Magnesium in PDB 5dji: Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound

All present enzymatic activity of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound:
3.1.3.11; 3.1.3.25; 3.1.3.7;

The structure of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound, PDB code: 5dji was solved by A.J.Fisher, A.I.Erickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.25 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.637, 58.200, 101.510, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 16.8

The binding sites of Magnesium atom in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound (pdb code 5dji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound, PDB code: 5dji:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:9.2 occ:1.00 OE1 A:GLU73 2.0 9.2 1.0 O A:HOH457 2.1 9.0 1.0 O A:LEU93 2.1 8.4 1.0 OD1 A:ASP91 2.1 7.8 1.0 O3 A:PO4304 2.2 10.8 1.0 O2 A:PO4304 2.2 8.4 1.0 P A:PO4304 2.7 14.5 1.0 CG A:ASP91 3.1 8.8 1.0 C A:LEU93 3.1 6.6 1.0 CD A:GLU73 3.2 14.4 1.0 OD2 A:ASP91 3.4 8.9 1.0 OE2 A:GLU73 3.7 16.8 1.0 O4 A:PO4304 3.7 17.3 1.0 MG A:MG302 3.7 12.9 1.0 N A:ASP94 3.9 7.1 1.0 CA A:ASP94 3.9 6.0 1.0 O1 A:PO4304 3.9 12.8 1.0 N A:LEU93 4.0 9.2 1.0 OE2 A:GLU74 4.0 12.6 1.0 CA A:LEU93 4.1 7.0 1.0 OG1 A:THR96 4.1 11.5 1.0 O A:HOH411 4.2 19.2 1.0 O A:HOH443 4.3 40.2 1.0 OD1 A:ASP50 4.3 12.5 1.0 CG A:GLU73 4.4 8.7 1.0 CB A:ASP91 4.4 6.5 1.0 CB A:GLU73 4.5 8.2 1.0 CB A:LEU93 4.6 7.2 1.0 CB A:ASP94 4.8 9.8 1.0 CA A:ASP91 4.8 7.0 1.0 N A:PRO92 4.8 6.4 1.0 C A:ASP91 4.8 7.3 1.0 CD A:PRO92 4.8 8.2 1.0 OD1 A:ASP94 4.8 15.7 1.0 O3' A:AMP303 4.9 13.2 1.0 C A:ASP94 5.0 9.3 1.0

Magnesium binding site 2 out of 2 in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 2MG Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.9 occ:1.00 OD1 A:ASP212 2.0 15.2 1.0 O2 A:PO4304 2.0 8.4 1.0 OD1 A:ASP94 2.0 15.7 1.0 OD2 A:ASP91 2.1 8.9 1.0 O3' A:AMP303 2.1 13.2 1.0 O A:HOH411 2.2 19.2 1.0 CG A:ASP212 3.1 14.2 1.0 CG A:ASP94 3.2 13.8 1.0 CG A:ASP91 3.2 8.8 1.0 C3' A:AMP303 3.3 12.1 1.0 P A:PO4304 3.3 14.5 1.0 O4 A:PO4304 3.6 17.3 1.0 C4' A:AMP303 3.7 13.6 1.0 OD1 A:ASP91 3.7 7.8 1.0 CB A:ASP94 3.7 9.8 1.0 MG A:MG301 3.7 9.2 1.0 OD2 A:ASP212 3.8 13.7 1.0 CA A:ASP94 3.9 6.0 1.0 O1 A:PO4304 4.0 12.8 1.0 OE1 A:GLU73 4.1 9.2 1.0 OD2 A:ASP94 4.2 11.0 1.0 CD1 A:TRP211 4.2 9.5 1.0 CB A:ASP212 4.3 9.7 1.0 O3 A:PO4304 4.4 10.8 1.0 CA A:ASP212 4.5 8.4 1.0 CB A:ASP91 4.5 6.5 1.0 OE2 A:GLU73 4.5 16.8 1.0 C2' A:AMP303 4.5 13.1 1.0 O4' A:AMP303 4.5 14.8 1.0 CD A:GLU73 4.5 14.4 1.0 NE1 A:TRP211 4.6 11.0 1.0 N A:GLY95 4.6 9.6 1.0 O A:LEU93 4.7 8.4 1.0 C1' A:AMP303 4.8 14.7 1.0 O2' A:AMP303 4.8 16.4 1.0 C A:ASP94 4.8 9.3 1.0 C5' A:AMP303 4.8 16.8 1.0 N A:ASP212 4.9 8.6 1.0 N A:ASP94 4.9 7.1 1.0

A.I.Erickson, R.D.Sarsam, A.J.Fisher. Crystal Structures of Mycobacterium Tuberculosis Cysq, with Substrate and Products Bound. Biochemistry V. 54 6830 2015.
ISSN: ISSN 0006-2960
PubMed: 26512869
DOI: 10.1021/ACS.BIOCHEM.5B01000