Magnesium in PDB 5jnb: Structure of Gld-2/Rnp-8 Complex

All present enzymatic activity of Structure of Gld-2/Rnp-8 Complex:
2.7.7.19;

The structure of Structure of Gld-2/Rnp-8 Complex, PDB code: 5jnb was solved by K.Nakel, F.Bonneau, C.Basquin, C.R.Eckmann, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.25 / 2.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.347, 86.435, 91.907, 89.88, 93.13, 90.22
R / Rfree (%)	19.2 / 24.2

The binding sites of Magnesium atom in the Structure of Gld-2/Rnp-8 Complex (pdb code 5jnb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Gld-2/Rnp-8 Complex, PDB code: 5jnb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Gld-2/Rnp-8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Gld-2/Rnp-8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:58.0 occ:1.00 OD2 A:ASP608 2.7 40.5 1.0 N F:THR177 2.8 35.7 1.0 O A:HOH1116 3.2 41.1 1.0 O1 A:SO41001 3.3 55.4 1.0 OG A:SER595 3.5 48.4 1.0 O A:HOH1118 3.6 36.4 1.0 CG A:ASP608 3.7 41.5 1.0 OD1 A:ASP608 3.9 44.8 1.0 CB A:SER595 4.0 38.1 1.0 CA F:THR177 4.2 42.4 1.0 O F:HOH306 4.3 46.1 1.0 N A:SER595 4.5 36.2 1.0 S A:SO41001 4.6 46.3 1.0 CB A:ASP606 4.7 39.9 1.0 O A:HOH1121 4.7 37.4 1.0 O4 A:SO41001 4.7 53.0 1.0 CB F:THR177 4.8 37.7 1.0 OD2 A:ASP606 4.9 53.8 1.0 CA A:SER595 5.0 38.1 1.0 CB A:ASP608 5.0 34.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Gld-2/Rnp-8 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Gld-2/Rnp-8 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1005 b:51.9 occ:1.00 N E:THR177 2.0 39.1 1.0 CA E:THR177 2.9 35.5 1.0 OD2 B:ASP608 3.0 44.7 1.0 CB E:THR177 3.4 37.5 1.0 N B:SER595 3.5 34.4 1.0 CG B:ASP608 3.6 42.1 1.0 OG B:SER595 3.6 38.9 1.0 O B:HOH1135 3.6 45.7 1.0 OD1 B:ASP608 3.9 37.7 1.0 CB B:SER595 4.0 34.4 1.0 CA B:GLY594 4.0 34.2 1.0 C E:THR177 4.2 36.7 1.0 OG1 E:THR177 4.3 39.1 1.0 C B:GLY594 4.3 32.1 1.0 CA B:SER595 4.4 33.9 1.0 O2 B:SO41001 4.5 43.6 1.0 CB B:ASP608 4.6 30.8 1.0 O B:HOH1107 4.6 33.0 1.0 CG2 E:THR177 4.6 33.6 1.0 O E:THR177 4.6 39.3 1.0 O B:HOH1128 4.8 38.5 1.0

K.Nakel, F.Bonneau, C.Basquin, B.Habermann, C.R.Eckmann, E.Conti. Structural Basis For the Antagonistic Roles of Rnp-8 and Gld-3 in Gld-2 Poly(A)-Polymerase Activity. Rna V. 22 1139 2016.
ISSN: ESSN 1469-9001
PubMed: 27288313
DOI: 10.1261/RNA.056598.116