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Magnesium in PDB 4rab: 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: 4rab 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) 41.53 / 2.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.728, 128.958, 62.938, 90.00, 103.04, 90.00
R / Rfree (%) 20.9 / 23.1

Other elements in 4rab:

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 also contains other interesting chemical elements:

Bromine (Br) 4 atoms

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

Magnesium binding site 1 out of 6 in 4rab

Go back to Magnesium Binding Sites List in 4rab
Magnesium binding site 1 out of 6 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:85.8
occ:1.00
 CD A:GLU133 2.0 50.6 1.0
OE2 A:GLU133 2.1 50.5 1.0
OE1 A:GLU133 2.2 53.2 1.0
OD1 A:ASP134 2.2 41.7 1.0
O A:HOH430 2.7 49.0 1.0
CG A:GLU133 2.8 47.9 1.0
O A:ILE135 2.8 33.7 1.0
CG A:ASP134 3.4 38.2 1.0
N A:ILE135 3.5 32.4 1.0
OAU A:3L3301 3.7 63.0 1.0
O A:HOH429 3.7 37.9 1.0
O A:HOH426 3.7 46.8 1.0
C A:ILE135 3.8 34.2 1.0
N A:ASP134 4.0 31.9 1.0
CG2 A:ILE135 4.0 35.1 1.0
OD2 A:ASP134 4.0 37.0 1.0
CAK A:3L3301 4.1 62.0 1.0
CA A:ILE135 4.2 34.3 1.0
CB A:GLU133 4.2 43.6 1.0
CAJ A:3L3301 4.3 62.5 1.0
C A:ASP134 4.5 35.0 1.0
CA A:ASP134 4.6 33.9 1.0
CB A:ASP134 4.6 36.6 1.0
CA A:GLU133 4.7 37.8 1.0
C A:GLU133 4.7 34.5 1.0
CAL A:3L3301 4.7 62.1 1.0
CB A:ILE135 4.8 35.3 1.0

Magnesium binding site 2 out of 6 in 4rab

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Magnesium binding site 2 out of 6 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
B:Mg302

b:77.0
occ:1.00
 CD B:GLU133 2.1 58.0 1.0
OE1 B:GLU133 2.1 59.1 1.0
OD1 B:ASP134 2.2 47.6 1.0
OE2 B:GLU133 2.2 60.0 1.0
CG B:GLU133 3.1 54.7 1.0
CG B:ASP134 3.3 44.2 1.0
OAU B:3L3301 3.5 69.2 1.0
CAJ B:3L3301 3.7 71.8 1.0
OD2 B:ASP134 3.8 42.8 1.0
O B:ILE135 3.9 43.6 1.0
O B:HOH417 3.9 54.3 1.0
N B:ASP134 4.1 39.5 1.0
N B:ILE135 4.1 41.3 1.0
CAL B:3L3301 4.4 72.3 1.0
CAK B:3L3301 4.4 67.5 1.0
CG2 B:ILE135 4.4 42.8 1.0
CB B:GLU133 4.4 47.3 1.0
CG1 B:VAL66 4.5 38.1 1.0
CB B:ASP134 4.6 42.4 1.0
CA B:ASP134 4.7 41.1 1.0
C B:ILE135 4.8 43.2 1.0
CA B:GLU133 4.8 40.7 1.0
CA B:ILE135 4.9 43.5 1.0
C B:GLU133 4.9 38.7 1.0
C B:ASP134 4.9 42.2 1.0
O4 B:PO4304 5.0 71.0 1.0

Magnesium binding site 3 out of 6 in 4rab

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Magnesium binding site 3 out of 6 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
C:Mg302

b:62.4
occ:1.00
 O C:HOH429 2.1 54.4 1.0
OD1 C:ASP134 2.1 43.1 1.0
OE1 C:GLU133 2.1 43.1 1.0
O C:HOH419 2.1 44.6 1.0
O C:HOH420 2.2 46.1 1.0
CD C:GLU133 2.9 44.1 1.0
OE2 C:GLU133 3.1 43.6 1.0
CG C:ASP134 3.2 43.4 1.0
CAJ C:3L3301 3.4 75.3 1.0
OD2 C:ASP134 3.6 43.1 1.0
O C:ILE135 3.6 40.1 1.0
OAU C:3L3301 3.6 76.3 1.0
N C:ILE135 3.9 40.7 1.0
CG2 C:ILE135 4.0 45.7 1.0
N C:ASP134 4.1 39.3 1.0
CG C:GLU133 4.3 42.5 1.0
CAK C:3L3301 4.5 76.3 1.0
CB C:ASP134 4.5 41.6 1.0
C C:ILE135 4.5 41.3 1.0
CB C:GLU133 4.6 39.1 1.0
CA C:ILE135 4.6 40.3 1.0
O2 C:PO4304 4.7 92.7 1.0
CA C:ASP134 4.7 40.0 1.0
CAL C:3L3301 4.8 75.3 1.0
C C:ASP134 4.8 39.9 1.0
CB C:ILE135 5.0 47.6 1.0
CA C:GLU133 5.0 36.7 1.0

Magnesium binding site 4 out of 6 in 4rab

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Magnesium binding site 4 out of 6 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
C:Mg303

b:71.2
occ:1.00
 O3 C:PO4304 1.9 93.2 1.0
O C:HOH421 2.0 67.7 1.0
OD1 C:ASP193 2.2 43.5 1.0
OAH C:3L3301 2.5 74.3 1.0
P C:PO4304 3.2 92.9 1.0
CG C:ASP193 3.2 41.3 1.0
O4 C:PO4304 3.3 93.0 1.0
OD2 C:ASP193 3.4 41.2 1.0
OAG C:3L3301 3.5 0.5 1.0
PBD C:3L3301 3.5 0.3 1.0
O C:HOH425 3.9 62.6 1.0
NH2 C:ARG199 3.9 33.3 1.0
O1 C:PO4304 4.1 92.2 1.0
O2 C:PO4304 4.2 92.7 1.0
CAN C:3L3301 4.3 75.5 1.0
CAQ C:3L3301 4.5 77.3 1.0
CB C:ASP193 4.6 39.2 1.0
O C:ASP193 4.7 35.8 1.0
OAD C:3L3301 4.7 0.9 1.0
NH1 C:ARG199 4.8 29.6 1.0
CZ C:ARG199 4.8 31.5 1.0

Magnesium binding site 5 out of 6 in 4rab

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Magnesium binding site 5 out of 6 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
D:Mg302

b:67.2
occ:1.00
 O D:HOH430 1.9 48.1 1.0
O D:HOH431 2.0 54.4 1.0
OD1 D:ASP134 2.1 39.7 1.0
OE1 D:GLU133 2.2 45.8 1.0
O D:HOH429 2.3 38.3 1.0
CG D:ASP134 2.9 39.2 1.0
CD D:GLU133 3.0 46.3 1.0
OD2 D:ASP134 3.2 41.8 1.0
OE2 D:GLU133 3.6 48.0 1.0
O2 D:PO4304 3.7 0.0 1.0
CG D:GLU133 4.0 44.1 1.0
CAL D:3L3301 4.1 62.9 1.0
N D:ASP134 4.2 31.2 1.0
CB D:ASP134 4.3 34.4 1.0
CAJ D:3L3301 4.4 61.2 1.0
OAU D:3L3301 4.4 60.4 1.0
N D:ILE135 4.4 31.6 1.0
CG1 D:VAL66 4.5 34.5 1.0
CG2 D:ILE135 4.6 41.7 1.0
O D:ILE135 4.6 38.2 1.0
CA D:ASP134 4.7 33.1 1.0
O D:VAL66 4.7 30.1 1.0
CAM D:3L3301 4.9 62.4 1.0
P D:PO4304 4.9 0.9 1.0

Magnesium binding site 6 out of 6 in 4rab

Go back to Magnesium Binding Sites List in 4rab
Magnesium binding site 6 out of 6 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
D:Mg303

b:60.2
occ:1.00
 OD1 D:ASP193 2.1 40.8 1.0
CG D:ASP193 3.0 41.8 1.0
OD2 D:ASP193 3.1 42.4 1.0
O4 D:PO4304 3.6 0.9 1.0
O D:ASP193 3.8 41.3 1.0
OAD D:3L3301 3.8 0.7 1.0
CAN D:3L3301 3.9 68.7 1.0
O3 D:PO4304 4.1 0.4 1.0
OAG D:3L3301 4.1 0.9 1.0
CB D:ASP193 4.4 40.1 1.0
PBD D:3L3301 4.4 0.3 1.0
C D:ASP193 4.4 41.5 1.0
P D:PO4304 4.5 0.9 1.0
CAQ D:3L3301 4.5 70.8 1.0
N3 D:3L3301 4.5 51.1 1.0
NH2 D:ARG199 4.6 33.0 1.0
CAO D:3L3301 4.7 60.4 1.0
CA D:ASP193 4.8 39.9 1.0
N D:ASP193 4.8 38.0 1.0
N2 D:3L3301 5.0 48.5 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 02:56:32 2024

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