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

Protein crystallography data

The structure of Crystal Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease, PDB code: 4rhy 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) 46.37 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.179, 85.525, 152.727, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.7

Magnesium Binding Sites:

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 4rhy). 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: 4rhy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4rhy

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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:Mg301

b:40.7
occ:1.00
 O A:HOH404 2.1 39.9 1.0
O A:HOH448 2.1 28.9 1.0
O A:HOH403 2.1 47.9 1.0
OD1 A:ASP123 2.1 40.8 1.0
OE1 A:GLU122 2.1 46.0 1.0
O A:HOH455 2.1 42.6 1.0
CD A:GLU122 3.0 45.1 1.0
CG A:ASP123 3.1 37.6 1.0
OE2 A:GLU122 3.3 48.2 1.0
OD2 A:ASP123 3.5 40.6 1.0
N A:ASP123 4.0 23.9 1.0
CAM A:3QG303 4.3 42.6 1.0
CG A:GLU122 4.4 39.1 1.0
O A:VAL124 4.4 24.3 1.0
CB A:ASP123 4.4 34.0 1.0
N A:VAL124 4.5 25.3 1.0
OAD A:3QG303 4.6 36.9 1.0
CB A:GLU122 4.7 29.5 1.0
CA A:ASP123 4.7 29.5 1.0
CA A:GLU122 4.8 27.8 1.0
O A:VAL64 4.9 32.8 1.0
C A:GLU122 4.9 25.9 1.0
CAN A:3QG303 5.0 42.3 1.0

Magnesium binding site 2 out of 8 in 4rhy

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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:Mg302

b:50.5
occ:1.00
 O A:HOH401 2.1 49.3 1.0
O A:HOH447 2.1 62.1 1.0
O A:HOH402 2.1 30.7 1.0
O A:HOH405 2.1 34.3 1.0
OD2 A:ASP182 2.1 35.9 1.0
OAJ A:3QG303 2.4 33.3 1.0
CG A:ASP182 3.1 32.0 1.0
OD1 A:ASP182 3.3 33.5 1.0
PBH A:3QG303 3.9 38.5 1.0
CAR A:3QG303 4.1 44.8 1.0
NH2 A:ARG188 4.1 35.4 1.0
O A:ASP182 4.3 34.2 1.0
CAV A:3QG303 4.3 45.7 1.0
CB A:ASP182 4.4 30.9 1.0
OAI A:3QG303 4.6 63.4 1.0
NH1 A:ARG188 4.6 29.2 1.0
O A:HOH452 4.7 44.9 1.0
CAU A:3QG303 4.7 61.1 1.0
N3 A:3QG303 4.7 35.9 1.0
CZ A:ARG188 4.8 34.3 1.0
N A:ASP182 4.8 29.1 1.0
C A:ASP182 4.8 32.3 1.0
OAD A:3QG303 4.9 36.9 1.0
CA A:ASP182 4.9 28.4 1.0

Magnesium binding site 3 out of 8 in 4rhy

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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:Mg301

b:36.2
occ:1.00
 O B:HOH455 2.1 65.7 1.0
O B:HOH450 2.1 61.4 1.0
O B:HOH403 2.1 38.6 1.0
O B:HOH402 2.1 45.9 1.0
OD1 B:ASP123 2.1 36.7 1.0
OE1 B:GLU122 2.1 41.0 1.0
CG B:ASP123 3.1 34.1 1.0
CD B:GLU122 3.2 43.9 1.0
OD2 B:ASP123 3.5 40.0 1.0
OE2 B:GLU122 3.6 51.0 1.0
N B:ASP123 4.0 22.5 1.0
O B:HOH412 4.2 43.3 1.0
CAM B:3QG303 4.2 42.1 1.0
OAG B:3QG303 4.2 39.7 1.0
CB B:ASP123 4.4 25.7 1.0
CG B:GLU122 4.5 36.9 1.0
N B:VAL124 4.7 22.9 1.0
O B:VAL124 4.7 30.9 1.0
CB B:GLU122 4.7 29.0 1.0
CA B:GLU122 4.8 26.8 1.0
CA B:ASP123 4.8 23.8 1.0
CAN B:3QG303 4.9 44.3 1.0
C B:GLU122 4.9 22.2 1.0

Magnesium binding site 4 out of 8 in 4rhy

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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:Mg302

b:42.5
occ:1.00
 O B:HOH401 2.1 48.1 1.0
O B:HOH405 2.1 43.2 1.0
O B:HOH404 2.1 37.4 1.0
OD1 B:ASP182 2.2 42.8 1.0
CG B:ASP182 3.0 40.1 1.0
OD2 B:ASP182 3.1 40.3 1.0
OAC B:3QG303 3.2 29.8 1.0
O B:HOH431 4.0 43.9 1.0
O B:ASP182 4.3 35.9 1.0
CAQ B:3QG303 4.4 42.0 1.0
CB B:ASP182 4.4 35.0 1.0
OAD B:3QG303 4.5 87.0 1.0
NH2 B:ARG188 4.5 32.3 1.0
PBG B:3QG303 4.5 30.0 1.0
CAU B:3QG303 4.7 47.8 1.0
C B:ASP182 4.8 32.4 1.0
O B:HOH416 4.8 45.4 1.0
O B:HOH454 4.8 41.6 1.0
CAR B:3QG303 4.8 48.1 1.0
N3 B:3QG303 4.8 37.1 1.0
N B:ASP182 4.9 24.1 1.0
CA B:ASP182 5.0 29.2 1.0

Magnesium binding site 5 out of 8 in 4rhy

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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:Mg301

b:35.9
occ:1.00
 O C:HOH401 2.1 32.2 1.0
O C:HOH403 2.1 46.4 1.0
O C:HOH446 2.1 57.1 1.0
O C:HOH402 2.1 43.2 1.0
OE1 C:GLU122 2.1 39.3 1.0
OD1 C:ASP123 2.1 33.5 1.0
CD C:GLU122 3.2 43.1 1.0
CG C:ASP123 3.2 32.2 1.0
OE2 C:GLU122 3.6 46.2 1.0
OD2 C:ASP123 3.6 34.9 1.0
CAM C:3QG303 4.1 53.3 1.0
N C:ASP123 4.1 31.5 1.0
O C:HOH447 4.1 37.2 1.0
O C:VAL124 4.4 34.5 1.0
CB C:ASP123 4.5 26.2 1.0
CG C:GLU122 4.5 37.9 1.0
O C:HOH448 4.5 48.2 1.0
N C:VAL124 4.6 29.7 1.0
CAN C:3QG303 4.6 54.8 1.0
OAI C:3QG303 4.6 47.9 1.0
O C:VAL64 4.7 28.9 1.0
CB C:GLU122 4.7 33.0 1.0
CA C:ASP123 4.8 30.6 1.0
CA C:GLU122 4.8 31.7 1.0
CAV C:3QG303 4.9 58.7 1.0
C C:GLU122 5.0 32.6 1.0

Magnesium binding site 6 out of 8 in 4rhy

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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:Mg302

b:39.1
occ:1.00
 O C:HOH408 2.1 34.6 1.0
O C:HOH405 2.1 25.6 1.0
O C:HOH445 2.1 49.6 1.0
O C:HOH404 2.1 34.7 1.0
OD1 C:ASP182 2.1 33.8 1.0
OAD C:3QG303 2.3 45.4 1.0
CG C:ASP182 3.0 32.9 1.0
OD2 C:ASP182 3.2 40.4 1.0
PBH C:3QG303 3.7 48.1 1.0
CAR C:3QG303 3.9 59.0 1.0
O C:HOH423 3.9 51.4 1.0
NBD C:3QG303 4.3 59.0 1.0
NH2 C:ARG188 4.3 27.5 1.0
CAV C:3QG303 4.4 58.7 1.0
CB C:ASP182 4.4 30.1 1.0
O C:ASP182 4.6 32.3 1.0
OAJ C:3QG303 4.7 36.3 1.0
O C:HOH431 4.7 46.9 1.0
OAI C:3QG303 4.8 47.9 1.0
N3 C:3QG303 4.8 27.8 1.0
CAQ C:3QG303 4.9 58.8 1.0
NH1 C:ARG188 4.9 26.2 1.0
C C:ASP182 5.0 31.8 1.0

Magnesium binding site 7 out of 8 in 4rhy

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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:Mg301

b:45.9
occ:1.00
 O D:HOH401 2.1 39.8 1.0
O D:HOH407 2.1 43.4 1.0
O D:HOH402 2.1 44.5 1.0
O D:HOH403 2.1 44.0 1.0
OE1 D:GLU122 2.1 46.4 1.0
OD1 D:ASP123 2.1 41.8 1.0
CD D:GLU122 3.0 46.6 1.0
CG D:ASP123 3.1 42.9 1.0
OE2 D:GLU122 3.2 52.2 1.0
OD2 D:ASP123 3.5 47.4 1.0
N D:ASP123 4.1 34.6 1.0
O D:HOH448 4.4 48.1 1.0
CB D:ASP123 4.4 39.8 1.0
CG D:GLU122 4.4 41.3 1.0
O D:VAL124 4.4 30.4 1.0
OAG D:3QG303 4.6 41.4 1.0
CAN D:3QG303 4.7 63.3 1.0
N D:VAL124 4.7 30.9 1.0
CB D:GLU122 4.8 37.8 1.0
O D:VAL64 4.8 27.1 1.0
CA D:ASP123 4.8 35.3 1.0
CA D:GLU122 4.9 33.5 1.0
CAP D:3QG303 4.9 59.5 1.0

Magnesium binding site 8 out of 8 in 4rhy

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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:Mg302

b:43.0
occ:1.00
 O D:HOH460 2.1 29.6 1.0
O D:HOH453 2.1 45.1 1.0
OD2 D:ASP182 2.1 34.2 1.0
O D:HOH413 2.1 34.9 1.0
O D:HOH406 2.1 26.2 1.0
OAC D:3QG303 2.3 42.4 1.0
CG D:ASP182 3.1 37.9 1.0
OD1 D:ASP182 3.3 34.5 1.0
PBG D:3QG303 3.7 42.4 1.0
CAQ D:3QG303 3.8 64.0 1.0
O D:HOH412 3.9 47.6 1.0
NH2 D:ARG188 4.1 33.7 1.0
O D:ASP182 4.3 35.1 1.0
CAU D:3QG303 4.4 69.4 1.0
CB D:ASP182 4.4 35.7 1.0
OAG D:3QG303 4.6 41.4 1.0
NH1 D:ARG188 4.6 33.2 1.0
N3 D:3QG303 4.7 34.0 1.0
OAH D:3QG303 4.7 79.9 1.0
CZ D:ARG188 4.8 33.3 1.0
C D:ASP182 4.8 34.6 1.0
N D:ASP182 4.8 33.6 1.0
CA D:ASP182 4.9 33.9 1.0

Reference:

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
Page generated: Tue Aug 20 03:07:22 2024

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