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Magnesium in PDB 4rac: Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents

Enzymatic activity of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents

All present enzymatic activity of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents:
2.4.2.8;

Protein crystallography data

The structure of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents, PDB code: 4rac was solved by D.T.Keough, D.Hockov, Z.Janeba, T.-H.Wang, L.Naesens, M.D.Edstein, M.Chavchich, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.823, 114.801, 67.661, 90.00, 98.33, 90.00
R / Rfree (%) 19.4 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents (pdb code 4rac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents, PDB code: 4rac:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4rac

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Magnesium binding site 1 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:32.8
occ:1.00
 O A:HOH420 2.1 46.5 1.0
O A:HOH416 2.1 41.3 1.0
O A:HOH456 2.1 28.2 1.0
OAH A:3L4301 2.2 29.0 1.0
O A:HOH417 2.3 39.1 1.0
OD1 A:ASP193 2.3 27.4 1.0
CG A:ASP193 3.3 31.9 1.0
PBB A:3L4301 3.4 28.5 1.0
OD2 A:ASP193 3.6 27.2 1.0
CAP A:3L4301 3.7 37.9 1.0
O A:HOH403 3.9 31.8 1.0
CAJ A:3L4301 4.0 42.5 1.0
NH2 A:ARG199 4.1 29.0 1.0
O A:HOH451 4.2 50.2 1.0
OAT A:3L4301 4.3 42.5 1.0
OAD A:3L4301 4.3 25.2 1.0
O A:ASP193 4.4 30.7 1.0
O A:HOH440 4.5 41.5 1.0
OAG A:3L4301 4.6 27.4 1.0
N3 A:3L4301 4.6 34.7 1.0
CAL A:3L4301 4.6 27.2 1.0
NH1 A:ARG199 4.6 26.2 1.0
CAN A:3L4301 4.6 37.4 1.0
CB A:ASP193 4.7 27.9 1.0
O A:HOH407 4.8 36.4 1.0
CZ A:ARG199 4.8 27.0 1.0
N A:ASP193 4.9 25.1 1.0
N2 A:3L4301 4.9 28.5 1.0
O A:HOH433 4.9 46.7 1.0
C A:ASP193 5.0 31.0 1.0

Magnesium binding site 2 out of 7 in 4rac

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Magnesium binding site 2 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:30.6
occ:1.00
 O A:HOH402 2.0 29.6 1.0
O A:HOH401 2.1 28.8 1.0
OD1 A:ASP134 2.1 28.2 1.0
OE1 A:GLU133 2.1 32.0 1.0
O A:HOH408 2.2 30.0 1.0
O A:HOH406 2.2 27.6 1.0
CD A:GLU133 3.0 32.2 1.0
CG A:ASP134 3.0 28.9 1.0
OE2 A:GLU133 3.2 37.6 1.0
OD2 A:ASP134 3.3 27.7 1.0
OAT A:3L4301 3.9 42.5 1.0
OAD A:3L4301 3.9 25.2 1.0
N A:ASP134 4.2 23.6 1.0
CAJ A:3L4301 4.3 42.5 1.0
O A:HOH414 4.3 33.5 1.0
CAK A:3L4301 4.4 38.5 1.0
CB A:ASP134 4.4 24.4 1.0
CG A:GLU133 4.4 31.8 1.0
N A:ILE135 4.4 25.9 1.0
O A:ILE135 4.5 35.0 1.0
O A:VAL66 4.5 28.0 1.0
CG1 A:VAL66 4.5 31.9 1.0
CG2 A:ILE135 4.7 21.8 1.0
O A:HOH446 4.8 49.2 1.0
CA A:ASP134 4.8 28.2 1.0
CB A:GLU133 4.8 31.7 1.0
O A:HOH403 4.9 31.8 1.0
CAP A:3L4301 4.9 37.9 1.0
PBB A:3L4301 5.0 28.5 1.0

Magnesium binding site 3 out of 7 in 4rac

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Magnesium binding site 3 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:46.2
occ:1.00
 O B:HOH419 2.0 48.7 1.0
O B:HOH406 2.0 40.0 1.0
OD1 B:ASP193 2.1 41.1 1.0
O B:HOH457 2.2 43.4 1.0
OAH B:3L4301 2.3 37.3 1.0
O B:HOH409 2.3 38.2 1.0
CG B:ASP193 3.1 38.0 1.0
OD2 B:ASP193 3.4 40.1 1.0
OAT B:3L4301 3.7 54.2 1.0
PBB B:3L4301 3.7 41.9 1.0
O B:HOH413 3.9 43.5 1.0
CAJ B:3L4301 3.9 54.0 1.0
NH2 B:ARG199 4.1 36.9 1.0
CAP B:3L4301 4.2 49.5 1.0
O B:HOH456 4.3 57.3 1.0
O B:ASP193 4.5 40.3 1.0
CB B:ASP193 4.5 35.7 1.0
OAD B:3L4301 4.5 41.6 1.0
OAG B:3L4301 4.6 29.6 1.0
NH1 B:ARG199 4.7 33.7 1.0
O B:HOH440 4.7 42.0 1.0
N B:ASP193 4.7 33.2 1.0
N2 B:3L4301 4.8 33.2 1.0
N3 B:3L4301 4.8 35.8 1.0
CZ B:ARG199 4.8 36.0 1.0
C B:ASP193 4.9 38.8 1.0
CA B:ASP193 4.9 34.6 1.0

Magnesium binding site 4 out of 7 in 4rac

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Magnesium binding site 4 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:36.0
occ:1.00
 O B:HOH446 1.9 44.5 1.0
OE1 B:GLU133 1.9 37.7 1.0
O B:HOH448 2.0 43.4 1.0
OD1 B:ASP134 2.1 30.6 1.0
O B:HOH434 2.2 43.1 1.0
O B:HOH402 2.3 40.4 1.0
CD B:GLU133 2.7 43.0 1.0
CG B:ASP134 3.0 35.8 1.0
OE2 B:GLU133 3.2 46.4 1.0
OD2 B:ASP134 3.4 35.2 1.0
CG B:GLU133 3.6 47.3 1.0
N B:ASP134 4.0 30.0 1.0
OAD B:3L4301 4.1 41.6 1.0
CAJ B:3L4301 4.2 54.0 1.0
O B:ILE135 4.3 38.1 1.0
CAK B:3L4301 4.4 46.9 1.0
CB B:ASP134 4.4 38.4 1.0
N B:ILE135 4.4 30.9 1.0
O B:HOH439 4.4 53.1 1.0
CG2 B:ILE135 4.6 36.2 1.0
CAP B:3L4301 4.7 49.5 1.0
O B:VAL66 4.7 31.1 1.0
CA B:ASP134 4.7 29.9 1.0
CG1 B:VAL66 4.7 32.3 1.0
CB B:GLU133 4.8 40.9 1.0
OAT B:3L4301 4.9 54.2 1.0
CA B:GLU133 4.9 32.2 1.0
C B:GLU133 5.0 31.8 1.0

Magnesium binding site 5 out of 7 in 4rac

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Magnesium binding site 5 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:34.5
occ:1.00
 OE1 C:GLU133 2.0 36.9 1.0
O C:HOH404 2.1 47.7 1.0
O C:HOH458 2.1 31.5 1.0
O C:HOH403 2.2 33.3 1.0
OD1 C:ASP134 2.2 32.0 1.0
O C:HOH401 2.4 31.8 1.0
CD C:GLU133 2.7 36.2 1.0
OE2 C:GLU133 3.1 40.7 1.0
CG C:ASP134 3.2 33.4 1.0
OD2 C:ASP134 3.5 37.0 1.0
CG C:GLU133 3.6 42.3 1.0
OAG C:3L4301 4.0 31.4 1.0
O C:HOH417 4.1 34.1 1.0
N C:ASP134 4.2 34.0 1.0
CAK C:3L4301 4.2 49.6 1.0
CG1 C:VAL66 4.2 26.0 1.0
O C:HOH426 4.2 43.6 1.0
CAJ C:3L4301 4.3 50.5 1.0
OAT C:3L4301 4.4 46.7 1.0
O C:ILE135 4.4 45.0 1.0
N C:ILE135 4.5 32.3 1.0
CB C:ASP134 4.5 32.5 1.0
O C:VAL66 4.5 25.6 1.0
CAP C:3L4301 4.8 44.5 1.0
CB C:VAL66 4.8 29.8 1.0
CB C:GLU133 4.8 34.3 1.0
CA C:ASP134 4.8 31.4 1.0
CG2 C:ILE135 4.9 36.4 1.0
CA C:GLU133 5.0 31.6 1.0

Magnesium binding site 6 out of 7 in 4rac

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Magnesium binding site 6 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:48.0
occ:1.00
 O C:HOH456 1.9 42.2 1.0
O C:HOH412 2.1 39.5 1.0
O C:HOH455 2.1 40.0 1.0
O C:HOH457 2.3 41.8 1.0
OAD C:3L4301 2.4 31.5 1.0
OD1 C:ASP193 2.4 40.0 1.0
CG C:ASP193 3.3 39.2 1.0
OD2 C:ASP193 3.5 39.9 1.0
PBB C:3L4301 3.7 34.2 1.0
OAT C:3L4301 3.7 46.7 1.0
CAP C:3L4301 3.9 44.5 1.0
O C:HOH415 4.1 47.1 1.0
NH2 C:ARG199 4.2 34.3 1.0
O C:HOH433 4.5 48.5 1.0
O C:ASP193 4.5 43.6 1.0
OAG C:3L4301 4.6 31.4 1.0
N3 C:3L4301 4.6 36.0 1.0
OAH C:3L4301 4.7 36.0 1.0
CB C:ASP193 4.7 34.3 1.0
O C:HOH432 4.8 51.0 1.0
CAL C:3L4301 4.8 47.6 1.0
O C:HOH434 4.8 51.9 1.0
NH1 C:ARG199 4.9 31.6 1.0
O C:HOH422 4.9 41.2 1.0
CAJ C:3L4301 4.9 50.5 1.0
N2 C:3L4301 4.9 33.0 1.0
CAN C:3L4301 5.0 47.0 1.0
CZ C:ARG199 5.0 32.7 1.0

Magnesium binding site 7 out of 7 in 4rac

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Magnesium binding site 7 out of 7 in the Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6- Oxopurine Phosphoribosyltransferases and Their Pro-Drugs As Antimalarial Agents within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.7
occ:1.00
 O D:HOH430 2.0 65.4 1.0
O D:HOH432 2.1 46.2 1.0
OD1 D:ASP134 2.1 43.8 1.0
OE1 D:GLU133 2.3 46.8 1.0
O D:HOH431 2.6 52.5 1.0
CG D:ASP134 3.0 41.7 1.0
CD D:GLU133 3.1 55.7 1.0
OD2 D:ASP134 3.2 42.2 1.0
OE2 D:GLU133 3.6 60.2 1.0
OAT D:3L4301 3.9 45.9 0.6
OAH D:3L4301 4.0 36.5 0.6
CG D:GLU133 4.0 54.1 1.0
CAK D:3L4301 4.3 54.6 0.6
N D:ASP134 4.3 44.1 1.0
CB D:ASP134 4.4 38.9 1.0
O D:ILE135 4.5 50.8 1.0
N D:ILE135 4.5 43.8 1.0
CAJ D:3L4301 4.6 50.3 0.6
CG1 D:VAL66 4.7 43.6 1.0
CG2 D:ILE135 4.8 47.4 1.0
O D:HOH426 4.8 48.7 1.0
CA D:ASP134 4.8 39.2 1.0
CAP D:3L4301 4.8 40.2 0.6
O D:VAL66 4.9 37.6 1.0

Reference:

D.T.Keough, D.Hockova, Z.Janeba, T.H.Wang, L.Naesens, M.D.Edstein, M.Chavchich, L.W.Guddat. Aza-Acyclic Nucleoside Phosphonates Containing A Second Phosphonate Group As Inhibitors of the Human, Plasmodium Falciparum and Vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs As Antimalarial Agents. J.Med.Chem. V. 58 827 2015.
ISSN: ISSN 0022-2623
PubMed: 25494538
DOI: 10.1021/JM501416T
Page generated: Tue Aug 20 02:56:52 2024

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