Magnesium in PDB 6d1v: Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna

The structure of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna, PDB code: 6d1v was solved by A.Gao, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.60 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	160.644, 191.986, 51.207, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22

The structure of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna (pdb code 6d1v). 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 E. Coli Rpph-Dapf Complex, Monomer Bound to Rna, PDB code: 6d1v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


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 E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:41.6 occ:1.00 OE2 B:GLU53 2.0 36.4 1.0 O1B C:APC1 2.0 35.5 1.0 O B:HOH369 2.1 33.1 1.0 O B:HOH314 2.1 43.5 1.0 O C:HOH102 2.2 42.9 1.0 O B:HOH327 2.3 40.6 1.0 CD B:GLU53 3.0 34.7 1.0 PB C:APC1 3.2 37.3 1.0 OE1 B:GLU53 3.4 32.5 1.0 MG B:MG202 3.6 32.6 1.0 O2B C:APC1 3.6 33.3 1.0 O B:HOH425 3.7 53.4 1.0 C3A C:APC1 3.8 35.1 1.0 OE2 B:GLU56 3.9 43.7 1.0 N B:GLY39 3.9 37.6 1.0 NH2 B:ARG52 4.1 44.9 1.0 O1A C:APC1 4.1 47.7 1.0 NH1 B:ARG52 4.1 43.6 1.0 O B:HOH421 4.2 58.0 1.0 O B:HOH304 4.3 58.5 1.0 O B:GLY39 4.3 41.1 1.0 O B:HOH325 4.3 52.7 1.0 CG B:GLU53 4.3 36.4 1.0 CA B:GLY38 4.5 30.8 1.0 OE1 B:GLU56 4.6 33.7 1.0 O3B C:APC1 4.6 39.4 1.0 CZ B:ARG52 4.6 42.0 1.0 PA C:APC1 4.7 49.1 1.0 CD B:GLU56 4.7 51.7 1.0 C B:GLY38 4.7 33.6 1.0 CA B:GLY39 4.7 41.6 1.0 OE2 B:GLU120 4.9 31.5 1.0 C B:GLY39 4.9 42.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


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 E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:32.6 occ:1.00 OE1 B:GLU53 2.0 32.5 1.0 OE2 B:GLU120 2.0 31.5 1.0 O2B C:APC1 2.1 33.3 1.0 OE1 B:GLU56 2.1 33.7 1.0 OE2 B:GLU57 2.2 30.8 1.0 O B:HOH369 2.2 33.1 1.0 CD B:GLU120 2.9 40.0 1.0 MG B:MG203 3.0 32.8 1.0 CD B:GLU53 3.1 34.7 1.0 CD B:GLU56 3.2 51.7 1.0 CD B:GLU57 3.2 35.3 1.0 PB C:APC1 3.2 37.3 1.0 OE1 B:GLU120 3.3 32.0 1.0 OE2 B:GLU53 3.4 36.4 1.0 CG B:GLU57 3.5 32.2 1.0 OE2 B:GLU56 3.5 43.7 1.0 MG B:MG201 3.6 41.6 1.0 O1B C:APC1 3.7 35.5 1.0 C3A C:APC1 3.7 35.1 1.0 O B:HOH337 4.0 49.8 1.0 O B:GLN37 4.0 28.4 1.0 O B:HOH425 4.0 53.4 1.0 CG B:GLU120 4.3 37.6 1.0 OE1 B:GLU57 4.3 32.2 1.0 CG B:GLU53 4.4 36.4 1.0 CA B:GLY38 4.5 30.8 1.0 CG B:GLU56 4.5 43.2 1.0 O3G C:APC1 4.5 40.3 0.6 O3B C:APC1 4.6 39.4 1.0 O B:HOH327 4.6 40.6 1.0 O B:HOH396 4.7 41.4 1.0 CB B:GLU53 4.7 36.6 1.0 O B:HOH344 4.8 27.6 1.0 C B:GLN37 5.0 26.4 1.0 O B:HOH388 5.0 51.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


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 E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:32.8 occ:1.00 O3G C:APC1 1.9 40.3 0.6 O B:GLN37 2.0 28.4 1.0 OE2 B:GLU57 2.0 30.8 1.0 O2B C:APC1 2.0 33.3 1.0 OE1 B:GLU120 2.0 32.0 1.0 O B:HOH344 2.1 27.6 1.0 CD B:GLU120 3.0 40.0 1.0 MG B:MG202 3.0 32.6 1.0 CD B:GLU57 3.0 35.3 1.0 PG C:APC1 3.2 47.8 0.6 C B:GLN37 3.2 26.4 1.0 PB C:APC1 3.2 37.3 1.0 OE2 B:GLU120 3.3 31.5 1.0 OE1 B:GLU57 3.3 32.2 1.0 O3B C:APC1 3.5 39.4 1.0 CA B:GLY38 3.9 30.8 1.0 OE1 B:GLU53 3.9 32.5 1.0 N B:GLY38 4.0 31.3 1.0 O2G C:APC1 4.0 51.6 0.6 N B:GLN37 4.1 28.5 1.0 O B:HOH400 4.1 35.8 1.0 C3A C:APC1 4.1 35.1 1.0 CA B:GLN37 4.3 29.3 1.0 O1G C:APC1 4.3 40.7 0.6 CG B:GLU57 4.3 32.2 1.0 CG B:GLU120 4.3 37.6 1.0 O1B C:APC1 4.4 35.5 1.0 CG B:GLN37 4.5 31.5 1.0 O C:HOH108 4.5 40.9 1.0 CB B:GLU120 4.7 33.6 1.0 O B:HOH369 4.8 33.1 1.0 OE1 B:GLU56 4.8 33.7 1.0 CD B:GLU53 4.9 34.7 1.0 CB B:GLN37 5.0 26.7 1.0

A.Gao, N.Vasilyev, D.J.Luciano, R.Levenson-Palmer, J.Richards, W.M.Marsiglia, N.J.Traaseth, J.G.Belasco, A.Serganov. Structural and Kinetic Insights Into Stimulation of Rpph-Dependent Rna Degradation By the Metabolic Enzyme Dapf. Nucleic Acids Res. V. 46 6841 2018.
ISSN: ESSN 1362-4962
PubMed: 29733359
DOI: 10.1093/NAR/GKY327