Atomistry » Magnesium » PDB 5hia-5hqw » 5hia
Atomistry »
  Magnesium »
    PDB 5hia-5hqw »
      5hia »

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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Go back to Magnesium Binding Sites List in 5hia
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy