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Magnesium in PDB 4raq: 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: 4raq 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) 58.90 / 2.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.328, 92.605, 115.013, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 26.9

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 4raq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 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: 4raq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4raq

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Magnesium binding site 1 out of 8 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:69.4
occ:1.00
 O A:HOH430 1.8 79.1 1.0
O A:HOH410 2.3 55.8 1.0
OAG A:3L8301 2.5 61.9 1.0
OD1 A:ASP193 2.9 58.5 1.0
CAJ A:3L8301 3.5 71.5 1.0
PBA A:3L8301 3.7 85.6 1.0
CAP A:3L8301 3.7 83.8 1.0
OAT A:3L8301 3.7 79.6 1.0
CG A:ASP193 3.8 55.7 1.0
OD2 A:ASP193 4.0 58.6 1.0
O A:HOH431 4.1 46.9 1.0
OAF A:3L8301 4.5 89.8 1.0
CAN A:3L8301 4.6 61.1 1.0
N3 A:3L8301 4.6 53.9 1.0
O A:ASP193 4.8 53.8 1.0
NH2 A:ARG199 4.8 76.2 1.0
OAC A:3L8301 4.8 84.7 1.0
CAK A:3L8301 4.9 65.5 1.0

Magnesium binding site 2 out of 8 in 4raq

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Magnesium binding site 2 out of 8 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:46.9
occ:1.00
 O A:HOH427 1.8 53.8 1.0
O A:HOH428 2.4 53.6 1.0
OD1 A:ASP134 2.5 53.1 1.0
OD2 A:ASP134 2.9 60.6 1.0
CG A:ASP134 3.0 51.2 1.0
OAT A:3L8301 3.0 79.6 1.0
OE1 A:GLU133 3.1 49.2 1.0
OAC A:3L8301 3.4 84.7 1.0
CD A:GLU133 3.6 51.2 1.0
CAP A:3L8301 3.7 83.8 1.0
OE2 A:GLU133 3.8 55.1 1.0
CAJ A:3L8301 4.0 71.5 1.0
PBA A:3L8301 4.2 85.6 1.0
CAK A:3L8301 4.3 65.5 1.0
O A:HOH422 4.4 59.1 1.0
CB A:ASP134 4.4 46.4 1.0
CG A:GLU133 4.6 41.9 1.0
O A:ILE135 4.7 65.3 1.0
N A:ASP134 4.7 57.0 1.0
CA A:GLY69 4.8 42.1 1.0
N A:ILE135 4.8 43.9 1.0
CAL A:3L8301 4.8 56.5 1.0
CG2 A:ILE135 4.9 62.8 1.0
N A:GLY69 4.9 53.6 1.0
OAG A:3L8301 4.9 61.9 1.0
CG1 A:VAL66 4.9 48.0 1.0
O A:LEU67 5.0 60.0 1.0

Magnesium binding site 3 out of 8 in 4raq

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Magnesium binding site 3 out of 8 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:73.1
occ:1.00
 O B:HOH422 2.1 64.5 1.0
O B:HOH433 2.3 47.0 1.0
O B:HOH407 2.3 72.4 1.0
OD1 B:ASP193 3.0 57.9 1.0
CAP B:3L8301 3.5 72.2 1.0
OD2 B:ASP193 3.5 54.2 1.0
CG B:ASP193 3.7 56.5 1.0
OAG B:3L8301 3.7 0.4 1.0
PBA B:3L8301 4.3 76.9 1.0
OAT B:3L8301 4.6 64.5 1.0
O B:ASP193 4.6 65.3 1.0
OE2 B:GLU196 4.7 73.5 1.0
CAJ B:3L8301 4.8 59.9 1.0

Magnesium binding site 4 out of 8 in 4raq

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Magnesium binding site 4 out of 8 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:50.7
occ:1.00
 O B:HOH430 1.9 53.5 1.0
O B:HOH431 2.0 44.7 1.0
O B:HOH425 2.4 58.0 1.0
OD1 B:ASP134 2.4 59.3 1.0
OAC B:3L8301 2.5 68.2 1.0
OE1 B:GLU133 2.9 56.2 1.0
CG B:ASP134 3.2 57.4 1.0
OD2 B:ASP134 3.2 68.5 1.0
CAK B:3L8301 3.4 57.6 1.0
OAT B:3L8301 3.6 64.5 1.0
CD B:GLU133 3.8 57.6 1.0
PBA B:3L8301 3.8 76.9 1.0
CAP B:3L8301 4.0 72.2 1.0
CAJ B:3L8301 4.0 59.9 1.0
OE2 B:GLU133 4.3 58.9 1.0
CG2 B:ILE135 4.5 48.0 1.0
NAX B:3L8301 4.6 54.4 1.0
O B:HOH432 4.6 57.8 1.0
CB B:ASP134 4.6 48.9 1.0
CAL B:3L8301 4.6 50.8 1.0
O B:ILE135 4.6 61.8 1.0
N B:ILE135 4.7 53.1 1.0
CG B:GLU133 4.7 50.1 1.0
OAG B:3L8301 4.8 0.4 1.0
OAF B:3L8301 4.8 48.0 1.0
CA B:GLY69 4.8 52.7 1.0
N B:ASP134 4.9 38.9 1.0
O B:HOH433 4.9 47.0 1.0
N B:GLY69 4.9 49.1 1.0

Magnesium binding site 5 out of 8 in 4raq

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Magnesium binding site 5 out of 8 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:57.5
occ:1.00
 O C:HOH430 2.0 52.2 1.0
O C:HOH431 2.5 50.1 1.0
OD1 C:ASP193 2.7 69.7 1.0
OD2 C:ASP193 2.8 66.4 1.0
O C:HOH432 3.0 70.2 1.0
CG C:ASP193 3.2 62.4 1.0
OAF C:3L8301 3.2 71.5 1.0
OAT C:3L8301 4.1 96.7 1.0
NH2 C:ARG199 4.2 62.6 1.0
CAP C:3L8301 4.3 0.9 1.0
PBA C:3L8301 4.4 86.2 1.0
OE2 C:GLU196 4.6 62.5 1.0
N C:ASN195 4.6 49.5 1.0
CB C:ASP193 4.7 51.2 1.0
CAJ C:3L8301 4.7 82.3 1.0
O C:ASP193 4.8 48.0 1.0
N C:GLU196 4.9 56.1 1.0

Magnesium binding site 6 out of 8 in 4raq

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Magnesium binding site 6 out of 8 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:82.0
occ:1.00
 OD1 C:ASP134 2.5 65.4 1.0
O C:HOH413 2.9 65.2 1.0
CG C:GLU133 3.1 68.0 1.0
OE1 C:GLU133 3.2 83.3 1.0
CG C:ASP134 3.5 63.7 1.0
CD C:GLU133 3.6 79.7 1.0
OD2 C:ASP134 3.7 67.2 1.0
CAK C:3L8301 3.9 66.6 1.0
CG2 C:THR141 4.0 56.6 1.0
O C:ILE135 4.0 60.6 1.0
CAM C:3L8301 4.2 66.3 1.0
CG1 C:VAL66 4.2 46.4 1.0
N C:ASP134 4.3 50.2 1.0
CB C:GLU133 4.5 51.2 1.0
N C:ILE135 4.6 53.7 1.0
OAC C:3L8301 4.6 78.6 1.0
NAX C:3L8301 4.6 59.9 1.0
CB C:VAL66 4.7 51.8 1.0
CB C:THR141 4.7 59.6 1.0
OE2 C:GLU133 4.8 78.4 1.0
CB C:ASP134 4.8 55.5 1.0
CAJ C:3L8301 4.8 82.3 1.0
OG1 C:THR141 4.9 66.5 1.0
CA C:GLU133 4.9 41.9 1.0

Magnesium binding site 7 out of 8 in 4raq

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Magnesium binding site 7 out of 8 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:54.6
occ:1.00
 OAC D:3L8301 2.3 88.9 1.0
OD1 D:ASP134 2.4 54.2 1.0
O D:HOH425 2.5 63.0 1.0
OE2 D:GLU133 2.9 59.0 1.0
CAJ D:3L8301 2.9 75.4 1.0
OD2 D:ASP134 3.0 70.0 1.0
CG D:ASP134 3.0 60.9 1.0
OE1 D:GLU133 3.1 55.4 1.0
CD D:GLU133 3.2 54.7 1.0
CAK D:3L8301 3.5 68.0 1.0
PBA D:3L8301 3.5 75.1 1.0
CAP D:3L8301 3.8 75.9 1.0
OAT D:3L8301 3.8 78.0 1.0
OAG D:3L8301 4.1 75.3 1.0
CG D:GLU133 4.4 50.0 1.0
CB D:ASP134 4.5 50.9 1.0
O D:ILE135 4.6 51.0 1.0
O D:HOH402 4.7 62.9 1.0
CG2 D:ILE135 4.7 44.8 1.0
N D:ASP134 4.7 44.1 1.0
N D:ILE135 4.7 55.3 1.0
NAX D:3L8301 4.8 58.2 1.0
OAF D:3L8301 4.8 41.7 1.0
N D:GLY69 4.9 47.7 1.0
CAL D:3L8301 4.9 50.1 1.0
O D:HOH407 4.9 63.2 1.0

Magnesium binding site 8 out of 8 in 4raq

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Magnesium binding site 8 out of 8 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 8 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:Mg303

b:50.2
occ:1.00
 OD1 D:ASP193 2.1 62.1 1.0
O D:HOH402 2.4 62.9 1.0
OAF D:3L8301 2.5 41.7 1.0
CG D:ASP193 2.9 59.0 1.0
OD2 D:ASP193 3.0 62.4 1.0
OAT D:3L8301 3.5 78.0 1.0
PBA D:3L8301 3.7 75.1 1.0
CAP D:3L8301 3.8 75.9 1.0
NH2 D:ARG199 4.0 60.1 1.0
CAJ D:3L8301 4.3 75.4 1.0
OAC D:3L8301 4.3 88.9 1.0
CB D:ASP193 4.4 56.6 1.0
O D:ASP193 4.6 59.1 1.0
OAG D:3L8301 4.9 75.3 1.0
C D:ASP193 4.9 60.0 1.0
CZ D:ARG199 4.9 52.0 1.0
N3 D:3L8301 5.0 60.7 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 02:59:25 2024

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