Magnesium in PDB 4okk: Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump

The structure of Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump, PDB code: 4okk was solved by 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 Dersar, B.J.Appelmelk, J.J.Geurtsen, R.Berisio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.95 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.489, 76.848, 105.244, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 25.9

The binding sites of Magnesium atom in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump (pdb code 4okk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump, PDB code: 4okk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


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 Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:50.0 occ:1.00 O A:HOH464 2.3 34.1 1.0 OD1 A:ASP6 2.5 42.0 1.0 O2P A:U5P201 2.5 80.7 1.0 OD1 A:ASP95 2.7 31.5 1.0 O A:THR7 2.8 34.5 1.0 C5' A:U5P201 3.2 75.5 1.0 CG A:ASP6 3.4 38.2 1.0 CG A:ASP95 3.4 32.7 1.0 OD2 A:ASP95 3.5 37.1 1.0 P A:U5P201 3.5 82.3 1.0 MG A:MG204 3.8 26.7 1.0 O5' A:U5P201 3.8 79.0 1.0 OD2 A:ASP6 3.8 41.1 1.0 N A:THR7 3.8 34.3 1.0 C A:THR7 3.9 33.9 1.0 O A:HOH411 3.9 54.3 1.0 O3P A:U5P201 4.0 83.6 1.0 CA A:THR7 4.4 34.3 1.0 C4' A:U5P201 4.5 74.5 1.0 CB A:ASP6 4.5 34.3 1.0 OG1 A:THR7 4.6 33.8 1.0 OE2 A:GLU8 4.6 39.2 1.0 CA A:ASP6 4.6 34.7 1.0 C A:ASP6 4.7 33.9 1.0 CE2 A:PHE9 4.8 33.4 1.0 CB A:ASP95 4.9 29.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


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 Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:46.5 occ:1.00 O A:TYR5 2.9 32.8 1.0 N A:TRP90 3.1 34.8 1.0 OD1 A:ASP145 3.4 54.5 1.0 OD1 A:ASP6 3.5 42.0 1.0 CG A:GLN149 3.5 37.5 1.0 CB A:ALA89 3.7 33.1 1.0 O A:TRP90 3.7 40.0 1.0 CA A:ALA89 3.7 33.2 1.0 CB A:ASP6 3.8 34.3 1.0 C A:ALA89 3.9 34.2 1.0 CB A:TRP90 3.9 36.9 1.0 C A:TYR5 3.9 33.0 1.0 CA A:ASP6 4.0 34.7 1.0 CA A:TRP90 4.0 37.1 1.0 CD A:GLN149 4.0 43.7 1.0 OE1 A:GLN149 4.0 49.6 1.0 O A:HOH464 4.0 34.1 1.0 CG A:ASP6 4.1 38.2 1.0 C A:TRP90 4.3 39.2 1.0 N A:ASP6 4.4 34.0 1.0 CG A:ASP145 4.5 49.2 1.0 CB A:GLN149 4.8 34.8 1.0 OD2 A:ASP95 4.8 37.1 1.0 NE2 A:GLN149 4.9 41.9 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


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 Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:26.7 occ:1.00 O2P A:U5P201 1.9 80.7 1.0 OE2 A:GLU8 1.9 39.2 1.0 O A:HOH331 1.9 66.3 1.0 OD2 A:ASP6 2.0 41.1 1.0 CG A:ASP6 2.8 38.2 1.0 P A:U5P201 2.9 82.3 1.0 OD1 A:ASP6 3.0 42.0 1.0 CD A:GLU8 3.0 40.7 1.0 OE1 A:GLU8 3.6 37.8 1.0 OD2 A:ASP145 3.7 57.1 1.0 CG A:ASP145 3.7 49.2 1.0 CB A:ASP145 3.7 41.7 1.0 MG A:MG202 3.8 50.0 1.0 O A:THR7 3.9 34.5 1.0 O5' A:U5P201 4.0 79.0 1.0 O3P A:U5P201 4.1 83.6 1.0 CA A:HIS140 4.2 54.9 1.0 CB A:ASP6 4.2 34.3 1.0 CG A:GLU8 4.3 36.3 1.0 O A:HOH464 4.4 34.1 1.0 OD1 A:ASP145 4.4 54.5 1.0 C5' A:U5P201 4.4 75.5 1.0 CA A:ALA142 4.6 40.1 1.0 C A:HIS140 4.6 51.8 1.0 N A:HIS140 4.6 56.8 1.0 C A:THR7 4.6 33.9 1.0 O A:ASP141 4.9 45.0 1.0 N A:ALA142 4.9 41.9 1.0 O A:HIS140 4.9 50.6 1.0 C A:ASP141 4.9 44.3 1.0 N A:THR7 5.0 34.3 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:43.7 occ:1.00 O B:HOH302 2.3 31.6 1.0 OD1 B:ASP6 2.3 36.8 1.0 O B:HOH431 2.4 46.5 1.0 O B:HOH379 2.6 55.9 1.0 O2P B:U5P201 2.8 54.8 1.0 O3P B:U5P201 2.9 50.4 1.0 P B:U5P201 3.2 58.7 1.0 O B:HOH460 3.4 67.1 1.0 CG B:ASP6 3.5 33.3 1.0 MG B:MG204 3.6 5.3 0.5 OD2 B:ASP95 3.9 29.2 1.0 OD2 B:ASP6 3.9 34.5 1.0 OD1 B:ASP95 4.0 29.7 1.0 O B:HOH332 4.1 49.8 1.0 O5' B:U5P201 4.3 59.4 1.0 C5' B:U5P201 4.3 59.4 1.0 CG B:ASP95 4.4 29.6 1.0 O B:HOH311 4.4 38.8 1.0 O B:THR7 4.4 30.1 1.0 O B:TRP90 4.5 39.9 1.0 CB B:ASP6 4.7 31.5 1.0 O B:HOH344 4.8 60.0 1.0 OD2 B:ASP145 4.9 49.4 1.0 O B:VAL91 5.0 40.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:52.2 occ:1.00 OE2 B:GLU37 2.5 45.4 1.0 O B:HOH387 2.8 66.8 1.0 O B:HOH402 2.9 49.9 1.0 N B:GLN67 3.1 38.0 1.0 CB B:GLN67 3.4 40.0 1.0 N B:ARG66 3.4 38.0 1.0 OG B:SER65 3.6 36.7 1.0 CB B:SER65 3.7 38.1 1.0 CD B:GLU37 3.7 48.4 1.0 CA B:GLN67 3.8 39.2 1.0 CB B:ARG66 3.9 37.5 1.0 CA B:ARG66 3.9 37.5 1.0 C B:ARG66 3.9 38.4 1.0 C B:SER65 4.1 38.5 1.0 OE1 B:GLU37 4.1 48.8 1.0 CA B:SER65 4.4 38.8 1.0 O B:HOH390 4.5 58.3 1.0 CG B:GLN67 4.7 47.0 1.0 O B:HOH380 4.8 51.1 1.0 CD B:GLN67 4.9 54.4 1.0 OE1 B:GLN67 4.9 56.8 1.0 CG B:GLU37 4.9 48.7 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rnase As From M Tuberculosis in Complex with Ump within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:5.3 occ:0.50 OD2 B:ASP6 1.8 34.5 1.0 O2P B:U5P201 1.8 54.8 1.0 OD2 B:ASP145 1.9 49.4 1.0 OE2 B:GLU8 2.0 39.2 1.0 CG B:ASP6 2.7 33.3 1.0 CG B:ASP145 2.9 45.9 1.0 OD1 B:ASP6 3.0 36.8 1.0 CD B:GLU8 3.1 40.2 1.0 P B:U5P201 3.2 58.7 1.0 CB B:ASP145 3.4 39.9 1.0 MG B:MG202 3.6 43.7 1.0 OE1 B:GLU8 3.6 40.7 1.0 O B:THR7 4.0 30.1 1.0 OD1 B:ASP145 4.1 51.7 1.0 O B:HOH302 4.1 31.6 1.0 CB B:ASP6 4.1 31.5 1.0 CA B:HIS140 4.3 69.5 1.0 O3P B:U5P201 4.3 50.4 1.0 O5' B:U5P201 4.3 59.4 1.0 CG B:GLU8 4.4 34.9 1.0 O B:HOH460 4.4 67.1 1.0 CA B:ALA142 4.4 42.0 1.0 O B:HOH344 4.6 60.0 1.0 N B:HIS140 4.7 73.1 1.0 C B:THR7 4.7 30.7 1.0 O B:ASP141 4.7 47.9 1.0 C5' B:U5P201 4.7 59.4 1.0 N B:ALA142 4.9 45.2 1.0 C B:HIS140 4.9 65.0 1.0 N B:THR7 4.9 29.2 1.0 C B:ASP141 4.9 50.0 1.0 CA B:ASP145 4.9 39.0 1.0 CB B:ALA142 5.0 41.0 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