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

Resolution Low / High (Å) 42.40 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.620, 93.942, 130.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.8

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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine (pdb code 6bnj). 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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine, PDB code: 6bnj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6bnj

Go back to Magnesium Binding Sites List in 6bnj
Magnesium binding site 1 out of 8 in the Human Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:29.5
occ:1.00
 O A:HOH421 2.1 27.4 1.0
O A:HOH467 2.1 19.2 1.0
O A:HOH436 2.1 22.6 1.0
OD1 A:ASP134 2.2 16.5 1.0
OE1 A:GLU133 2.2 22.5 1.0
O A:HOH479 2.4 23.1 1.0
CD A:GLU133 2.7 19.4 1.0
OE2 A:GLU133 3.0 24.9 1.0
CG A:ASP134 3.2 16.8 1.0
OD2 A:ASP134 3.6 18.0 1.0
CG A:GLU133 3.8 23.9 1.0
OAD A:WPG301 3.9 26.4 1.0
O A:HOH505 4.0 35.3 1.0
N A:ASP134 4.3 14.4 1.0
O A:ILE135 4.3 17.1 1.0
O A:HOH474 4.4 31.4 1.0
N A:ILE135 4.4 14.3 1.0
OAT A:WPG301 4.5 24.9 1.0
CB A:ASP134 4.5 15.8 1.0
O A:HOH456 4.6 40.7 1.0
CG1 A:VAL66 4.6 15.7 1.0
CAO A:WPG301 4.7 27.4 1.0
CG2 A:ILE135 4.8 16.5 1.0
CAL A:WPG301 4.8 28.3 1.0
CA A:ASP134 4.9 14.5 1.0
O A:VAL66 4.9 13.1 1.0
CB A:GLU133 4.9 20.0 1.0

Magnesium binding site 2 out of 8 in 6bnj

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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-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:26.6
occ:1.00
 OAB A:WPG301 2.0 29.2 1.0
OD1 A:ASP193 2.0 13.6 1.0
OAG A:WPG301 2.1 29.9 1.0
O A:HOH488 2.1 20.9 1.0
O A:HOH493 2.2 22.2 1.0
O A:HOH507 2.3 26.1 1.0
CAU A:WPG301 3.0 29.5 1.0
CG A:ASP193 3.1 13.3 1.0
PBE A:WPG301 3.4 29.0 1.0
OD2 A:ASP193 3.4 14.1 1.0
O A:HOH439 3.6 28.9 1.0
CAM A:WPG301 3.7 26.8 1.0
CAL A:WPG301 3.9 28.3 1.0
NBC A:WPG301 3.9 28.9 1.0
NH2 A:ARG199 4.0 12.5 1.0
CAP A:WPG301 4.1 31.2 1.0
O A:ASP193 4.2 14.4 1.0
OAD A:WPG301 4.3 26.4 1.0
NH1 A:ARG199 4.4 11.3 1.0
CB A:ASP193 4.4 12.5 1.0
OAH A:WPG301 4.5 22.2 1.0
N A:ASP193 4.5 11.7 1.0
O A:HOH490 4.6 39.5 1.0
O A:HOH535 4.6 41.5 1.0
CZ A:ARG199 4.6 11.8 1.0
N3 A:WPG301 4.6 20.6 1.0
O A:HOH426 4.7 32.7 1.0
C A:ASP193 4.8 13.4 1.0
O A:HOH436 4.8 22.6 1.0
CA A:ASP193 4.8 12.1 1.0
N2 A:WPG301 4.9 18.7 1.0
CBB A:WPG301 5.0 28.1 1.0

Magnesium binding site 3 out of 8 in 6bnj

Go back to Magnesium Binding Sites List in 6bnj
Magnesium binding site 3 out of 8 in the Human Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:41.1
occ:1.00
 O B:HOH444 2.0 36.4 1.0
OE1 B:GLU133 2.3 15.7 1.0
OD1 B:ASP134 2.4 19.4 1.0
O B:HOH446 2.4 29.2 1.0
CD B:GLU133 2.8 19.9 1.0
OE2 B:GLU133 2.9 26.6 1.0
CG B:ASP134 3.3 18.2 1.0
OD2 B:ASP134 3.6 23.5 1.0
OAG B:WPG301 3.7 33.7 1.0
CG B:GLU133 4.1 23.8 1.0
CG1 B:VAL66 4.2 15.8 1.0
O B:HOH509 4.2 42.8 1.0
N B:ASP134 4.5 14.3 1.0
O B:HOH445 4.6 27.0 1.0
CB B:ASP134 4.7 17.3 1.0
O B:VAL66 4.7 14.2 1.0
CB B:VAL66 4.8 15.0 1.0
O B:ILE135 4.8 21.7 1.0
N B:ILE135 4.8 12.2 1.0
CAL B:WPG301 4.9 31.4 1.0
OAT B:WPG301 4.9 36.2 1.0

Magnesium binding site 4 out of 8 in 6bnj

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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-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:33.6
occ:1.00
 OAB B:WPG301 1.9 36.5 1.0
OD1 B:ASP193 2.1 15.7 1.0
O B:HOH416 2.1 26.0 1.0
O B:HOH486 2.2 25.1 1.0
O B:HOH488 2.2 30.9 1.0
OAH B:WPG301 2.3 37.1 1.0
CAU B:WPG301 3.0 35.5 1.0
CG B:ASP193 3.1 16.2 1.0
OD2 B:ASP193 3.4 17.2 1.0
PBE B:WPG301 3.5 41.4 1.0
CAM B:WPG301 3.5 23.7 1.0
O B:HOH436 3.6 22.6 1.0
CAL B:WPG301 3.8 31.4 1.0
NBC B:WPG301 3.9 34.2 1.0
NH2 B:ARG199 4.0 16.5 1.0
CAP B:WPG301 4.1 30.2 1.0
O B:ASP193 4.2 16.4 1.0
CB B:ASP193 4.4 15.8 1.0
NH1 B:ARG199 4.5 14.2 1.0
OAD B:WPG301 4.5 39.2 1.0
OAG B:WPG301 4.5 33.7 1.0
N B:ASP193 4.6 14.5 1.0
CZ B:ARG199 4.7 17.0 1.0
N3 B:WPG301 4.7 22.4 1.0
C B:ASP193 4.7 16.3 1.0
O B:HOH449 4.7 36.7 1.0
O B:HOH446 4.8 29.2 1.0
CA B:ASP193 4.8 15.4 1.0
CBB B:WPG301 4.9 26.8 1.0
N2 B:WPG301 4.9 21.4 1.0

Magnesium binding site 5 out of 8 in 6bnj

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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-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:24.3
occ:1.00
 OD1 C:ASP134 2.1 13.7 1.0
OE1 C:GLU133 2.1 17.5 1.0
O C:HOH407 2.2 16.6 1.0
O C:HOH424 2.2 20.7 1.0
O C:HOH446 2.3 18.6 1.0
O C:HOH423 2.3 17.7 1.0
CD C:GLU133 3.0 16.8 1.0
CG C:ASP134 3.1 16.6 1.0
OE2 C:GLU133 3.3 16.9 1.0
OD2 C:ASP134 3.4 17.0 1.0
OAH C:WPG301 3.7 25.0 1.0
N C:ASP134 4.1 10.4 1.0
O C:HOH515 4.1 29.9 1.0
O C:ILE135 4.3 16.3 1.0
CG C:GLU133 4.3 18.7 1.0
N C:ILE135 4.4 10.4 1.0
CB C:ASP134 4.4 11.9 1.0
OAT C:WPG301 4.5 22.4 1.0
CG1 C:VAL66 4.5 12.7 1.0
O C:HOH505 4.7 24.9 1.0
CB C:GLU133 4.7 13.3 1.0
O C:VAL66 4.7 11.8 1.0
CG2 C:ILE135 4.7 17.9 1.0
CA C:ASP134 4.7 9.5 1.0
CAO C:WPG301 4.7 25.2 1.0
O C:HOH504 4.8 25.1 1.0
CA C:GLU133 4.9 8.4 1.0
CAL C:WPG301 4.9 20.6 1.0
N C:GLY70 5.0 12.1 1.0
CB C:VAL66 5.0 16.0 1.0
C C:GLU133 5.0 11.1 1.0

Magnesium binding site 6 out of 8 in 6bnj

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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-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:27.4
occ:1.00
 OD1 C:ASP193 2.0 15.1 1.0
OAB C:WPG301 2.1 23.3 1.0
OAD C:WPG301 2.1 24.6 1.0
O C:HOH425 2.1 22.2 1.0
O C:HOH495 2.2 22.4 1.0
O C:HOH437 2.3 23.9 1.0
CG C:ASP193 3.0 16.6 1.0
CAU C:WPG301 3.1 25.0 1.0
PBE C:WPG301 3.3 28.3 1.0
OD2 C:ASP193 3.4 15.2 1.0
O C:HOH430 3.5 30.9 1.0
CAM C:WPG301 3.8 20.4 1.0
NH2 C:ARG199 3.9 17.7 1.0
NBC C:WPG301 4.0 25.8 1.0
CAL C:WPG301 4.0 20.6 1.0
CAP C:WPG301 4.1 23.7 1.0
OAH C:WPG301 4.3 25.0 1.0
O C:ASP193 4.3 18.4 1.0
NH1 C:ARG199 4.3 15.3 1.0
CB C:ASP193 4.4 13.4 1.0
OAG C:WPG301 4.4 23.9 1.0
CZ C:ARG199 4.5 16.4 1.0
O C:HOH429 4.5 42.7 1.0
N C:ASP193 4.5 11.9 1.0
O C:HOH498 4.6 24.3 1.0
O C:HOH545 4.7 32.5 1.0
N3 C:WPG301 4.7 16.5 1.0
C C:ASP193 4.8 17.5 1.0
CA C:ASP193 4.8 12.8 1.0
O C:HOH407 4.9 16.6 1.0
N2 C:WPG301 4.9 18.2 1.0

Magnesium binding site 7 out of 8 in 6bnj

Go back to Magnesium Binding Sites List in 6bnj
Magnesium binding site 7 out of 8 in the Human Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:31.3
occ:1.00
 OD1 D:ASP134 2.0 21.0 1.0
O D:HOH442 2.1 29.6 1.0
O D:HOH423 2.1 26.2 1.0
OE1 D:GLU133 2.2 21.9 1.0
O D:HOH468 2.2 26.5 1.0
O D:HOH443 2.4 22.1 1.0
CD D:GLU133 2.8 24.5 1.0
CG D:ASP134 2.9 21.0 1.0
OE2 D:GLU133 3.3 28.6 1.0
OD2 D:ASP134 3.3 22.5 1.0
CG D:GLU133 3.8 25.9 1.0
OAG D:WPG301 4.0 29.1 1.0
N D:ASP134 4.0 18.1 1.0
O D:HOH485 4.0 34.3 1.0
N D:ILE135 4.2 17.8 1.0
CB D:ASP134 4.3 19.2 1.0
O D:ILE135 4.3 21.6 1.0
O D:HOH444 4.6 30.1 1.0
CA D:ASP134 4.6 17.6 1.0
CG2 D:ILE135 4.6 20.4 1.0
OAT D:WPG301 4.6 37.7 1.0
O D:HOH488 4.7 32.0 1.0
CG1 D:VAL66 4.8 15.9 1.0
CAO D:WPG301 4.9 32.7 1.0
CB D:GLU133 4.9 19.2 1.0
O D:VAL66 4.9 14.1 1.0
C D:ASP134 4.9 16.9 1.0

Magnesium binding site 8 out of 8 in 6bnj

Go back to Magnesium Binding Sites List in 6bnj
Magnesium binding site 8 out of 8 in the Human Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3R,4R]-4-Guanin-9-Yl-3-((R)-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-((R)-2-Hydroxy-2-Phosphonoethyl)Oxy-1-N- (Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:29.7
occ:1.00
 OAB D:WPG301 2.0 32.3 1.0
OD1 D:ASP193 2.0 15.8 1.0
OAH D:WPG301 2.1 28.1 1.0
O D:HOH483 2.1 23.8 1.0
O D:HOH475 2.2 28.0 1.0
O D:HOH416 2.2 25.9 1.0
CG D:ASP193 3.0 20.6 1.0
CAU D:WPG301 3.0 31.3 1.0
PBE D:WPG301 3.3 31.8 1.0
OD2 D:ASP193 3.3 19.9 1.0
O D:HOH408 3.6 26.2 1.0
CAM D:WPG301 3.7 28.6 1.0
NBC D:WPG301 3.9 31.5 1.0
CAL D:WPG301 3.9 30.4 1.0
NH2 D:ARG199 4.0 16.3 1.0
CAP D:WPG301 4.0 30.8 1.0
O D:ASP193 4.0 16.1 1.0
OAD D:WPG301 4.2 32.2 1.0
CB D:ASP193 4.3 17.9 1.0
OAG D:WPG301 4.4 29.1 1.0
N D:ASP193 4.4 13.8 1.0
NH1 D:ARG199 4.5 14.3 1.0
C D:ASP193 4.6 15.5 1.0
CZ D:ARG199 4.6 15.1 1.0
O D:HOH501 4.6 42.7 1.0
O D:HOH418 4.6 34.8 1.0
N3 D:WPG301 4.6 22.4 1.0
O D:HOH519 4.7 50.5 1.0
CA D:ASP193 4.7 14.5 1.0
N2 D:WPG301 4.8 18.3 1.0
O D:HOH515 4.8 48.1 1.0
O D:HOH423 4.8 26.2 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 19:50:34 2024

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