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Magnesium in PDB 4rao: 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: 4rao 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) 35.41 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.602, 92.853, 114.849, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23

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

Magnesium binding site 1 out of 8 in 4rao

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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:28.6
occ:1.00
 O A:HOH449 2.2 42.4 1.0
O A:HOH450 2.3 40.6 1.0
O A:HOH418 2.3 34.6 1.0
OE1 A:GLU133 2.3 40.9 1.0
OD1 A:ASP134 2.4 28.7 1.0
O A:HOH426 2.4 42.2 1.0
CD A:GLU133 2.7 42.2 1.0
OE2 A:GLU133 2.7 44.7 1.0
CG A:ASP134 3.4 29.8 1.0
OD2 A:ASP134 3.7 38.0 1.0
CG A:GLU133 3.9 40.5 1.0
CAP A:3L7301 4.1 73.3 1.0
CG1 A:VAL66 4.3 32.1 1.0
N A:ASP134 4.4 23.6 1.0
OAE A:3L7301 4.4 61.3 1.0
O A:ILE135 4.5 26.3 1.0
O A:HOH411 4.6 40.2 1.0
CAJ A:3L7301 4.6 59.9 1.0
N A:ILE135 4.7 27.1 1.0
CB A:ASP134 4.7 29.5 1.0
O A:VAL66 4.7 25.0 1.0
NAY A:3L7301 4.7 42.7 1.0
CB A:VAL66 4.9 30.3 1.0
O A:HOH444 4.9 48.8 1.0
CAK A:3L7301 5.0 72.8 1.0

Magnesium binding site 2 out of 8 in 4rao

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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:45.8
occ:1.00
 OD1 A:ASP193 2.3 37.5 1.0
OAD A:3L7301 2.4 60.8 1.0
O A:HOH451 2.6 49.4 1.0
O A:HOH452 2.7 50.2 1.0
CG A:ASP193 3.1 32.5 1.0
OD2 A:ASP193 3.2 35.7 1.0
CAK A:3L7301 3.8 72.8 1.0
PBA A:3L7301 3.9 66.7 1.0
O A:HOH448 4.0 40.8 1.0
NH2 A:ARG199 4.1 32.2 1.0
CAP A:3L7301 4.3 73.3 1.0
O A:ASP193 4.4 36.1 1.0
CB A:ASP193 4.5 31.0 1.0
OAE A:3L7301 4.7 61.3 1.0
OAB A:3L7301 4.8 58.2 1.0
C A:ASP193 4.9 37.9 1.0
CZ A:ARG199 4.9 30.2 1.0
NH1 A:ARG199 4.9 28.3 1.0
N A:ASP193 5.0 27.9 1.0

Magnesium binding site 3 out of 8 in 4rao

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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:75.0
occ:1.00
 OE1 B:GLU133 2.1 35.9 0.5
OD1 B:ASP134 2.1 31.8 1.0
OE1 B:GLU133 2.2 33.2 0.1
CAJ B:3L7301 2.2 42.7 0.6
CD B:GLU133 2.5 31.5 0.5
OAU B:3L7301 2.6 42.7 0.6
CAL B:3L7301 2.8 41.2 0.6
OE2 B:GLU133 2.8 35.0 0.5
CAK B:3L7301 3.1 39.2 0.6
CG B:ASP134 3.1 31.7 1.0
CD B:GLU133 3.4 31.5 0.1
OD2 B:ASP134 3.5 41.4 1.0
CG B:GLU133 3.6 28.9 0.5
OE2 B:GLU133 3.9 32.0 0.1
CAL B:3L7301 4.0 40.9 0.3
N B:ASP134 4.1 22.9 1.0
NAY B:3L7301 4.2 40.2 0.3
O B:ILE135 4.2 31.1 1.0
NAY B:3L7301 4.3 40.5 0.6
CG1 B:VAL66 4.3 30.3 1.0
N B:ILE135 4.3 27.2 1.0
CB B:ASP134 4.4 30.8 1.0
OE1 B:GLU133 4.5 30.3 0.5
CG B:GLU133 4.5 29.2 0.1
CAP B:3L7301 4.6 35.5 0.6
CG B:GLU133 4.6 29.9 0.5
OG1 B:THR141 4.6 39.8 0.3
CA B:ASP134 4.7 23.0 1.0
CG2 B:THR141 4.7 39.9 0.7
CB B:GLU133 4.7 27.3 0.5
CG2 B:ILE135 4.8 38.8 1.0
O B:VAL66 4.8 24.4 1.0
CB B:GLU133 4.8 27.5 0.5
CB B:VAL66 4.8 31.6 1.0
CAN B:3L7301 4.8 38.4 0.6
CB B:GLU133 4.9 26.8 0.1
CA B:GLU133 5.0 25.3 0.5
CA B:GLU133 5.0 25.7 0.5
C B:GLU133 5.0 24.9 0.5
CA B:GLU133 5.0 25.8 0.1

Magnesium binding site 4 out of 8 in 4rao

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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:36.8
occ:1.00
 O B:HOH447 2.0 41.2 1.0
OD1 B:ASP193 2.2 29.8 1.0
O B:HOH448 2.3 44.5 1.0
OAE B:3L7301 2.3 27.3 0.6
O B:HOH446 2.3 37.2 1.0
O B:HOH421 2.5 37.7 1.0
CG B:ASP193 3.0 30.6 1.0
OD2 B:ASP193 3.2 29.4 1.0
PBA B:3L7301 3.6 32.0 0.6
OAB B:3L7301 3.7 60.9 0.3
O B:HOH414 4.1 48.2 1.0
CAP B:3L7301 4.1 35.5 0.6
OAD B:3L7301 4.1 31.2 0.6
NH2 B:ARG199 4.1 29.8 1.0
O B:ASP193 4.2 25.6 1.0
O B:HOH441 4.4 44.4 1.0
OAU B:3L7301 4.4 43.1 0.3
CB B:ASP193 4.4 24.1 1.0
CAJ B:3L7301 4.5 40.1 0.3
O B:HOH429 4.5 44.5 1.0
C B:ASP193 4.7 25.7 1.0
N3 B:3L7301 4.7 33.9 0.6
N3 B:3L7301 4.8 33.9 0.3
OAB B:3L7301 4.8 26.8 0.6
N B:ASP193 4.8 26.7 1.0
NH1 B:ARG199 4.9 25.4 1.0
CAK B:3L7301 4.9 42.9 0.3
CA B:ASP193 4.9 22.4 1.0
CZ B:ARG199 4.9 28.2 1.0
CAK B:3L7301 4.9 39.2 0.6
PBA B:3L7301 5.0 62.5 0.3
CAM B:3L7301 5.0 38.9 0.3

Magnesium binding site 5 out of 8 in 4rao

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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:27.6
occ:1.00
 O C:HOH450 1.8 57.3 1.0
OE1 C:GLU133 2.2 39.3 1.0
O C:HOH448 2.2 43.6 1.0
OD1 C:ASP134 2.3 33.7 1.0
O C:HOH405 2.3 32.1 1.0
O C:HOH411 2.5 35.1 1.0
O C:HOH451 2.6 38.6 1.0
CD C:GLU133 2.8 43.9 1.0
OE2 C:GLU133 3.1 43.3 1.0
CG C:ASP134 3.3 34.9 1.0
OD2 C:ASP134 3.8 39.8 1.0
CG C:GLU133 3.8 41.2 1.0
OAD C:3L7301 4.1 32.8 0.8
N C:ASP134 4.2 29.1 1.0
O C:HOH449 4.2 58.6 1.0
CAK C:3L7301 4.3 53.5 0.8
O C:ILE135 4.4 32.1 1.0
O C:HOH407 4.5 38.6 1.0
N C:ILE135 4.5 33.3 1.0
CG1 C:VAL66 4.5 34.5 1.0
CB C:ASP134 4.6 32.7 1.0
NAY C:3L7301 4.6 38.5 0.8
CG2 C:ILE135 4.7 40.3 1.0
O C:VAL66 4.8 28.4 1.0
CA C:ASP134 4.8 30.2 1.0
CAJ C:3L7301 4.8 46.2 0.8
CB C:GLU133 5.0 30.9 1.0
CB C:VAL66 5.0 31.6 1.0

Magnesium binding site 6 out of 8 in 4rao

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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:41.7
occ:1.00
 O C:HOH452 2.1 60.9 1.0
OD1 C:ASP193 2.2 33.1 1.0
O C:HOH453 2.2 81.3 1.0
O C:HOH421 2.3 38.3 1.0
O C:HOH412 2.5 41.3 1.0
OAB C:3L7301 2.5 45.5 0.8
O C:HOH438 2.7 57.4 1.0
CG C:ASP193 3.1 33.4 1.0
OD2 C:ASP193 3.3 32.0 1.0
PBA C:3L7301 3.8 43.0 0.8
CAK C:3L7301 4.2 53.5 0.8
NH2 C:ARG199 4.2 35.5 1.0
CAP C:3L7301 4.3 51.5 0.8
O C:HOH436 4.3 47.4 1.0
O C:HOH415 4.3 46.8 1.0
O C:ASP193 4.3 32.8 1.0
O C:HOH451 4.4 38.6 1.0
OAD C:3L7301 4.5 32.8 0.8
CB C:ASP193 4.5 30.6 1.0
NH1 C:ARG199 4.7 36.2 1.0
N3 C:3L7301 4.7 30.8 0.8
N C:ASP193 4.8 29.5 1.0
C C:ASP193 4.9 32.5 1.0
CZ C:ARG199 4.9 33.3 1.0
OAU C:3L7301 4.9 52.3 0.8
OAE C:3L7301 5.0 39.6 0.8
CA C:ASP193 5.0 30.2 1.0

Magnesium binding site 7 out of 8 in 4rao

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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:26.2
occ:1.00
 O D:HOH447 1.9 49.3 1.0
O D:HOH445 2.1 36.6 1.0
OE1 D:GLU133 2.1 29.4 1.0
O D:HOH410 2.3 43.0 1.0
O D:HOH401 2.3 37.8 1.0
OD1 D:ASP134 2.4 29.1 1.0
CD D:GLU133 2.8 31.3 1.0
OE2 D:GLU133 3.1 32.7 1.0
CG D:ASP134 3.4 30.6 1.0
OD2 D:ASP134 3.8 33.5 1.0
CG D:GLU133 3.9 34.5 1.0
CAK D:3L7301 4.2 76.5 1.0
CG1 D:VAL66 4.2 31.1 1.0
OAB D:3L7301 4.3 79.3 1.0
N D:ASP134 4.3 28.1 1.0
CAP D:3L7301 4.5 78.1 1.0
O D:ILE135 4.5 30.0 1.0
O D:HOH421 4.5 38.1 1.0
N D:ILE135 4.6 28.8 1.0
CB D:ASP134 4.7 25.9 1.0
NAY D:3L7301 4.7 54.5 1.0
O D:VAL66 4.7 22.3 1.0
CAJ D:3L7301 4.7 68.3 1.0
CB D:VAL66 4.9 26.2 1.0
CA D:ASP134 4.9 21.9 1.0
OAU D:3L7301 5.0 74.4 1.0

Magnesium binding site 8 out of 8 in 4rao

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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:45.2
occ:1.00
 OD1 D:ASP193 2.2 33.9 1.0
O D:HOH425 2.3 42.9 1.0
O D:HOH446 2.3 53.5 1.0
OAE D:3L7301 2.7 0.7 1.0
CG D:ASP193 3.0 33.1 1.0
OD2 D:ASP193 3.2 35.7 1.0
CAP D:3L7301 3.3 78.1 1.0
PBA D:3L7301 3.6 81.7 1.0
NH2 D:ARG199 4.3 31.1 1.0
O D:ASP193 4.3 34.1 1.0
CB D:ASP193 4.4 31.0 1.0
O D:HOH431 4.5 47.4 1.0
OAB D:3L7301 4.6 79.3 1.0
CAK D:3L7301 4.7 76.5 1.0
N3 D:3L7301 4.7 39.7 1.0
OAD D:3L7301 4.7 80.1 1.0
C D:ASP193 4.8 33.3 1.0
N D:ASP193 4.8 28.7 1.0
NH1 D:ARG199 4.8 30.3 1.0
O D:HOH401 4.9 37.8 1.0
CA D:ASP193 4.9 30.3 1.0
CZ D:ARG199 5.0 31.8 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 02:58:39 2024

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