLU152 3.8 36.2 1.0 NE2 C:GLN153 3.9 25.8 1.0 OE2 C:GLU198 4.0 34.6 1.0 O C:HOH523 4.2 45.7 1.0 OE1 C:GLU198 4.3 36.7 1.0 CA C:GLY134 4.4 28.6 1.0 CG C:GLU149 4.4 27.4 1.0 O C:ARG133 4.5 30.5 1.0 O C:HOH485 4.5 50.7 1.0 O C:HOH435 4.5 33.0 1.0 CD C:GLU198 4.5 35.4 1.0 NH1 C:ARG148 4.7 32.4 1.0 CD C:GLU152 4.8 34.2 1.0 CB C:GLU149 4.9 29.5 1.0

R.A.Aglietti, S.N.Floor, C.L.Mcclendon, M.P.Jacobson, J.D.Gross. Active Site Conformational Dynamics Are Coupled to Catalysis in the Mrna Decapping Enzyme DCP2. Structure V. 21 1571 2013.
ISSN: ISSN 0969-2126
PubMed: 23911090
DOI: 10.1016/J.STR.2013.06.021