Magnesium in PDB 4s2y: Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions

The structure of Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions, PDB code: 4s2y was solved by N.Vasilyev, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.45 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.631, 36.484, 58.073, 90.00, 102.30, 90.00
R / Rfree (%)	17.2 / 19.9

The structure of Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions (pdb code 4s2y). 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 E. Coli Rpph Bound to Rna and Three Magnesium Ions, PDB code: 4s2y:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:14.8 occ:0.70 OE1 A:GLU54 2.0 23.1 1.0 O A:HOH308 2.1 19.3 0.9 OE2 A:GLU58 2.1 19.4 1.0 OE1 A:GLU121 2.1 26.6 1.0 O B:HOH201 2.2 22.7 0.9 O1B B:APC1 2.3 26.8 0.8 CD A:GLU121 3.1 27.1 1.0 CD A:GLU54 3.1 18.3 1.0 MG A:MG202 3.1 16.4 0.6 CD A:GLU58 3.1 18.8 1.0 PB B:APC1 3.3 29.9 0.8 OE2 A:GLU121 3.4 23.3 1.0 CG A:GLU58 3.4 20.8 1.0 OE2 A:GLU54 3.4 20.2 1.0 O2B B:APC1 3.6 29.4 0.8 MG B:MG101 3.6 17.1 0.8 OE2 A:GLU57 3.9 27.1 1.0 O3B B:APC1 3.9 35.7 0.8 O A:HOH355 4.1 26.1 0.8 O A:GLN38 4.1 16.4 1.0 O A:HOH387 4.2 38.0 1.0 O A:HOH316 4.3 23.0 1.0 OE1 A:GLU58 4.3 16.7 1.0 O A:HOH339 4.4 27.6 0.9 CG A:GLU121 4.4 26.9 1.0 CG A:GLU54 4.4 19.5 1.0 CA A:GLY39 4.5 28.8 1.0 O2A B:APC1 4.6 30.6 0.8 CB A:GLU54 4.8 19.8 1.0 O A:HOH310 4.9 17.4 0.8 C3A B:APC1 4.9 33.5 0.8 CB A:GLU58 4.9 16.3 1.0 CB A:GLU57 5.0 18.5 1.0

Magnesium binding site 2 out of 3 in the Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.4 occ:0.64 O1B B:APC1 1.9 26.8 0.8 O A:GLN38 2.0 16.4 1.0 O2A B:APC1 2.0 30.6 0.8 OE2 A:GLU121 2.0 23.3 1.0 OE2 A:GLU58 2.0 19.4 1.0 O A:HOH310 2.1 17.4 0.8 CD A:GLU121 3.0 27.1 1.0 CD A:GLU58 3.0 18.8 1.0 MG A:MG201 3.1 14.8 0.7 PA B:APC1 3.2 37.5 0.8 C A:GLN38 3.3 18.1 1.0 PB B:APC1 3.3 29.9 0.8 OE1 A:GLU121 3.3 26.6 1.0 OE1 A:GLU58 3.3 16.7 1.0 C3A B:APC1 3.8 33.5 0.8 O A:HOH360 3.9 31.1 0.8 O3B B:APC1 4.0 35.7 0.8 O A:HOH359 4.0 45.6 0.9 N A:GLN38 4.1 15.8 1.0 CA A:GLY39 4.1 28.8 1.0 N A:GLY39 4.1 18.6 1.0 OE1 A:GLU54 4.1 23.1 1.0 CA A:GLN38 4.2 18.1 1.0 O5' B:APC1 4.3 42.5 0.8 CG A:GLU121 4.3 26.9 1.0 CG A:GLU58 4.3 20.8 1.0 O1A B:APC1 4.4 39.4 0.8 O2B B:APC1 4.5 29.4 0.8 O B:HOH204 4.5 30.9 1.0 CG A:GLN38 4.5 20.8 1.0 O B:HOH201 4.7 22.7 0.9 O B:HOH203 4.7 29.8 0.7 CB A:GLU121 4.7 21.3 1.0 CB A:GLN38 5.0 21.6 1.0 O A:HOH308 5.0 19.3 0.9

Magnesium binding site 3 out of 3 in the Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of E. Coli Rpph Bound to Rna and Three Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:17.1 occ:0.75 O A:HOH316 2.0 23.0 1.0 O2B B:APC1 2.0 29.4 0.8 O B:HOH202 2.0 25.3 0.9 O B:HOH201 2.0 22.7 0.9 OE2 A:GLU54 2.1 20.2 1.0 O A:HOH314 2.1 21.9 0.9 CD A:GLU54 3.2 18.3 1.0 PB B:APC1 3.3 29.9 0.8 O2G B:APC1 3.4 54.5 0.8 OE1 A:GLU54 3.6 23.1 1.0 MG A:MG201 3.6 14.8 0.7 O1B B:APC1 3.9 26.8 0.8 NH1 A:ARG53 3.9 19.7 1.0 O3B B:APC1 3.9 35.7 0.8 N A:GLY40 4.0 19.5 1.0 O A:HOH387 4.0 38.0 1.0 PG B:APC1 4.0 50.7 0.8 OE2 A:GLU57 4.1 27.1 1.0 O3G B:APC1 4.2 53.9 0.8 O A:HOH362 4.2 48.0 1.0 NH1 A:ARG9 4.3 50.5 1.0 O A:GLY40 4.4 22.1 1.0 O A:HOH308 4.4 19.3 0.9 CG A:GLU54 4.5 19.5 1.0 CA A:GLY39 4.6 28.8 1.0 CA A:GLY40 4.7 21.0 1.0 C3A B:APC1 4.7 33.5 0.8 C A:GLY39 4.8 20.0 1.0 CZ A:ARG53 4.9 19.9 1.0 NH2 A:ARG53 4.9 20.2 1.0

N.Vasilyev, A.Serganov. Structures of Escherichia Coli Rpph-Rna Complexes Unveil the Basis For Specific 5 -End-Dependent Mrna Decay To Be Published.