Magnesium in PDB 6s0m: Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence

The structure of Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence, PDB code: 6s0m was solved by R.Berisio, M.Romano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.464, 77.068, 104.572, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 24.2

The binding sites of Magnesium atom in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence (pdb code 6s0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence, PDB code: 6s0m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:44.8 occ:1.00 O A:HOH354 2.0 35.0 1.0 O A:HOH317 2.1 31.5 1.0 OD1 A:ASP6 2.2 28.2 1.0 O A:HOH466 2.2 48.1 1.0 O A:HOH411 2.3 38.3 1.0 CG A:ASP6 3.3 27.7 1.0 OD2 A:ASP6 3.7 33.2 1.0 OD2 A:ASP95 3.8 24.9 1.0 OD1 A:ASP95 3.9 23.7 1.0 O A:HOH382 4.0 45.6 1.0 O A:HOH364 4.2 22.4 1.0 CG A:ASP95 4.2 21.0 1.0 O A:THR7 4.3 22.4 1.0 O A:TRP90 4.4 27.1 1.0 CB A:ASP6 4.5 22.2 1.0 O A:HOH423 4.6 34.6 1.0 O A:HOH439 4.8 73.7 1.0 N A:THR7 4.8 23.1 1.0 CA A:ASP6 4.9 22.2 1.0

Magnesium binding site 2 out of 4 in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:48.1 occ:1.00 O B:HOH308 2.1 32.6 1.0 O B:HOH384 2.2 47.6 1.0 OP3 C:G211 2.3 78.2 1.0 OD1 B:ASP6 2.4 25.9 1.0 O B:HOH303 2.5 24.5 1.0 P C:G211 3.5 81.2 1.0 CG B:ASP6 3.5 23.9 1.0 OP1 C:G211 3.6 81.9 1.0 OD2 B:ASP6 3.8 22.6 1.0 OD2 B:ASP95 3.9 24.3 1.0 O5' C:G211 4.0 80.5 1.0 MG B:MG202 4.0 42.6 1.0 OD1 B:ASP95 4.0 22.0 1.0 O B:TRP90 4.2 26.3 1.0 O B:HOH346 4.3 27.5 1.0 C5' C:G211 4.4 79.8 1.0 O B:HOH377 4.4 46.3 1.0 CG B:ASP95 4.4 22.5 1.0 O B:HOH408 4.5 34.7 1.0 O B:THR7 4.5 20.3 1.0 O B:HOH332 4.6 63.0 1.0 OP2 C:G211 4.7 80.6 1.0 CB B:ASP6 4.8 20.5 1.0 O B:VAL91 4.9 24.9 1.0

Magnesium binding site 3 out of 4 in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:42.6 occ:1.00 OD2 B:ASP6 1.8 22.6 1.0 OE2 B:GLU8 2.1 38.2 1.0 OD2 B:ASP145 2.1 38.9 1.0 OP3 C:G211 2.4 78.2 1.0 CG B:ASP6 2.9 23.9 1.0 CG B:ASP145 3.2 36.5 1.0 OP2 C:G211 3.2 80.6 1.0 CD B:GLU8 3.2 32.2 1.0 P C:G211 3.3 81.2 1.0 OD1 B:ASP6 3.4 25.9 1.0 CB B:ASP145 3.6 27.4 1.0 O B:HOH332 3.6 63.0 1.0 O B:THR7 3.8 20.3 1.0 OE1 B:GLU8 3.9 34.2 1.0 MG B:MG201 4.0 48.1 1.0 CA B:HIS140 4.1 45.3 1.0 CA B:ALA142 4.2 23.5 1.0 CB B:ASP6 4.2 20.5 1.0 CG B:GLU8 4.2 22.9 1.0 OD1 B:ASP145 4.3 42.2 1.0 N B:HIS140 4.4 49.0 1.0 O B:HOH303 4.4 24.5 1.0 OP1 C:G211 4.4 81.9 1.0 O5' C:G211 4.4 80.5 1.0 C5' C:G211 4.5 79.8 1.0 C B:THR7 4.6 19.9 1.0 O B:ASP141 4.6 27.2 1.0 CB B:ALA142 4.6 22.9 1.0 C B:HIS140 4.6 41.3 1.0 O B:HOH384 4.6 47.6 1.0 N B:ALA142 4.6 25.1 1.0 C B:ASP141 4.7 28.9 1.0 ND1 B:HIS140 4.8 52.7 1.0 N B:THR7 4.9 20.2 1.0 N B:ASP141 5.0 35.3 1.0

Magnesium binding site 4 out of 4 in the Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:34.3 occ:1.00 O B:HOH452 2.5 44.8 1.0 OE2 B:GLU37 2.6 28.4 1.0 O B:HOH447 2.8 39.9 1.0 N B:GLN67 3.0 22.8 1.0 CB B:GLN67 3.5 25.9 1.0 N B:ARG66 3.6 20.9 1.0 CD B:GLU37 3.7 32.4 1.0 CB B:SER65 3.7 21.8 1.0 O B:HOH420 3.7 51.8 1.0 CA B:GLN67 3.8 24.6 1.0 OG B:SER65 3.9 20.8 1.0 CB B:ARG66 3.9 20.8 1.0 C B:ARG66 3.9 22.9 1.0 CA B:ARG66 3.9 21.4 1.0 OE1 B:GLU37 4.0 33.0 1.0 C B:SER65 4.3 21.5 1.0 O B:HOH336 4.5 42.4 1.0 CA B:SER65 4.5 22.8 1.0 CG B:GLN67 4.9 33.7 1.0 CG B:GLU37 4.9 29.8 1.0

L.Calvanese, F.Squeglia, M.Romano, G.D'auria, L.Falcigno, R.Berisio. Structural and Dynamic Studies Provide Insights Into Specificity and Allosteric Regulation of Ribonuclease As, A Key Enzyme in Mycobacterial Virulence. J.Biomol.Struct.Dyn. 1 2019.
ISSN: ESSN 1538-0254
PubMed: 31299874
DOI: 10.1080/07391102.2019.1643786