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Magnesium in PDB 5hia: Human 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 Human 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 Human 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 Human 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: 5hia 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) 47.61 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.718, 97.606, 130.329, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human 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 5hia). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human 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: 5hia:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5hia

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Magnesium binding site 1 out of 8 in the Human 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 Human 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:30.6
occ:1.00
 OD1 A:ASP193 2.0 22.3 1.0
O A:HOH464 2.2 27.4 1.0
OAB A:YPG301 2.2 29.1 1.0
OAD A:YPG301 2.2 27.5 1.0
O A:HOH468 2.2 36.0 1.0
O A:HOH423 2.3 28.8 1.0
CG A:ASP193 3.0 23.9 1.0
CAU A:YPG301 3.1 27.7 1.0
OD2 A:ASP193 3.3 24.1 1.0
PBE A:YPG301 3.5 28.2 1.0
O A:HOH458 3.7 30.6 1.0
CAM A:YPG301 3.8 24.1 1.0
NH2 A:ARG199 3.9 22.1 1.0
CAL A:YPG301 4.0 24.2 1.0
NBC A:YPG301 4.0 30.1 1.0
CAP A:YPG301 4.2 30.7 1.0
O A:ASP193 4.2 25.9 1.0
CB A:ASP193 4.3 22.6 1.0
OAH A:YPG301 4.4 24.9 1.0
NH1 A:ARG199 4.5 20.7 1.0
O A:HOH412 4.5 40.3 1.0
OAG A:YPG301 4.5 27.6 1.0
N A:ASP193 4.5 20.9 1.0
CZ A:ARG199 4.6 21.3 1.0
C A:ASP193 4.7 24.8 1.0
CA A:ASP193 4.7 21.5 1.0
N3 A:YPG301 4.8 24.6 1.0
O A:HOH426 5.0 25.8 1.0
N2 A:YPG301 5.0 27.8 1.0

Magnesium binding site 2 out of 8 in 5hia

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Magnesium binding site 2 out of 8 in the Human 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 Human 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:Mg303

b:27.4
occ:1.00
 O A:HOH426 1.9 25.8 1.0
OD1 A:ASP134 2.0 24.1 1.0
OE1 A:GLU133 2.1 25.3 1.0
O A:HOH406 2.2 33.0 1.0
O A:HOH465 2.2 27.5 1.0
O A:HOH438 2.2 24.0 1.0
CD A:GLU133 2.9 29.7 1.0
CG A:ASP134 3.0 25.8 1.0
OD2 A:ASP134 3.3 28.6 1.0
OE2 A:GLU133 3.4 32.9 1.0
OAH A:YPG301 3.8 24.9 1.0
CG A:GLU133 3.9 32.4 1.0
O A:HOH466 4.0 41.9 1.0
N A:ASP134 4.1 19.6 1.0
CB A:ASP134 4.3 22.6 1.0
O A:ILE135 4.4 22.1 1.0
N A:ILE135 4.4 20.9 1.0
O A:HOH452 4.5 35.1 1.0
OAT A:YPG301 4.6 28.7 1.0
CAO A:YPG301 4.7 28.4 1.0
CG1 A:VAL66 4.7 24.7 1.0
CA A:ASP134 4.7 19.2 1.0
CG2 A:ILE135 4.8 21.5 1.0
O A:VAL66 4.8 21.0 1.0
CAL A:YPG301 4.8 24.2 1.0
CA A:GLY69 5.0 20.2 1.0
N A:GLY70 5.0 20.9 1.0
OAF A:YPG301 5.0 28.8 1.0

Magnesium binding site 3 out of 8 in 5hia

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Magnesium binding site 3 out of 8 in the Human 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 Human 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:28.2
occ:1.00
 OAB B:YPG301 2.0 22.5 1.0
OD1 B:ASP193 2.1 18.4 1.0
OAD B:YPG301 2.1 25.6 1.0
O B:HOH414 2.2 24.1 1.0
O B:HOH485 2.2 25.5 1.0
O B:HOH488 2.3 20.5 1.0
CG B:ASP193 3.0 18.6 1.0
CAU B:YPG301 3.0 22.1 1.0
OD2 B:ASP193 3.3 19.9 1.0
PBE B:YPG301 3.4 25.2 1.0
O B:HOH422 3.7 26.5 1.0
CAM B:YPG301 3.7 18.5 1.0
NH2 B:ARG199 3.8 20.1 1.0
NBC B:YPG301 3.9 24.0 1.0
CAL B:YPG301 3.9 21.2 1.0
CAP B:YPG301 4.0 22.5 1.0
O B:ASP193 4.3 17.6 1.0
OAH B:YPG301 4.3 25.4 1.0
CB B:ASP193 4.4 17.7 1.0
OAG B:YPG301 4.4 24.5 1.0
NH1 B:ARG199 4.4 18.1 1.0
O B:HOH491 4.5 34.6 1.0
CZ B:ARG199 4.5 19.0 1.0
N B:ASP193 4.6 16.1 1.0
N3 B:YPG301 4.7 21.0 1.0
O B:HOH411 4.8 18.9 1.0
C B:ASP193 4.8 17.4 1.0
CA B:ASP193 4.8 16.7 1.0
N2 B:YPG301 4.9 22.1 1.0

Magnesium binding site 4 out of 8 in 5hia

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Magnesium binding site 4 out of 8 in the Human 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 Human 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:Mg303

b:21.6
occ:1.00
 OD1 B:ASP134 2.1 15.1 1.0
O B:HOH411 2.1 18.9 1.0
O B:HOH419 2.1 24.3 1.0
O B:HOH444 2.1 21.1 1.0
OE2 B:GLU133 2.2 18.3 1.0
O B:HOH424 2.2 24.0 1.0
CD B:GLU133 3.1 20.8 1.0
CG B:ASP134 3.1 17.1 1.0
OE1 B:GLU133 3.3 21.4 1.0
OD2 B:ASP134 3.5 20.4 1.0
OAH B:YPG301 3.8 25.4 1.0
N B:ASP134 4.1 15.2 1.0
O B:ILE135 4.4 19.4 1.0
N B:ILE135 4.4 14.1 1.0
CB B:ASP134 4.4 15.6 1.0
CG1 B:VAL66 4.4 19.2 1.0
CG B:GLU133 4.5 19.6 1.0
OAT B:YPG301 4.5 21.9 1.0
O B:HOH524 4.5 38.2 1.0
CAO B:YPG301 4.6 21.0 1.0
O B:HOH457 4.6 22.2 1.0
O B:VAL66 4.6 13.3 1.0
CG2 B:ILE135 4.7 17.9 1.0
CA B:ASP134 4.8 13.5 1.0
CB B:GLU133 4.8 17.5 1.0
CAL B:YPG301 4.9 21.2 1.0
CB B:VAL66 4.9 18.0 1.0
OAF B:YPG301 5.0 21.9 1.0

Magnesium binding site 5 out of 8 in 5hia

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Magnesium binding site 5 out of 8 in the Human 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 Human 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:26.7
occ:1.00
 OD1 C:ASP193 1.9 22.4 1.0
O C:HOH484 2.0 18.5 1.0
OAB C:YPG301 2.1 26.6 1.0
OAD C:YPG301 2.1 25.3 1.0
O C:HOH488 2.2 32.8 1.0
O C:HOH434 2.2 26.5 1.0
CG C:ASP193 2.9 23.2 1.0
CAU C:YPG301 3.1 24.5 1.0
OD2 C:ASP193 3.3 24.1 1.0
PBE C:YPG301 3.5 28.6 1.0
O C:HOH419 3.6 36.1 1.0
NBC C:YPG301 3.9 24.7 1.0
CAM C:YPG301 3.9 25.6 1.0
NH2 C:ARG199 3.9 22.8 1.0
CAP C:YPG301 4.0 24.9 1.0
CAL C:YPG301 4.0 25.4 1.0
O C:ASP193 4.2 22.1 1.0
CB C:ASP193 4.3 19.1 1.0
NH1 C:ARG199 4.3 22.5 1.0
OAH C:YPG301 4.3 29.1 1.0
O C:HOH501 4.3 37.5 1.0
N C:ASP193 4.5 17.2 1.0
CZ C:ARG199 4.5 21.0 1.0
OAG C:YPG301 4.5 34.3 1.0
O C:HOH449 4.6 36.6 1.0
N3 C:YPG301 4.6 21.8 1.0
C C:ASP193 4.7 22.4 1.0
CA C:ASP193 4.7 17.5 1.0
N2 C:YPG301 4.8 24.4 1.0
O C:HOH408 4.9 21.3 1.0
CBB C:YPG301 5.0 23.8 1.0

Magnesium binding site 6 out of 8 in 5hia

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Magnesium binding site 6 out of 8 in the Human 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 Human 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:Mg303

b:23.4
occ:1.00
 O C:HOH408 2.0 21.3 1.0
OD1 C:ASP134 2.1 17.9 1.0
OE2 C:GLU133 2.1 21.4 1.0
O C:HOH450 2.1 19.5 1.0
O C:HOH431 2.2 24.4 1.0
O C:HOH474 2.3 24.8 1.0
CD C:GLU133 3.0 21.4 1.0
CG C:ASP134 3.1 18.4 1.0
OE1 C:GLU133 3.3 20.0 1.0
OD2 C:ASP134 3.4 17.4 1.0
OAH C:YPG301 3.7 29.1 1.0
N C:ASP134 4.2 14.2 1.0
O C:HOH502 4.3 33.8 1.0
CG C:GLU133 4.4 21.9 1.0
N C:ILE135 4.4 13.3 1.0
O C:ILE135 4.4 19.0 1.0
CG1 C:VAL66 4.4 16.4 1.0
CB C:ASP134 4.4 14.0 1.0
OAT C:YPG301 4.6 24.1 1.0
O C:VAL66 4.6 16.5 1.0
O C:HOH460 4.6 37.5 1.0
O C:HOH455 4.7 22.9 1.0
CB C:GLU133 4.7 16.1 1.0
CG2 C:ILE135 4.8 19.9 1.0
CAO C:YPG301 4.8 24.9 1.0
CA C:ASP134 4.8 13.0 1.0
OAF C:YPG301 4.9 27.3 1.0
CB C:VAL66 4.9 15.9 1.0
CA C:GLU133 5.0 15.1 1.0
N C:GLY70 5.0 18.6 1.0
O C:HOH419 5.0 36.1 1.0
CAL C:YPG301 5.0 25.4 1.0

Magnesium binding site 7 out of 8 in 5hia

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Magnesium binding site 7 out of 8 in the Human 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 Human 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:24.8
occ:1.00
 OD1 D:ASP193 1.9 17.7 1.0
OAB D:YPG301 2.1 21.4 1.0
OAD D:YPG301 2.1 26.2 1.0
O D:HOH414 2.1 22.0 1.0
O D:HOH458 2.2 21.1 1.0
O D:HOH475 2.3 25.1 1.0
CG D:ASP193 2.9 17.9 1.0
CAU D:YPG301 3.1 20.5 1.0
OD2 D:ASP193 3.2 16.8 1.0
PBE D:YPG301 3.4 25.6 1.0
O D:HOH416 3.8 27.0 1.0
CAM D:YPG301 3.8 20.0 1.0
NH2 D:ARG199 3.9 14.1 1.0
NBC D:YPG301 4.0 22.2 1.0
CAL D:YPG301 4.0 21.0 1.0
O D:ASP193 4.0 16.5 1.0
CAP D:YPG301 4.1 22.3 1.0
CB D:ASP193 4.2 16.8 1.0
OAH D:YPG301 4.3 23.3 1.0
NH1 D:ARG199 4.3 12.3 1.0
OAG D:YPG301 4.5 23.9 1.0
CZ D:ARG199 4.5 13.0 1.0
O D:HOH450 4.5 33.7 1.0
N D:ASP193 4.5 14.2 1.0
C D:ASP193 4.6 15.4 1.0
CA D:ASP193 4.7 13.1 1.0
N3 D:YPG301 4.8 25.5 1.0
O D:HOH411 4.9 22.0 1.0
O D:HOH440 4.9 33.3 1.0
N2 D:YPG301 4.9 22.4 1.0

Magnesium binding site 8 out of 8 in 5hia

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Magnesium binding site 8 out of 8 in the Human 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 Human 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:Mg303

b:21.7
occ:1.00
 OE1 D:GLU133 2.0 17.9 1.0
OD1 D:ASP134 2.1 15.4 1.0
O D:HOH411 2.1 22.0 1.0
O D:HOH441 2.1 20.6 1.0
O D:HOH439 2.1 24.7 1.0
O D:HOH413 2.1 23.7 1.0
CD D:GLU133 3.0 21.0 1.0
CG D:ASP134 3.1 18.3 1.0
OE2 D:GLU133 3.3 23.7 1.0
OD2 D:ASP134 3.5 19.1 1.0
OAH D:YPG301 3.7 23.3 1.0
N D:ASP134 4.1 14.9 1.0
CG D:GLU133 4.4 22.2 1.0
O D:HOH497 4.4 35.9 1.0
CB D:ASP134 4.4 16.6 1.0
N D:ILE135 4.5 17.2 1.0
O D:ILE135 4.5 18.0 1.0
CG1 D:VAL66 4.6 21.1 1.0
O D:VAL66 4.6 16.7 1.0
OAT D:YPG301 4.6 20.1 1.0
O D:HOH426 4.7 27.4 1.0
CB D:GLU133 4.7 18.0 1.0
CA D:ASP134 4.8 12.8 1.0
CAO D:YPG301 4.8 21.4 1.0
CA D:GLY69 4.8 17.6 1.0
N D:GLY70 4.9 16.7 1.0
CAL D:YPG301 4.9 21.0 1.0
OAF D:YPG301 4.9 21.5 1.0
CG2 D:ILE135 4.9 17.9 1.0
CB D:VAL66 5.0 18.3 1.0
CA D:GLU133 5.0 14.3 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. 2017.
ISSN: ESSN 1554-8937
PubMed: 29161011
DOI: 10.1021/ACSCHEMBIO.7B00916
Page generated: Sun Sep 29 15:56:52 2024

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