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

Protein crystallography data

The structure of Structures of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase Which Is A Potential Target For Drug Development Against This Disease, PDB code: 4rhx 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) 44.97 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.439, 85.723, 88.139, 90.00, 98.77, 90.00
R / Rfree (%) 18.7 / 22.6

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4rhx

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Magnesium binding site 1 out of 8 in the 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 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:27.6
occ:1.00
 OD2 A:ASP182 2.1 21.1 1.0
O A:HOH585 2.1 23.5 1.0
O A:HOH421 2.1 21.7 1.0
O A:HOH419 2.1 19.1 1.0
O A:HOH410 2.1 18.4 1.0
OAF A:3QF301 2.1 22.1 0.6
OAF A:3QF301 2.1 22.0 0.2
OAF A:3QF301 2.1 22.1 0.3
CG A:ASP182 3.1 21.2 1.0
OD1 A:ASP182 3.5 21.2 1.0
PBE A:3QF301 3.6 22.1 0.2
PBE A:3QF301 3.6 22.3 0.6
PBE A:3QF301 3.6 22.0 0.3
O A:HOH428 3.6 23.4 1.0
NH2 A:ARG188 4.0 22.8 1.0
CAP A:3QF301 4.0 14.4 0.2
CAP A:3QF301 4.1 14.4 0.3
N2 A:3QF301 4.2 16.9 0.3
O A:HOH500 4.2 29.3 1.0
N2 A:3QF301 4.2 16.9 0.2
CAS A:3QF301 4.3 14.5 0.6
CAS A:3QF301 4.3 14.5 0.2
OAC A:3QF301 4.3 21.9 0.3
CAP A:3QF301 4.3 14.4 0.6
N2 A:3QF301 4.3 16.8 0.6
OAC A:3QF301 4.3 21.9 0.2
O A:ASP182 4.3 20.2 1.0
NH1 A:ARG188 4.4 17.2 1.0
CAS A:3QF301 4.4 14.6 0.3
OAG A:3QF301 4.4 20.9 0.6
OAC A:3QF301 4.4 21.9 0.6
CB A:ASP182 4.4 18.9 1.0
OAG A:3QF301 4.4 21.4 0.2
O A:HOH578 4.5 41.7 1.0
O A:HOH447 4.5 25.0 1.0
OAG A:3QF301 4.5 21.2 0.3
N A:ASP182 4.6 18.1 1.0
CZ A:ARG188 4.6 18.9 1.0
N3 A:3QF301 4.6 16.7 0.3
N3 A:3QF301 4.7 16.5 0.6
N3 A:3QF301 4.7 16.7 0.2
CAL A:3QF301 4.7 11.7 0.3
C A:ASP182 4.8 19.6 1.0
CA A:ASP182 4.9 19.8 1.0
O A:HOH408 4.9 20.3 1.0
CAK A:3QF301 4.9 9.1 0.3
C2 A:3QF301 5.0 16.7 0.3
C2 A:3QF301 5.0 16.7 0.2

Magnesium binding site 2 out of 8 in 4rhx

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Magnesium binding site 2 out of 8 in the 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 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:20.6
occ:1.00
 O A:HOH586 2.1 20.8 1.0
O A:HOH402 2.1 17.9 1.0
OD1 A:ASP123 2.1 17.6 1.0
O A:HOH405 2.1 19.1 1.0
O A:HOH408 2.1 20.3 1.0
OE1 A:GLU122 2.1 20.2 1.0
CG A:ASP123 3.0 20.9 1.0
CD A:GLU122 3.1 21.7 1.0
OD2 A:ASP123 3.3 24.8 1.0
OE2 A:GLU122 3.3 23.5 1.0
OAC A:3QF301 3.9 21.9 0.2
OAC A:3QF301 4.0 21.9 0.3
OAC A:3QF301 4.0 21.9 0.6
N A:ASP123 4.1 16.5 1.0
CAP A:3QF301 4.2 14.4 0.6
CAP A:3QF301 4.2 14.4 0.3
NBC A:3QF301 4.3 17.6 0.2
CB A:ASP123 4.4 17.9 1.0
O A:VAL124 4.4 21.3 1.0
CG A:GLU122 4.4 20.6 1.0
NBC A:3QF301 4.5 17.7 0.6
NBC A:3QF301 4.5 17.6 0.3
N A:VAL124 4.5 17.6 1.0
CAP A:3QF301 4.5 14.4 0.2
CG1 A:VAL64 4.5 19.1 1.0
O A:VAL64 4.6 20.1 1.0
OAE A:3QF301 4.6 8.0 0.6
CAO A:3QF301 4.7 17.3 0.2
CAN A:3QF301 4.7 17.3 0.2
O A:HOH430 4.7 24.8 1.0
CAM A:3QF301 4.7 14.5 0.6
CA A:ASP123 4.8 18.1 1.0
CAO A:3QF301 4.8 17.2 0.6
CAO A:3QF301 4.8 17.3 0.3
CAS A:3QF301 4.8 14.6 0.3
CB A:GLU122 4.8 19.4 1.0
CAM A:3QF301 4.8 14.3 0.3
CB A:VAL64 4.8 17.3 1.0
CG1 A:VAL124 4.9 26.4 1.0
CAS A:3QF301 4.9 14.5 0.2
CAN A:3QF301 4.9 17.1 0.6
CAM A:3QF301 5.0 15.1 0.2

Magnesium binding site 3 out of 8 in 4rhx

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Magnesium binding site 3 out of 8 in the 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 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:18.4
occ:1.00
 OD2 B:ASP182 2.0 18.1 1.0
O B:HOH407 2.1 21.0 1.0
OAF B:3QF301 2.1 21.2 0.7
O B:HOH402 2.1 17.9 1.0
O B:HOH405 2.1 13.5 1.0
O B:HOH406 2.1 13.4 1.0
OAF B:3QF301 2.1 21.2 0.3
CG B:ASP182 3.0 20.4 1.0
OD1 B:ASP182 3.3 22.4 1.0
PBE B:3QF301 3.5 20.8 0.7
PBE B:3QF301 3.6 21.0 0.3
O B:HOH425 3.7 20.2 1.0
O B:ASP182 4.2 18.8 1.0
CAP B:3QF301 4.2 19.9 0.3
NH2 B:ARG188 4.2 15.8 1.0
CAS B:3QF301 4.2 20.0 0.3
O B:HOH517 4.2 50.7 1.0
CAS B:3QF301 4.2 19.9 0.7
CAP B:3QF301 4.3 20.0 0.7
OAG B:3QF301 4.3 21.4 0.7
CB B:ASP182 4.4 20.5 1.0
OAG B:3QF301 4.4 21.4 0.3
OAC B:3QF301 4.4 21.6 0.7
OAC B:3QF301 4.4 21.5 0.3
NH1 B:ARG188 4.4 16.2 1.0
N2 B:3QF301 4.6 16.4 0.7
N2 B:3QF301 4.7 16.5 0.3
N B:ASP182 4.7 17.8 1.0
CAL B:3QF301 4.7 18.2 0.3
C B:ASP182 4.7 18.3 1.0
CZ B:ARG188 4.7 16.9 1.0
CA B:ASP182 4.8 19.1 1.0
N3 B:3QF301 4.9 17.5 0.7
N3 B:3QF301 5.0 17.4 0.3

Magnesium binding site 4 out of 8 in 4rhx

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Magnesium binding site 4 out of 8 in the 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 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:22.0
occ:1.00
 O B:HOH403 2.1 23.2 1.0
OD1 B:ASP123 2.1 20.5 1.0
OE1 B:GLU122 2.1 22.7 1.0
O B:HOH408 2.1 22.4 1.0
O B:HOH404 2.1 17.9 1.0
O B:HOH401 2.1 19.0 1.0
CD B:GLU122 3.0 23.2 1.0
CG B:ASP123 3.1 21.9 1.0
OE2 B:GLU122 3.3 23.5 1.0
OD2 B:ASP123 3.4 22.8 1.0
OAC B:3QF301 4.0 21.6 0.7
OAC B:3QF301 4.0 21.5 0.3
N B:ASP123 4.1 18.9 1.0
CAP B:3QF301 4.2 20.0 0.7
CAP B:3QF301 4.3 19.9 0.3
O B:VAL124 4.4 16.5 1.0
CB B:ASP123 4.4 20.8 1.0
CG B:GLU122 4.4 23.3 1.0
N B:VAL124 4.4 17.5 1.0
NBC B:3QF301 4.4 19.6 0.3
NBC B:3QF301 4.5 19.8 0.7
CG1 B:VAL64 4.5 20.1 1.0
O B:VAL64 4.5 17.1 1.0
OAE B:3QF301 4.7 15.8 0.7
CB B:VAL64 4.7 18.5 1.0
CB B:GLU122 4.7 21.8 1.0
CA B:ASP123 4.7 18.9 1.0
CAO B:3QF301 4.8 19.0 0.7
CAO B:3QF301 4.8 19.1 0.3
CG1 B:VAL124 4.8 25.3 1.0
CAM B:3QF301 4.8 19.4 0.3
O B:HOH424 4.8 22.6 1.0
CAM B:3QF301 4.9 19.6 0.7
CAN B:3QF301 4.9 19.2 0.3
CA B:GLU122 5.0 20.3 1.0

Magnesium binding site 5 out of 8 in 4rhx

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Magnesium binding site 5 out of 8 in the 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 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:23.4
occ:1.00
 OD1 C:ASP123 2.1 24.9 1.0
OE1 C:GLU122 2.1 30.3 1.0
O C:HOH406 2.1 24.4 1.0
O C:HOH409 2.1 23.4 1.0
O C:HOH402 2.1 29.5 1.0
O C:HOH407 2.1 27.4 1.0
CG C:ASP123 3.1 24.9 1.0
CD C:GLU122 3.1 31.4 1.0
OE2 C:GLU122 3.4 31.9 1.0
OD2 C:ASP123 3.4 25.4 1.0
N C:ASP123 4.1 25.3 1.0
OAC C:3QF301 4.1 29.5 0.7
OAC C:3QF301 4.1 29.6 0.3
CAP C:3QF301 4.2 20.6 0.3
CAP C:3QF301 4.3 20.6 0.7
O C:VAL124 4.3 29.0 1.0
CB C:ASP123 4.4 23.1 1.0
NBC C:3QF301 4.4 23.2 0.3
CG C:GLU122 4.4 30.4 1.0
NBC C:3QF301 4.4 23.4 0.7
N C:VAL124 4.4 22.8 1.0
CG1 C:VAL64 4.5 32.8 1.0
OAE C:3QF301 4.5 18.0 0.7
O C:VAL64 4.6 23.3 1.0
CB C:GLU122 4.7 27.6 1.0
O C:HOH455 4.7 36.6 1.0
CAO C:3QF301 4.7 23.3 0.3
CAO C:3QF301 4.7 23.2 0.7
CA C:ASP123 4.7 23.9 1.0
CAM C:3QF301 4.8 20.4 0.3
CB C:VAL64 4.8 32.0 1.0
CAM C:3QF301 4.8 20.9 0.7
CAN C:3QF301 4.9 22.3 0.3
CA C:GLU122 4.9 26.1 1.0
CG1 C:VAL124 4.9 25.1 1.0
CAN C:3QF301 5.0 22.6 0.7

Magnesium binding site 6 out of 8 in 4rhx

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Magnesium binding site 6 out of 8 in the 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 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:27.4
occ:1.00
 OD2 C:ASP182 2.1 25.5 1.0
O C:HOH410 2.1 29.1 1.0
O C:HOH508 2.1 29.6 1.0
O C:HOH404 2.1 21.2 1.0
O C:HOH412 2.1 29.7 1.0
OAF C:3QF301 2.2 29.3 0.7
OAF C:3QF301 2.2 29.5 0.3
CG C:ASP182 3.1 25.8 1.0
OD1 C:ASP182 3.4 30.4 1.0
O C:HOH433 3.5 34.3 1.0
PBE C:3QF301 3.6 29.5 0.7
PBE C:3QF301 3.7 29.8 0.3
O C:ASP182 4.1 16.7 1.0
NH2 C:ARG188 4.2 22.6 1.0
O C:HOH483 4.3 39.0 1.0
CAP C:3QF301 4.3 20.6 0.7
CAS C:3QF301 4.3 21.4 0.7
CAP C:3QF301 4.3 20.6 0.3
CAS C:3QF301 4.4 21.9 0.3
N2 C:3QF301 4.4 23.2 0.3
N2 C:3QF301 4.4 23.1 0.7
CB C:ASP182 4.4 21.5 1.0
OAG C:3QF301 4.4 30.2 0.7
OAG C:3QF301 4.5 30.2 0.3
OAC C:3QF301 4.5 29.5 0.7
NH1 C:ARG188 4.5 18.3 1.0
OAC C:3QF301 4.6 29.6 0.3
CAL C:3QF301 4.6 19.0 0.3
N C:ASP182 4.6 20.4 1.0
N3 C:3QF301 4.7 23.4 0.7
N3 C:3QF301 4.7 23.4 0.3
C C:ASP182 4.7 18.0 1.0
CZ C:ARG188 4.8 21.2 1.0
CA C:ASP182 4.8 19.7 1.0

Magnesium binding site 7 out of 8 in 4rhx

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Magnesium binding site 7 out of 8 in the 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 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:19.2
occ:1.00
 OD1 D:ASP123 2.0 21.5 1.0
O D:HOH406 2.1 21.3 1.0
O D:HOH404 2.1 25.0 1.0
O D:HOH401 2.1 20.8 1.0
O D:HOH402 2.1 16.5 1.0
OE1 D:GLU122 2.1 22.4 1.0
CD D:GLU122 3.0 22.9 1.0
CG D:ASP123 3.0 23.2 1.0
OE2 D:GLU122 3.3 24.6 1.0
OD2 D:ASP123 3.4 26.0 1.0
OAC D:3QF301 3.9 29.5 1.0
N D:ASP123 4.1 19.6 1.0
CAN D:3QF301 4.2 35.0 1.0
OAE D:3QF301 4.2 26.2 1.0
O D:VAL124 4.3 22.8 1.0
CB D:ASP123 4.4 21.5 1.0
N D:VAL124 4.4 19.7 1.0
CG D:GLU122 4.4 23.3 1.0
CG1 D:VAL64 4.5 26.9 1.0
CAP D:3QF301 4.5 28.0 1.0
O D:VAL64 4.6 25.5 1.0
O D:HOH426 4.7 23.8 1.0
CA D:ASP123 4.7 19.9 1.0
CG1 D:VAL124 4.8 27.6 1.0
CAM D:3QF301 4.8 30.1 1.0
CB D:GLU122 4.8 22.3 1.0
CB D:VAL64 4.8 25.0 1.0
CAQ D:3QF301 4.8 33.5 1.0
O D:HOH479 4.8 36.9 1.0
NBC D:3QF301 5.0 34.8 1.0
CAK D:3QF301 5.0 27.5 1.0
CA D:GLU122 5.0 20.4 1.0

Magnesium binding site 8 out of 8 in 4rhx

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Magnesium binding site 8 out of 8 in the 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 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:26.5
occ:1.00
 O D:HOH405 2.1 28.1 1.0
OAF D:3QF301 2.1 28.6 1.0
O D:HOH403 2.1 20.8 1.0
O D:HOH534 2.1 26.6 1.0
O D:HOH409 2.1 28.1 1.0
OD2 D:ASP182 2.1 27.8 1.0
CG D:ASP182 3.1 30.9 1.0
OD1 D:ASP182 3.3 33.4 1.0
PBE D:3QF301 3.5 29.4 1.0
O D:HOH479 3.5 36.9 1.0
CAP D:3QF301 3.9 28.0 1.0
NH2 D:ARG188 3.9 24.8 1.0
CAS D:3QF301 4.1 21.6 1.0
O D:HOH446 4.2 42.1 1.0
OAC D:3QF301 4.3 29.5 1.0
NH1 D:ARG188 4.3 22.0 1.0
N2 D:3QF301 4.3 24.1 1.0
O D:HOH535 4.4 54.1 1.0
O D:HOH464 4.4 37.9 1.0
CB D:ASP182 4.4 28.6 1.0
OAG D:3QF301 4.4 30.3 1.0
O D:ASP182 4.5 25.5 1.0
O D:HOH455 4.5 29.7 1.0
CZ D:ARG188 4.6 23.4 1.0
N3 D:3QF301 4.7 20.8 1.0
N D:ASP182 4.8 24.9 1.0
O D:HOH402 4.9 16.5 1.0
C D:ASP182 5.0 29.0 1.0
CA D:ASP182 5.0 27.8 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 03:05:43 2024

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