Magnesium in PDB 4rht: Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease

The structure of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease, PDB code: 4rht was solved by W.S.Eng, D.Hockova, P.Spacek, N.P.West, K.Woods, L.M.J.Naesens, D.T.Keough, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.10 / 2.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.417, 85.580, 156.644, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28.4

The binding sites of Magnesium atom in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease (pdb code 4rht). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease, PDB code: 4rht:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:65.0 occ:1.00 OD1 A:ASP123 2.5 53.5 1.0 O A:HOH401 2.6 57.3 1.0 O A:HOH417 2.6 80.6 1.0 OE1 A:GLU122 2.8 63.3 1.0 CG A:ASP123 3.3 50.3 1.0 OD2 A:ASP123 3.5 53.6 1.0 CD A:GLU122 3.5 60.1 1.0 OE2 A:GLU122 3.6 65.1 1.0 O4 A:POP301 4.4 82.2 1.0 N A:ASP123 4.5 34.8 1.0 O A:VAL124 4.7 61.2 1.0 CB A:ASP123 4.7 41.7 1.0 O1 A:POP301 4.7 64.8 1.0 CG A:GLU122 4.9 46.8 1.0 N A:VAL124 4.9 43.0 1.0 O2' A:5GP302 4.9 75.6 1.0

Magnesium binding site 2 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:63.5 occ:1.00 OD2 A:ASP182 2.2 58.5 1.0 O2 A:POP301 2.6 68.9 1.0 O5 A:POP301 3.1 76.0 1.0 CG A:ASP182 3.2 59.0 1.0 O4 A:POP301 3.6 82.2 1.0 OD1 A:ASP182 3.7 63.9 1.0 P1 A:POP301 3.7 66.6 1.0 O4' A:5GP302 3.7 81.6 1.0 P2 A:POP301 3.8 75.6 1.0 O1 A:POP301 3.9 64.8 1.0 O A:ASP182 4.0 56.3 1.0 N3 A:5GP302 4.1 64.9 1.0 O A:POP301 4.2 0.3 1.0 C1' A:5GP302 4.4 76.6 1.0 CB A:ASP182 4.4 54.0 1.0 N A:ASP182 4.5 47.2 1.0 N2 A:5GP302 4.5 65.1 1.0 C A:ASP182 4.5 54.6 1.0 C4' A:5GP302 4.6 83.7 1.0 NH2 A:ARG188 4.7 42.5 1.0 CA A:ASP182 4.7 51.6 1.0 C2 A:5GP302 4.8 65.8 1.0 NH1 A:ARG188 4.9 37.9 1.0 O3 A:POP301 5.0 69.6 1.0

Magnesium binding site 3 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:65.3 occ:1.00 O B:HOH415 2.3 72.8 1.0 OE2 B:GLU122 2.4 79.3 1.0 OD1 B:ASP123 2.6 54.1 1.0 CG B:ASP123 3.3 56.0 1.0 OD2 B:ASP123 3.4 63.3 1.0 CD B:GLU122 3.5 72.8 1.0 OE1 B:GLU122 4.3 76.8 1.0 O4 B:POP301 4.3 72.2 1.0 CG B:GLU122 4.4 56.4 1.0 O B:VAL64 4.5 43.8 1.0 O2' B:5GP302 4.6 84.2 1.0 N B:ASP123 4.6 40.7 1.0 CB B:ASP123 4.7 50.8 1.0 N B:GLY67 4.8 56.1 1.0 CA B:GLY67 4.9 56.7 1.0 O6 B:POP301 4.9 70.4 1.0 O B:POP301 5.0 72.4 1.0 P2 B:POP301 5.0 67.2 1.0

Magnesium binding site 4 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:50.5 occ:1.00 OD2 B:ASP182 2.0 64.1 1.0 O1 B:POP301 2.2 87.0 1.0 O B:HOH401 2.3 44.7 1.0 O B:HOH413 2.5 51.5 1.0 O5 B:POP301 2.6 69.3 1.0 CG B:ASP182 2.8 60.0 1.0 OD1 B:ASP182 2.9 59.7 1.0 O3 B:POP301 3.0 87.8 1.0 P1 B:POP301 3.0 86.9 1.0 P2 B:POP301 3.4 67.2 1.0 O4 B:POP301 3.5 72.2 1.0 O B:POP301 3.6 72.4 1.0 NH2 B:ARG188 3.9 52.8 1.0 CB B:ASP182 4.2 53.7 1.0 O2 B:POP301 4.4 87.8 1.0 O B:ASP182 4.5 38.8 1.0 CZ B:ARG188 4.6 46.5 1.0 NH1 B:ARG188 4.6 45.3 1.0 N B:ASP182 4.7 44.4 1.0 C B:ASP182 4.8 40.2 1.0 O6 B:POP301 4.8 70.4 1.0 CA B:ASP182 4.8 45.0 1.0 N3 B:5GP302 4.9 62.1 1.0 N2 B:5GP302 5.0 64.8 1.0

Magnesium binding site 5 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:67.1 occ:1.00 O2 C:POP301 2.2 90.5 1.0 OD2 C:ASP182 2.5 0.9 1.0 O6 C:POP301 2.6 0.0 1.0 CG C:ASP182 3.2 0.5 1.0 OD1 C:ASP182 3.4 1.0 1.0 P1 C:POP301 3.5 90.5 1.0 P2 C:POP301 3.8 0.3 1.0 O C:ASP182 3.8 0.1 1.0 O C:POP301 3.8 64.8 1.0 O4' C:5GP302 4.3 0.9 1.0 O1 C:POP301 4.3 88.2 1.0 O4 C:POP301 4.4 0.0 1.0 C C:ASP182 4.4 0.4 1.0 C1' C:5GP302 4.4 1.0 1.0 CB C:ASP182 4.5 0.1 1.0 O3 C:POP301 4.6 92.7 1.0 O2' C:5GP302 4.7 0.3 1.0 N C:ASP182 4.7 93.7 1.0 CA C:ASP182 4.8 97.5 1.0 C4' C:5GP302 4.9 0.7 1.0 N3 C:5GP302 4.9 0.7 1.0 O5 C:POP301 5.0 0.6 1.0

Magnesium binding site 6 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg304 b:83.2 occ:1.00 OE2 C:GLU122 2.1 89.9 1.0 OD1 C:ASP123 2.8 0.2 1.0 O C:HOH404 2.9 73.3 1.0 O C:HOH403 2.9 71.3 1.0 CD C:GLU122 3.3 88.1 1.0 CG C:ASP123 3.6 1.0 1.0 OD2 C:ASP123 3.6 0.1 1.0 O C:VAL124 3.8 97.5 1.0 O2' C:5GP302 3.9 0.3 1.0 CG C:GLU122 3.9 91.2 1.0 OE1 C:GLU122 4.2 84.8 1.0 O4 C:POP301 4.4 0.0 1.0 C2' C:5GP302 4.5 0.3 1.0 O3 C:POP301 4.6 92.7 1.0 N C:VAL124 4.6 90.8 1.0 CG1 C:VAL124 4.7 86.3 1.0 C C:VAL124 4.9 97.8 1.0 N C:ASP123 4.9 93.5 1.0

Magnesium binding site 7 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:96.5 occ:1.00 OD1 D:ASP182 2.0 0.1 1.0 O4 D:POP301 2.1 0.3 1.0 O1 D:POP301 2.4 97.0 1.0 CG D:ASP182 3.0 0.6 1.0 OD2 D:ASP182 3.3 0.2 1.0 P2 D:POP301 3.4 0.5 1.0 P1 D:POP301 3.7 96.2 1.0 N2 D:5GP302 3.7 1.0 1.0 O D:POP301 3.8 0.8 1.0 O5 D:POP301 4.0 0.5 1.0 N3 D:5GP302 4.0 0.4 1.0 O D:ASP182 4.1 0.5 1.0 O4' D:5GP302 4.1 0.7 1.0 O5' D:5GP302 4.2 0.7 1.0 C2 D:5GP302 4.3 0.3 1.0 CB D:ASP182 4.4 0.3 1.0 O2 D:POP301 4.5 95.8 1.0 O6 D:POP301 4.5 0.4 1.0 N D:ASP182 4.6 92.2 1.0 C D:ASP182 4.6 0.1 1.0 O3 D:POP301 4.7 96.4 1.0 CA D:ASP182 4.7 0.4 1.0 C5' D:5GP302 4.8 0.2 1.0 NH2 D:ARG188 4.9 97.0 1.0 C4' D:5GP302 4.9 0.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:78.1 occ:1.00 OE1 D:GLU122 2.2 80.8 1.0 OD1 D:ASP123 2.4 0.5 1.0 O D:HOH406 2.4 71.5 1.0 O D:HOH404 2.6 76.7 1.0 CG D:ASP123 3.1 0.0 1.0 OD2 D:ASP123 3.2 0.6 1.0 CD D:GLU122 3.4 84.2 1.0 O2 D:POP301 3.8 95.8 1.0 OE2 D:GLU122 4.1 82.3 1.0 CG D:GLU122 4.3 89.4 1.0 O5 D:POP301 4.4 0.5 1.0 N D:ASP123 4.5 0.8 1.0 CB D:ASP123 4.5 0.1 1.0 O D:VAL64 4.7 70.3 1.0 N D:VAL124 4.9 0.8 1.0

W.S.Eng, D.Hockova, P.Spacek, Z.Janeba, N.P.West, K.Woods, L.Naesens, D.T.Keough, L.W.Guddat. The First Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with Gmp and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25915781
DOI: 10.1021/ACS.JMEDCHEM.5B00611