Magnesium in PDB 4oke: Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo

The structure of Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo, PDB code: 4oke 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)	15.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.433, 76.664, 104.372, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.2

The binding sites of Magnesium atom in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo (pdb code 4oke). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo, PDB code: 4oke:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:31.9 occ:1.00 O A:HOH471 2.0 27.7 1.0 O2P A:AMP201 2.0 30.9 1.0 O A:HOH302 2.1 27.7 1.0 O A:HOH476 2.1 37.2 1.0 OD1 A:ASP6 2.2 22.1 1.0 O A:HOH464 2.3 38.2 1.0 P A:AMP201 3.3 33.5 1.0 CG A:ASP6 3.3 26.1 1.0 O A:HOH333 3.7 36.1 1.0 O5' A:AMP201 3.8 29.3 1.0 OD2 A:ASP6 3.9 30.9 1.0 O3P A:AMP201 3.9 34.5 1.0 OD2 A:ASP95 3.9 26.9 1.0 OD1 A:ASP95 4.0 17.8 1.0 O A:HOH410 4.0 36.6 1.0 C5' A:AMP201 4.0 24.5 1.0 O A:THR7 4.3 17.3 1.0 CG A:ASP95 4.4 17.8 1.0 O A:HOH301 4.4 18.2 1.0 O A:TRP90 4.4 24.2 1.0 O1P A:AMP201 4.4 28.2 1.0 CB A:ASP6 4.6 17.3 1.0 O A:HOH422 4.8 42.3 1.0 N A:THR7 4.8 17.9 1.0 O A:HOH371 4.9 35.4 1.0 O A:VAL91 4.9 24.5 1.0

Magnesium binding site 2 out of 4 in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:17.4 occ:1.00 O B:HOH343 2.2 31.1 1.0 O B:HOH433 2.3 26.0 1.0 O B:HOH380 2.3 27.2 1.0 O1P B:AMP201 2.3 19.1 1.0 OD1 B:ASP6 2.4 27.7 1.0 O B:HOH302 2.5 15.9 1.0 O3' A:AMP203 2.5 36.8 1.0 O2' A:AMP203 2.9 39.1 1.0 CG B:ASP6 3.3 20.5 1.0 P B:AMP201 3.5 24.0 1.0 OD2 B:ASP6 3.6 26.0 1.0 C3' A:AMP203 3.6 36.6 1.0 O B:HOH462 3.7 38.5 1.0 MG B:MG203 3.7 30.9 1.0 C2' A:AMP203 3.8 38.7 1.0 O2P B:AMP201 3.9 25.1 1.0 O5' B:AMP201 4.0 22.2 1.0 C4' A:AMP203 4.2 33.9 1.0 C5' B:AMP201 4.3 19.2 1.0 OD2 B:ASP95 4.3 18.4 1.0 OD1 B:ASP95 4.3 16.0 1.0 O B:HOH313 4.5 17.6 1.0 O A:HOH337 4.5 26.8 1.0 O B:TRP90 4.5 23.9 1.0 O B:HOH374 4.6 30.6 1.0 O B:THR7 4.6 14.9 1.0 CB B:ASP6 4.6 15.7 1.0 CG B:ASP95 4.7 16.6 1.0 O3P B:AMP201 4.7 24.5 1.0 C1' A:AMP203 4.9 40.2 1.0

Magnesium binding site 3 out of 4 in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:30.9 occ:1.00 OE2 B:GLU8 2.1 23.4 1.0 OD2 B:ASP6 2.2 26.0 1.0 OD2 B:ASP145 2.2 23.1 1.0 O1P B:AMP201 2.2 19.1 1.0 O3P B:AMP201 2.9 24.5 1.0 P B:AMP201 3.1 24.0 1.0 CD B:GLU8 3.2 20.3 1.0 CG B:ASP6 3.2 20.5 1.0 CG B:ASP145 3.2 23.4 1.0 O B:HOH343 3.3 31.1 1.0 OD1 B:ASP6 3.6 27.7 1.0 CB B:ASP145 3.6 16.8 1.0 O B:HOH374 3.7 30.6 1.0 MG B:MG202 3.7 17.4 1.0 OE1 B:GLU8 3.8 20.3 1.0 O B:THR7 3.8 14.9 1.0 CA B:HIS140 4.0 25.9 1.0 O2P B:AMP201 4.1 25.1 1.0 O B:HOH302 4.2 15.9 1.0 O5' B:AMP201 4.3 22.2 1.0 CG B:GLU8 4.3 16.7 1.0 N B:HIS140 4.3 25.9 1.0 OD1 B:ASP145 4.4 26.7 1.0 CA B:ALA142 4.4 17.0 1.0 CB B:ASP6 4.5 15.7 1.0 C B:HIS140 4.5 23.9 1.0 C5' B:AMP201 4.6 19.2 1.0 C B:THR7 4.6 14.4 1.0 O B:ASP141 4.7 17.3 1.0 ND1 B:HIS140 4.7 31.3 1.0 C B:ASP141 4.8 19.2 1.0 N B:ALA142 4.8 18.2 1.0 O3' A:AMP203 4.8 36.8 1.0 N B:ASP141 4.9 21.4 1.0 CB B:ALA142 4.9 16.5 1.0 O B:HIS140 5.0 26.1 1.0 N B:THR7 5.0 14.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:20.0 occ:1.00 O B:HOH404 2.7 37.2 1.0 O B:HOH389 2.8 39.2 1.0 OE2 B:GLU37 2.8 22.3 1.0 N B:GLN67 2.9 18.7 1.0 CB B:GLN67 3.4 21.1 1.0 N B:ARG66 3.5 18.4 1.0 CB B:SER65 3.7 19.1 1.0 CA B:GLN67 3.7 19.9 1.0 OG B:SER65 3.8 20.1 1.0 C B:ARG66 3.8 19.2 1.0 CD B:GLU37 3.9 25.1 1.0 O B:HOH392 3.9 43.1 1.0 CB B:ARG66 3.9 18.6 1.0 CA B:ARG66 3.9 18.1 1.0 OE1 B:GLU37 4.2 23.6 1.0 C B:SER65 4.2 18.6 1.0 CA B:SER65 4.5 18.8 1.0 O B:HOH382 4.8 39.2 1.0 CG B:GLN67 4.8 28.2 1.0 C B:GLN67 4.9 18.3 1.0 O B:ARG66 4.9 19.9 1.0 N B:GLN68 5.0 16.5 1.0

M.Romano, R.Van De Weerd, F.C.C.Brouwer, G.N.Roviello, R.Lacroix, M.Sparrius, G.Van Den Brink-Van Stempvoort, J.J.Maaskant, A.M.Van Der Sar, B.J.Appelmelk, J.J.Geurtsen, R.Berisio. Structure and Function of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo Structure V. 22 719 2014.
ISSN: ISSN 0969-2126
PubMed: 24704253
DOI: 10.1016/J.STR.2014.01.014