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Magnesium in PDB 6bo7: Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine

Enzymatic activity of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine

All present enzymatic activity of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine, PDB code: 6bo7 was solved by L.W.Guddat, D.T.Keough, D.Rejman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.17 / 2.86
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.784, 219.854, 254.139, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 25.6

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine (pdb code 6bo7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine, PDB code: 6bo7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in 6bo7

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Magnesium binding site 1 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:59.0
occ:1.00
 OE1 A:GLU144 2.8 63.3 1.0
OE2 A:GLU144 2.9 64.7 1.0
OD1 A:ASP145 2.9 50.1 1.0
CD A:GLU144 3.1 64.1 1.0
OAH A:YPG303 3.6 51.7 1.0
CG A:ASP145 3.8 48.4 1.0
OAT A:YPG303 4.0 46.1 1.0
OD2 A:ASP145 4.1 49.1 1.0
OAF A:YPG303 4.3 56.4 1.0
CG A:GLU144 4.4 62.0 1.0
CAO A:YPG303 4.5 49.4 1.0
CAL A:YPG303 4.7 44.1 1.0
O A:ILE146 4.8 44.3 1.0
CBA A:YPG303 4.8 47.4 1.0
O A:LEU75 4.9 43.6 1.0
N A:ASP145 5.0 46.6 1.0
OG A:SER79 5.0 45.3 1.0
CAN A:YPG303 5.0 49.1 1.0

Magnesium binding site 2 out of 27 in 6bo7

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Magnesium binding site 2 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:65.2
occ:1.00
 OAB A:YPG303 1.9 49.9 1.0
OD1 A:ASP204 2.2 48.1 1.0
CG A:ASP204 3.0 47.0 1.0
OAD A:YPG303 3.0 49.4 1.0
CAU A:YPG303 3.0 48.2 1.0
OD2 A:ASP204 3.2 46.7 1.0
CAP A:YPG303 3.6 47.0 1.0
O A:ASP204 3.6 42.3 1.0
NBC A:YPG303 3.7 48.0 1.0
PBE A:YPG303 4.2 51.3 1.0
CAL A:YPG303 4.2 44.1 1.0
C A:ASP204 4.2 43.2 1.0
CAM A:YPG303 4.3 52.8 1.0
CB A:ASP204 4.3 43.4 1.0
N3 A:YPG303 4.5 39.6 1.0
N A:ASP204 4.6 44.3 1.0
CA A:ASP204 4.6 41.5 1.0
NH2 A:ARG210 4.6 48.6 1.0
CBB A:YPG303 4.8 44.6 1.0
N2 A:YPG303 4.9 38.8 1.0

Magnesium binding site 3 out of 27 in 6bo7

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Magnesium binding site 3 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:65.4
occ:1.00
 OD1 B:ASP145 2.4 56.9 1.0
OE1 B:GLU144 2.7 64.4 1.0
OE2 B:GLU144 2.9 66.9 1.0
CD B:GLU144 3.0 64.4 1.0
CG B:ASP145 3.3 55.3 1.0
OD2 B:ASP145 3.6 59.1 1.0
OAH B:YPG303 3.9 48.7 1.0
OAT B:YPG303 4.0 50.8 1.0
CG B:GLU144 4.2 57.4 1.0
O B:ILE146 4.2 37.2 1.0
OAF B:YPG303 4.5 41.3 1.0
OG B:SER79 4.5 37.4 1.0
CG2 B:ILE146 4.5 36.1 1.0
N B:ASP145 4.6 43.9 1.0
N B:ILE146 4.6 31.8 1.0
CAO B:YPG303 4.7 48.5 1.0
CB B:ASP145 4.7 49.0 1.0
CBA B:YPG303 4.9 49.0 1.0
CAN B:YPG303 4.9 49.7 1.0

Magnesium binding site 4 out of 27 in 6bo7

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Magnesium binding site 4 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:51.5
occ:1.00
 OD1 B:ASP204 2.0 54.1 1.0
OAB B:YPG303 2.0 48.5 1.0
OAD B:YPG303 2.2 49.5 1.0
CG B:ASP204 2.7 52.7 1.0
OD2 B:ASP204 2.8 55.6 1.0
CAU B:YPG303 3.1 42.4 1.0
PBE B:YPG303 3.4 50.6 1.0
CAM B:YPG303 3.6 45.1 1.0
NH2 B:ARG210 3.8 52.2 1.0
CAL B:YPG303 3.9 43.1 1.0
NBC B:YPG303 4.1 41.5 1.0
CB B:ASP204 4.2 47.8 1.0
OAG B:YPG303 4.2 49.9 1.0
CAP B:YPG303 4.3 40.9 1.0
O B:ASP204 4.4 50.4 1.0
OAH B:YPG303 4.5 48.7 1.0
N B:ASP204 4.7 45.0 1.0
CZ B:ARG210 4.7 49.0 1.0
C B:ASP204 4.8 49.6 1.0
CA B:ASP204 4.8 46.4 1.0
NH1 B:ARG210 4.9 45.1 1.0

Magnesium binding site 5 out of 27 in 6bo7

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Magnesium binding site 5 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:61.5
occ:1.00
 OD1 C:ASP145 2.5 71.9 1.0
OE2 C:GLU144 3.0 67.1 1.0
OE1 C:GLU144 3.1 69.4 1.0
CD C:GLU144 3.2 68.8 1.0
CG C:ASP145 3.4 68.5 1.0
OAT C:YPG303 3.5 53.6 1.0
OD2 C:ASP145 3.6 66.5 1.0
OAH C:YPG303 3.8 51.4 1.0
OAF C:YPG303 4.1 50.2 1.0
O C:ILE146 4.3 51.2 1.0
CG C:GLU144 4.4 66.9 1.0
CAO C:YPG303 4.4 53.2 1.0
CG2 C:ILE146 4.5 47.7 1.0
CBA C:YPG303 4.5 51.9 1.0
CAN C:YPG303 4.5 56.1 1.0
N C:ILE146 4.6 45.6 1.0
CAZ C:YPG303 4.7 52.7 1.0
N C:ASP145 4.8 63.9 1.0
CBB C:YPG303 4.8 59.4 1.0
CB C:ASP145 4.8 64.7 1.0
OG C:SER79 4.9 40.9 1.0
NBC C:YPG303 4.9 50.6 1.0
CAL C:YPG303 5.0 50.4 1.0

Magnesium binding site 6 out of 27 in 6bo7

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Magnesium binding site 6 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:60.4
occ:1.00
 OD1 C:ASP204 2.0 63.1 1.0
OAB C:YPG303 2.0 50.6 1.0
OAD C:YPG303 2.4 48.6 1.0
OD2 C:ASP204 2.7 61.6 1.0
CG C:ASP204 2.7 61.4 1.0
CAU C:YPG303 3.1 50.5 1.0
PBE C:YPG303 3.5 54.0 1.0
CAM C:YPG303 3.6 50.1 1.0
NH2 C:ARG210 3.8 54.0 1.0
CAL C:YPG303 4.0 50.4 1.0
CB C:ASP204 4.1 57.3 1.0
NBC C:YPG303 4.2 50.6 1.0
OAG C:YPG303 4.3 48.4 1.0
O C:ASP204 4.3 62.7 1.0
CAP C:YPG303 4.4 50.8 1.0
C C:ASP204 4.7 62.5 1.0
OAH C:YPG303 4.7 51.4 1.0
CZ C:ARG210 4.7 49.5 1.0
N C:ASP204 4.7 59.9 1.0
CA C:ASP204 4.7 59.6 1.0

Magnesium binding site 7 out of 27 in 6bo7

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Magnesium binding site 7 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:62.9
occ:1.00
 OD1 D:ASP145 2.4 77.7 1.0
OE1 D:GLU144 2.8 51.4 1.0
OE2 D:GLU144 2.9 49.6 1.0
CD D:GLU144 3.0 48.3 1.0
CG D:ASP145 3.3 77.6 1.0
OD2 D:ASP145 3.5 80.7 1.0
OAH D:YPG303 3.7 59.1 1.0
OAT D:YPG303 3.8 52.7 1.0
CG D:GLU144 4.2 43.2 1.0
CAO D:YPG303 4.3 47.0 1.0
OAF D:YPG303 4.4 55.9 1.0
O D:ILE146 4.6 61.2 1.0
CBA D:YPG303 4.6 50.4 1.0
N D:ASP145 4.6 65.5 1.0
CB D:ASP145 4.7 72.3 1.0
OG D:SER79 4.7 46.8 1.0
CAN D:YPG303 4.8 51.7 1.0
CG2 D:ILE146 4.8 63.6 1.0
N D:ILE146 4.8 62.6 1.0
CAL D:YPG303 4.9 52.4 1.0
CAZ D:YPG303 5.0 53.8 1.0
CBB D:YPG303 5.0 54.4 1.0

Magnesium binding site 8 out of 27 in 6bo7

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Magnesium binding site 8 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:52.2
occ:1.00
 OAB D:YPG303 2.0 67.6 1.0
OD1 D:ASP204 2.0 51.8 1.0
OAD D:YPG303 2.2 51.7 1.0
CG D:ASP204 2.7 49.1 1.0
OD2 D:ASP204 2.7 47.3 1.0
CAU D:YPG303 3.1 58.1 1.0
PBE D:YPG303 3.2 56.1 1.0
CAM D:YPG303 3.4 47.7 1.0
NH2 D:ARG210 3.4 46.5 1.0
CAL D:YPG303 3.8 52.4 1.0
OAG D:YPG303 3.9 56.4 1.0
CB D:ASP204 4.1 46.0 1.0
NBC D:YPG303 4.1 51.2 1.0
CZ D:ARG210 4.4 47.2 1.0
CAP D:YPG303 4.4 50.4 1.0
OAH D:YPG303 4.4 59.1 1.0
O D:ASP204 4.6 44.1 1.0
NH1 D:ARG210 4.8 44.0 1.0
N D:ASP204 4.8 39.7 1.0
CA D:ASP204 4.9 42.8 1.0
C D:ASP204 4.9 43.0 1.0

Magnesium binding site 9 out of 27 in 6bo7

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Magnesium binding site 9 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:55.0
occ:1.00
 OD1 E:ASP145 2.5 48.3 1.0
OE2 E:GLU144 2.9 60.4 1.0
OE1 E:GLU144 2.9 56.7 1.0
CD E:GLU144 3.1 56.9 1.0
OAH E:YPG304 3.3 48.8 1.0
CG E:ASP145 3.3 47.2 1.0
OD2 E:ASP145 3.5 46.6 1.0
OAT E:YPG304 3.9 41.9 1.0
CG E:GLU144 4.4 51.7 1.0
CAO E:YPG304 4.4 42.4 1.0
O E:ILE146 4.4 40.5 1.0
CG2 E:ILE146 4.4 42.7 1.0
OAF E:YPG304 4.4 58.6 1.0
CBA E:YPG304 4.7 42.6 1.0
PBE E:YPG304 4.7 45.0 1.0
N E:ILE146 4.7 38.5 1.0
CAL E:YPG304 4.7 51.1 1.0
CB E:ASP145 4.8 44.0 1.0
N E:ASP145 4.8 43.8 1.0
OG E:SER79 4.8 48.6 1.0
NBC E:YPG304 4.9 47.5 1.0
CBB E:YPG304 4.9 50.3 1.0
CAN E:YPG304 5.0 50.9 1.0

Magnesium binding site 10 out of 27 in 6bo7

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Magnesium binding site 10 out of 27 in the Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Plasmodium Vivax Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3- ((S)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N-(Phosphonopropionyl) Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:48.4
occ:1.00
 OAB E:YPG304 2.0 51.2 1.0
OD1 E:ASP204 2.0 64.7 1.0
OAD E:YPG304 2.0 46.3 1.0
CG E:ASP204 2.9 61.0 1.0
OD2 E:ASP204 3.1 61.3 1.0
CAU E:YPG304 3.1 46.9 1.0
PBE E:YPG304 3.3 45.0 1.0
CAM E:YPG304 3.6 58.5 1.0
NH2 E:ARG210 3.8 57.1 1.0
CAL E:YPG304 3.9 51.1 1.0
NBC E:YPG304 4.0 47.5 1.0
OAG E:YPG304 4.2 42.5 1.0
CAP E:YPG304 4.2 48.1 1.0
CB E:ASP204 4.3 56.6 1.0
OAH E:YPG304 4.3 48.8 1.0
O E:ASP204 4.4 60.8 1.0
N E:ASP204 4.6 57.0 1.0
CZ E:ARG210 4.6 52.9 1.0
NH1 E:ARG210 4.8 49.9 1.0
CA E:ASP204 4.8 56.0 1.0
C E:ASP204 4.8 58.2 1.0

Reference:

D.T.Keough, D.Rejman, R.Pohl, E.Zbornikova, D.Hockova, T.Croll, M.D.Edstein, G.W.Birrell, M.Chavchich, L.M.J.Naesens, G.K.Pierens, I.M.Brereton, L.W.Guddat. Design of Plasmodium Vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors As Potential Antimalarial Therapeutics. Acs Chem. Biol. V. 13 82 2018.
ISSN: ESSN 1554-8937
PubMed: 29161011
DOI: 10.1021/ACSCHEMBIO.7B00916
Page generated: Mon Sep 30 19:52:18 2024

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