Magnesium in PDB 8tpv: Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine

Enzymatic activity of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine

All present enzymatic activity of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine:
2.4.2.8;

Protein crystallography data

The structure of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine, PDB code: 8tpv was solved by L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.98 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.636, 129.595, 64.325, 90, 103.8, 90
R / Rfree (%) 17.2 / 23.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 8tpv

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Magnesium binding site 1 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

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

b:44.6
occ:1.00
 O A:HOH417 1.9 33.9 1.0
OE1 A:GLU133 2.0 44.8 1.0
OD1 A:ASP134 2.3 49.9 1.0
O A:HOH407 2.4 42.8 1.0
O A:HOH406 2.4 37.8 1.0
CD A:GLU133 2.8 46.2 1.0
CG A:ASP134 3.3 44.8 1.0
OE2 A:GLU133 3.4 50.2 1.0
H231 A:JEI301 3.6 49.3 1.0
H061 A:JEI301 3.6 42.4 1.0
OD2 A:ASP134 3.6 39.2 1.0
H241 A:JEI301 3.7 46.9 1.0
CG A:GLU133 3.8 52.8 1.0
O01 A:JEI301 4.1 40.2 1.0
N A:ASP134 4.2 33.7 1.0
CG1 A:VAL66 4.3 42.0 1.0
O A:ILE135 4.4 42.9 1.0
H262 A:JEI301 4.4 52.5 1.0
O A:VAL66 4.5 38.4 1.0
N A:ILE135 4.5 34.9 1.0
C23 A:JEI301 4.5 41.1 1.0
O A:HOH420 4.6 39.9 1.0
C24 A:JEI301 4.6 39.1 1.0
CB A:ASP134 4.6 35.2 1.0
C06 A:JEI301 4.7 35.3 1.0
CB A:VAL66 4.8 41.5 1.0
CG2 A:ILE135 4.8 35.2 1.0
CA A:ASP134 4.9 34.1 1.0
CB A:GLU133 5.0 43.4 1.0

Magnesium binding site 2 out of 8 in 8tpv

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Magnesium binding site 2 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:41.5
occ:1.00
 O A:HOH423 2.0 40.6 1.0
O A:HOH419 2.0 40.7 1.0
O32 A:JEI301 2.1 43.0 1.0
O A:HOH434 2.3 35.6 1.0
OD1 A:ASP193 2.3 35.5 1.0
O03 A:JEI301 2.4 40.6 1.0
C07 A:JEI301 2.8 41.8 1.0
H092 A:JEI301 3.1 46.7 1.0
CG A:ASP193 3.3 42.4 1.0
H052 A:JEI301 3.3 38.7 1.0
N08 A:JEI301 3.5 41.8 1.0
C09 A:JEI301 3.5 38.9 1.0
P02 A:JEI301 3.6 45.1 1.0
H091 A:JEI301 3.6 46.7 1.0
OD2 A:ASP193 3.6 41.9 1.0
H191 A:JEI301 3.7 46.6 1.0
C05 A:JEI301 3.7 32.2 1.0
C06 A:JEI301 3.9 35.3 1.0
O A:ASP193 4.2 34.6 1.0
H061 A:JEI301 4.3 42.4 1.0
NH2 A:ARG199 4.3 32.0 1.0
N20 A:JEI301 4.5 37.0 1.0
O01 A:JEI301 4.5 40.2 1.0
O04 A:JEI301 4.6 55.5 1.0
N19 A:JEI301 4.6 38.8 1.0
H231 A:JEI301 4.6 49.3 1.0
C23 A:JEI301 4.6 41.1 1.0
CB A:ASP193 4.6 32.9 1.0
NH1 A:ARG199 4.7 32.8 1.0
H062 A:JEI301 4.8 42.4 1.0
H051 A:JEI301 4.8 38.7 1.0
N A:ASP193 4.8 30.1 1.0
C A:ASP193 4.8 34.2 1.0
O A:HOH421 5.0 50.4 1.0
CZ A:ARG199 5.0 32.6 1.0

Magnesium binding site 3 out of 8 in 8tpv

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Magnesium binding site 3 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

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

b:48.5
occ:1.00
 OE2 B:GLU133 2.2 47.3 1.0
O B:HOH412 2.2 37.5 1.0
O B:HOH402 2.3 34.9 1.0
O B:HOH425 2.4 37.7 1.0
OD1 B:ASP134 2.8 47.5 1.0
CD B:GLU133 3.0 51.5 1.0
H061 B:JEI301 3.2 43.5 1.0
H231 B:JEI301 3.3 53.2 1.0
OE1 B:GLU133 3.4 60.4 1.0
CG B:ASP134 3.8 47.3 1.0
O03 B:JEI301 3.9 40.8 1.0
H241 B:JEI301 3.9 57.5 1.0
OD2 B:ASP134 4.0 43.7 1.0
O25 B:JEI301 4.2 57.6 1.0
CG B:GLU133 4.2 49.0 1.0
C06 B:JEI301 4.2 36.3 1.0
C23 B:JEI301 4.2 44.3 1.0
C24 B:JEI301 4.3 47.9 1.0
H062 B:JEI301 4.4 43.5 1.0
CG1 B:VAL66 4.5 33.3 1.0
O B:ILE135 4.6 35.4 1.0
O B:HOH440 4.7 36.6 1.0
CG2 B:ILE135 4.9 35.2 1.0
O B:VAL66 4.9 34.5 1.0
N B:ASP134 5.0 30.0 1.0

Magnesium binding site 4 out of 8 in 8tpv

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Magnesium binding site 4 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:46.5
occ:1.00
 OD1 B:ASP193 2.4 40.3 1.0
O32 B:JEI301 2.5 42.3 1.0
O04 B:JEI301 2.5 38.0 1.0
O B:HOH404 2.6 45.2 1.0
OD2 B:ASP193 2.9 41.2 1.0
CG B:ASP193 2.9 43.5 1.0
H052 B:JEI301 3.3 41.0 1.0
C07 B:JEI301 3.5 36.6 1.0
P02 B:JEI301 3.7 49.6 1.0
C05 B:JEI301 3.9 34.1 1.0
NH2 B:ARG199 3.9 40.0 1.0
O B:HOH429 3.9 43.1 1.0
H092 B:JEI301 4.2 45.2 1.0
C06 B:JEI301 4.3 36.3 1.0
N08 B:JEI301 4.3 32.2 1.0
H091 B:JEI301 4.4 45.2 1.0
CB B:ASP193 4.4 32.3 1.0
C09 B:JEI301 4.5 37.7 1.0
O01 B:JEI301 4.6 41.6 1.0
H191 B:JEI301 4.6 43.3 1.0
CZ B:ARG199 4.7 33.3 1.0
NH1 B:ARG199 4.7 32.9 1.0
O B:ASP193 4.7 41.4 1.0
O B:HOH432 4.8 40.0 1.0
O03 B:JEI301 4.8 40.8 1.0
H061 B:JEI301 4.8 43.5 1.0
H051 B:JEI301 4.9 41.0 1.0
OE2 B:GLU196 4.9 59.6 1.0
C B:ASP193 5.0 37.2 1.0

Magnesium binding site 5 out of 8 in 8tpv

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Magnesium binding site 5 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.0
occ:1.00
 OD1 C:ASP134 1.9 43.9 1.0
O C:HOH426 1.9 41.3 1.0
O C:HOH408 2.0 36.3 1.0
O C:HOH405 2.0 42.3 1.0
OE1 C:GLU133 2.1 43.7 1.0
O C:HOH409 2.3 43.7 1.0
CG C:ASP134 2.9 47.5 1.0
CD C:GLU133 3.1 44.0 1.0
OD2 C:ASP134 3.3 49.3 1.0
OE2 C:GLU133 3.5 49.9 1.0
H231 C:JEI301 3.5 46.5 1.0
H061 C:JEI301 3.7 44.6 1.0
N C:ASP134 4.1 40.9 1.0
O C:ILE135 4.2 44.7 1.0
O01 C:JEI301 4.2 44.2 1.0
N C:ILE135 4.3 30.8 1.0
CB C:ASP134 4.3 39.8 1.0
CG1 C:VAL66 4.4 33.4 1.0
C23 C:JEI301 4.5 38.7 1.0
CG C:GLU133 4.5 45.2 1.0
CG2 C:ILE135 4.6 42.5 1.0
O25 C:JEI301 4.6 55.9 1.0
CA C:ASP134 4.7 35.4 1.0
C06 C:JEI301 4.8 37.2 1.0
O C:VAL66 4.8 36.9 1.0
H221 C:JEI301 4.8 51.7 1.0
CB C:GLU133 4.8 38.8 1.0
H241 C:JEI301 4.9 64.0 1.0
C24 C:JEI301 5.0 53.3 1.0
CA C:GLU133 5.0 36.0 1.0

Magnesium binding site 6 out of 8 in 8tpv

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Magnesium binding site 6 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:57.4
occ:1.00
 OD1 C:ASP193 2.2 40.0 1.0
O32 C:JEI301 2.3 59.3 1.0
O03 C:JEI301 2.4 37.6 1.0
O C:HOH432 2.5 51.8 1.0
O C:HOH420 2.6 47.2 1.0
C07 C:JEI301 2.9 41.6 1.0
H092 C:JEI301 3.0 50.7 1.0
H191 C:JEI301 3.2 47.9 1.0
CG C:ASP193 3.3 49.2 1.0
N08 C:JEI301 3.5 41.5 1.0
C09 C:JEI301 3.6 42.2 1.0
P02 C:JEI301 3.7 58.8 1.0
OD2 C:ASP193 3.8 37.1 1.0
H052 C:JEI301 3.8 37.6 1.0
O C:ASP193 3.9 36.1 1.0
C06 C:JEI301 3.9 37.2 1.0
C05 C:JEI301 4.0 31.3 1.0
H091 C:JEI301 4.0 50.7 1.0
N20 C:JEI301 4.1 33.5 1.0
H061 C:JEI301 4.1 44.6 1.0
N19 C:JEI301 4.2 39.9 1.0
N C:ASP193 4.3 35.9 1.0
H231 C:JEI301 4.4 46.5 1.0
O01 C:JEI301 4.4 44.2 1.0
CB C:ASP193 4.5 34.2 1.0
C23 C:JEI301 4.5 38.7 1.0
C C:ASP193 4.5 43.1 1.0
NH2 C:ARG199 4.6 32.1 1.0
C18 C:JEI301 4.7 37.4 1.0
CA C:ASP193 4.7 46.1 1.0
NH1 C:ARG199 4.7 29.6 1.0
O04 C:JEI301 4.8 54.7 1.0
O C:HOH405 4.8 42.3 1.0
H062 C:JEI301 4.9 44.6 1.0
H192 C:JEI301 4.9 47.9 1.0

Magnesium binding site 7 out of 8 in 8tpv

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Magnesium binding site 7 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:42.4
occ:1.00
 OE1 D:GLU133 2.1 47.4 1.0
O D:HOH436 2.1 44.2 1.0
O D:HOH408 2.1 45.7 1.0
O D:HOH405 2.1 41.6 1.0
O D:HOH429 2.2 44.9 1.0
OD1 D:ASP134 2.4 50.8 1.0
CD D:GLU133 2.8 47.4 1.0
OE2 D:GLU133 3.1 50.3 1.0
CG D:ASP134 3.3 48.9 1.0
H061 D:JEI301 3.5 54.4 1.0
H231 D:JEI301 3.6 64.0 1.0
OD2 D:ASP134 3.7 46.3 1.0
CG D:GLU133 3.9 54.3 1.0
H241 D:JEI301 3.9 60.2 1.0
O01 D:JEI301 4.2 45.6 1.0
O25 D:JEI301 4.2 56.9 1.0
N D:ASP134 4.3 38.4 1.0
CG1 D:VAL66 4.3 38.4 1.0
O D:HOH402 4.4 40.0 1.0
C24 D:JEI301 4.4 50.1 1.0
C23 D:JEI301 4.5 53.4 1.0
O D:ILE135 4.5 40.3 1.0
C06 D:JEI301 4.5 45.3 1.0
CB D:ASP134 4.6 45.7 1.0
N D:ILE135 4.6 33.4 1.0
O D:VAL66 4.7 38.2 1.0
H062 D:JEI301 4.7 54.4 1.0
CG2 D:ILE135 4.8 42.9 1.0
CA D:ASP134 5.0 37.8 1.0
CB D:VAL66 5.0 38.6 1.0

Magnesium binding site 8 out of 8 in 8tpv

Go back to Magnesium Binding Sites List in 8tpv
Magnesium binding site 8 out of 8 in the Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Human Hypoxanthine Guanine Phosphoribzosyltransferase in Complex with [2S,4R]-4-Guanin-9-Yl-2-(2-Phosphonoethoxymethyl)-1-N- (3-Phosphonopropionyl)Pyrrolidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:45.4
occ:1.00
 O32 D:JEI301 2.0 51.1 1.0
O03 D:JEI301 2.2 44.0 1.0
OD1 D:ASP193 2.2 38.4 1.0
O D:HOH418 2.4 45.2 1.0
O D:HOH411 2.4 38.6 1.0
O D:HOH417 2.4 43.7 1.0
C07 D:JEI301 2.6 45.1 1.0
H092 D:JEI301 3.1 63.7 1.0
CG D:ASP193 3.2 41.6 1.0
N08 D:JEI301 3.3 47.8 1.0
P02 D:JEI301 3.4 55.2 1.0
H052 D:JEI301 3.4 42.2 1.0
OD2 D:ASP193 3.5 41.6 1.0
C09 D:JEI301 3.6 53.0 1.0
C06 D:JEI301 3.6 45.3 1.0
C05 D:JEI301 3.7 35.2 1.0
H091 D:JEI301 3.7 63.7 1.0
H061 D:JEI301 4.0 54.4 1.0
O D:HOH421 4.0 48.3 1.0
H191 D:JEI301 4.0 44.0 1.0
H231 D:JEI301 4.3 64.0 1.0
O04 D:JEI301 4.3 55.8 1.0
O01 D:JEI301 4.4 45.6 1.0
O D:ASP193 4.4 38.5 1.0
C23 D:JEI301 4.4 53.4 1.0
NH2 D:ARG199 4.5 35.7 1.0
CB D:ASP193 4.5 31.4 1.0
H062 D:JEI301 4.6 54.4 1.0
N20 D:JEI301 4.6 32.2 1.0
NH1 D:ARG199 4.7 29.9 1.0
H051 D:JEI301 4.7 42.2 1.0
N D:ASP193 4.9 29.9 1.0
O D:HOH405 4.9 41.6 1.0
N19 D:JEI301 4.9 36.7 1.0
C D:ASP193 5.0 31.5 1.0

Reference:

D.T.Keough, M.Petrova, G.King, M.Kratochvil, R.Pohl, E.Dolezelova, A.Zikova, L.W.Guddat, D.Rejman. Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38651522
DOI: 10.1021/ACS.JMEDCHEM.4C00021
Page generated: Fri Oct 4 20:53:32 2024

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