Magnesium in PDB 5djh: Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG Bound

All present enzymatic activity of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG 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 3MG Bound, PDB code: 5djh 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)	38.17 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.636, 58.140, 101.198, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 16.9

The binding sites of Magnesium atom in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG Bound (pdb code 5djh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG Bound, PDB code: 5djh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG 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 3MG Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:9.5 occ:1.00 OE1 A:GLU73 2.0 9.9 1.0 O A:LEU93 2.1 9.8 1.0 O A:HOH439 2.1 10.8 1.0 OD1 A:ASP91 2.1 9.3 1.0 O2 A:PO4305 2.1 9.6 1.0 O3 A:PO4305 2.2 11.9 1.0 P A:PO4305 2.8 12.2 1.0 CG A:ASP91 3.1 8.7 1.0 C A:LEU93 3.1 8.4 1.0 CD A:GLU73 3.1 12.6 1.0 OD2 A:ASP91 3.4 9.8 1.0 MG A:MG302 3.7 10.7 1.0 OE2 A:GLU73 3.7 17.8 1.0 O4 A:PO4305 3.8 14.1 1.0 N A:ASP94 3.9 9.2 1.0 O1 A:PO4305 3.9 13.1 1.0 CA A:ASP94 3.9 7.4 1.0 N A:LEU93 4.0 9.0 1.0 OE2 A:GLU74 4.0 13.4 1.0 CA A:LEU93 4.1 8.0 1.0 OG1 A:THR96 4.1 11.8 1.0 O A:HOH442 4.1 14.3 1.0 O A:HOH414 4.2 21.6 1.0 OD1 A:ASP50 4.3 11.6 1.0 CG A:GLU73 4.3 9.8 1.0 CB A:ASP91 4.4 7.5 1.0 CB A:GLU73 4.5 9.3 1.0 MG A:MG303 4.5 24.7 1.0 CB A:LEU93 4.7 8.1 1.0 CB A:ASP94 4.8 9.2 1.0 CA A:ASP91 4.8 8.3 1.0 N A:PRO92 4.8 7.9 1.0 C A:ASP91 4.8 8.3 1.0 CD A:PRO92 4.8 9.3 1.0 OD1 A:ASP94 4.8 12.6 1.0 O3' A:AMP304 4.9 11.9 1.0 C A:ASP94 5.0 10.7 1.0

Magnesium binding site 2 out of 3 in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG 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 3MG Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:10.7 occ:1.00 OD1 A:ASP212 2.0 13.4 1.0 O2 A:PO4305 2.0 9.6 1.0 OD2 A:ASP91 2.1 9.8 1.0 OD1 A:ASP94 2.1 12.6 1.0 O3' A:AMP304 2.2 11.9 1.0 O A:HOH442 2.3 14.3 1.0 CG A:ASP212 3.1 11.0 1.0 CG A:ASP91 3.2 8.7 1.0 CG A:ASP94 3.2 11.7 1.0 P A:PO4305 3.3 12.2 1.0 C3' A:AMP304 3.3 11.6 1.0 O4 A:PO4305 3.6 14.1 1.0 C4' A:AMP304 3.7 10.7 1.0 OD1 A:ASP91 3.7 9.3 1.0 MG A:MG301 3.7 9.5 1.0 CB A:ASP94 3.7 9.2 1.0 OD2 A:ASP212 3.7 12.1 1.0 CA A:ASP94 3.9 7.4 1.0 O1 A:PO4305 4.0 13.1 1.0 OE1 A:GLU73 4.0 9.9 1.0 OD2 A:ASP94 4.2 10.8 1.0 CD1 A:TRP211 4.3 11.9 1.0 CB A:ASP212 4.3 10.1 1.0 O3 A:PO4305 4.4 11.9 1.0 CB A:ASP91 4.4 7.5 1.0 O4' A:AMP304 4.5 12.6 1.0 CA A:ASP212 4.5 9.4 1.0 C2' A:AMP304 4.5 11.8 1.0 CD A:GLU73 4.6 12.6 1.0 OE2 A:GLU73 4.6 17.8 1.0 NE1 A:TRP211 4.6 12.1 1.0 O A:LEU93 4.6 9.8 1.0 O A:HOH466 4.6 24.2 1.0 N A:GLY95 4.7 9.9 1.0 C1' A:AMP304 4.8 14.0 1.0 C A:ASP94 4.8 10.7 1.0 O2' A:AMP304 4.8 13.0 1.0 MG A:MG303 4.8 24.7 1.0 C5' A:AMP304 4.8 12.4 1.0 N A:ASP94 4.9 9.2 1.0 N A:ASP212 4.9 9.7 1.0

Magnesium binding site 3 out of 3 in the Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of M. Tuberculosis Cysq, A Pap Phosphatase with Amp, PO4, and 3MG Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.7 occ:1.00 O4 A:PO4305 1.9 14.1 1.0 O A:HOH497 2.1 22.5 1.0 OE2 A:GLU73 2.1 17.8 1.0 O A:HOH414 2.1 21.6 1.0 O A:HOH466 2.2 24.2 1.0 P A:PO4305 3.1 12.2 1.0 CD A:GLU73 3.3 12.6 1.0 O3 A:PO4305 3.3 11.9 1.0 O A:HOH442 3.7 14.3 1.0 OE1 A:GLU73 3.8 9.9 1.0 O2' A:AMP304 3.8 13.0 1.0 O2 A:PO4305 3.9 9.6 1.0 O A:HOH457 4.0 35.2 1.0 O3' A:AMP304 4.0 11.9 1.0 O A:HOH537 4.1 43.0 1.0 O1 A:PO4305 4.2 13.1 1.0 O A:HOH445 4.2 21.9 1.0 O A:HOH643 4.4 36.6 1.0 CG A:GLU73 4.5 9.8 1.0 MG A:MG301 4.5 9.5 1.0 MG A:MG302 4.8 10.7 1.0 C2' A:AMP304 4.9 11.8 1.0 C3' A:AMP304 5.0 11.6 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