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Magnesium in PDB 6apu: Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid, PDB code: 6apu was solved by D.Teran, L.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.49 / 1.84
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.883, 108.890, 44.970, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 19.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid (pdb code 6apu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid, PDB code: 6apu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6apu

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Magnesium binding site 1 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.4
occ:1.00
 O A:HOH509 2.3 27.8 0.5
CAI A:3L6307 2.4 25.6 0.5
OD1 A:ASP114 2.9 41.2 1.0
O A:HOH509 3.0 17.8 0.5
CAJ A:3L6307 3.1 21.8 0.5
O A:HOH510 3.2 56.0 1.0
CG A:GLU113 3.6 29.8 1.0
CD A:GLU113 3.7 44.1 1.0
CG A:ASP114 3.9 33.0 1.0
OE2 A:GLU113 4.0 32.4 1.0
CG1 A:VAL52 4.2 26.3 1.0
CB A:ALA81 4.2 43.5 1.0
OE1 A:GLU113 4.2 41.9 1.0
OD2 A:ASP114 4.2 50.8 1.0
O4 A:SO4301 4.3 79.2 1.0
NAV A:3L6307 4.4 20.8 0.5
O1 A:SO4301 4.4 89.2 1.0
CAJ A:3L6307 4.5 27.5 0.5
NAV A:3L6307 4.5 18.7 0.5
O A:ILE115 4.6 20.2 1.0
CB A:VAL52 4.7 22.2 1.0
O A:VAL52 4.8 21.9 1.0
N A:ASP114 4.9 16.9 1.0
CAN A:3L6307 4.9 13.8 0.5
OG A:SER56 4.9 15.8 0.4
CG2 A:THR121 5.0 27.8 1.0
N A:ILE115 5.0 13.7 1.0
CB A:GLU113 5.0 19.7 1.0

Magnesium binding site 2 out of 7 in 6apu

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Magnesium binding site 2 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:33.9
occ:0.39
 MG A:MG303 0.0 33.9 0.4
O3 A:SO4301 2.3 78.4 1.0
MG A:MG303 2.4 45.3 0.6
O A:HOH513 2.4 51.1 1.0
OD1 A:ASP173 2.6 23.7 1.0
O A:HOH481 2.9 46.1 1.0
O A:HOH405 2.9 49.2 1.0
O1 A:SO4301 3.4 89.2 1.0
S A:SO4301 3.4 83.7 1.0
CG A:ASP173 3.5 29.6 1.0
OD2 A:ASP173 3.6 26.0 1.0
O A:HOH466 3.8 43.3 1.0
O A:HOH510 4.2 56.0 1.0
O4 A:SO4301 4.4 79.2 1.0
O2 A:SO4301 4.4 80.4 1.0
NH1 A:ARG179 4.4 15.6 1.0
CAJ A:3L6307 4.5 27.5 0.5
O A:HOH403 4.6 34.9 1.0
O A:HOH490 4.7 34.0 1.0
CAI A:3L6307 4.7 20.4 0.5
NH2 A:ARG179 4.9 14.8 1.0
O A:ASP173 4.9 19.2 1.0
N2 A:3L6307 5.0 9.9 0.5
CB A:ASP173 5.0 15.5 1.0

Magnesium binding site 3 out of 7 in 6apu

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Magnesium binding site 3 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:45.3
occ:0.61
 MG A:MG303 0.0 45.3 0.6
O1 A:SO4301 2.3 89.2 1.0
MG A:MG303 2.4 33.9 0.4
CAJ A:3L6307 2.5 27.5 0.5
O A:HOH513 2.6 51.1 1.0
CAI A:3L6307 2.8 20.4 0.5
O3 A:SO4301 3.2 78.4 1.0
S A:SO4301 3.3 83.7 1.0
O A:HOH510 3.5 56.0 1.0
CAJ A:3L6307 3.8 21.8 0.5
NAV A:3L6307 3.8 20.8 0.5
O4 A:SO4301 4.2 79.2 1.0
O A:HOH405 4.3 49.2 1.0
NAV A:3L6307 4.3 18.7 0.5
O2 A:SO4301 4.3 80.4 1.0
CAK A:3L6307 4.3 21.5 0.5
CAM A:3L6307 4.5 19.4 0.5
O A:HOH481 4.6 46.1 1.0
O A:HOH466 4.7 43.3 1.0
CAK A:3L6307 4.8 21.6 0.5
OD1 A:ASP173 4.9 23.7 1.0
CAL A:3L6307 4.9 17.8 0.5

Magnesium binding site 4 out of 7 in 6apu

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Magnesium binding site 4 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:45.5
occ:1.00
 NH2 A:ARG30 1.9 29.1 1.0
O A:HOH570 2.0 31.1 1.0
CD A:ARG30 2.7 22.8 1.0
O A:HOH472 2.8 33.3 1.0
CZ A:ARG30 2.9 33.3 1.0
NE A:ARG30 3.2 29.2 1.0
O A:HOH574 3.9 38.5 1.0
CG2 A:VAL27 3.9 14.0 1.0
O A:HOH468 4.0 23.4 1.0
NH1 A:ARG30 4.1 31.5 1.0
O A:HOH464 4.2 18.2 1.0
CG A:ARG30 4.3 23.1 1.0
CA A:VAL27 4.5 12.7 1.0
O A:HOH477 4.7 19.3 1.0
N A:VAL27 4.7 11.2 1.0
CB A:VAL27 4.8 17.2 1.0
O A:GLY26 4.8 14.8 1.0
C A:GLY26 4.9 15.6 1.0
O A:VAL158 4.9 14.6 1.0
CB A:ARG30 5.0 19.6 1.0

Magnesium binding site 5 out of 7 in 6apu

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Magnesium binding site 5 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:49.0
occ:1.00
 NH2 A:ARG25 1.9 31.6 1.0
O A:HOH504 2.1 43.0 1.0
NE A:ARG25 2.4 21.1 1.0
CZ A:ARG25 2.4 24.8 1.0
OG1 A:THR22 3.2 22.4 1.0
CA A:THR22 3.5 12.9 1.0
CB A:THR22 3.7 14.9 1.0
NH1 A:ARG25 3.7 23.3 1.0
CG2 A:THR22 3.8 13.7 1.0
CD A:ARG25 3.8 19.3 1.0
O A:HOH450 4.2 26.4 1.0
O A:HOH463 4.2 21.2 1.0
N A:THR22 4.3 11.3 1.0
O A:HOH586 4.6 47.8 1.0
C A:THR22 4.6 15.8 1.0
O A:THR22 4.6 12.8 1.0
CG A:ARG25 4.6 14.1 1.0
CB A:ARG25 4.7 11.9 1.0
O A:HIS21 4.8 12.2 1.0
C A:HIS21 4.9 11.7 1.0

Magnesium binding site 6 out of 7 in 6apu

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Magnesium binding site 6 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:77.3
occ:1.00
 OD2 B:ASP114 2.4 30.2 1.0
OG B:SER56 2.8 27.1 1.0
O B:VAL52 3.0 21.2 1.0
CG B:ASP114 3.3 31.2 1.0
CG B:GLU113 3.3 31.2 1.0
N B:ASP114 3.7 13.3 1.0
OD1 B:ASP114 3.8 46.5 1.0
O3 B:SO4301 3.9 21.9 0.7
N B:SER56 4.0 15.6 1.0
CG1 B:VAL52 4.0 26.6 1.0
C B:VAL52 4.0 25.3 1.0
CB B:VAL52 4.0 23.9 1.0
CB B:SER56 4.2 20.3 1.0
CA B:GLU113 4.3 17.9 1.0
CD B:GLU113 4.3 40.5 1.0
N B:GLY55 4.3 18.8 1.0
CB B:ASP114 4.4 15.5 1.0
CB B:GLU113 4.4 20.1 1.0
CA B:GLY55 4.4 21.7 1.0
C B:GLY55 4.5 23.9 1.0
C B:GLU113 4.5 21.4 1.0
O B:LEU53 4.6 21.5 1.0
CA B:SER56 4.6 13.9 1.0
CA B:VAL52 4.6 18.4 1.0
CA B:ASP114 4.6 14.9 1.0
C B:LEU53 4.7 24.2 1.0
OE1 B:GLU113 4.8 40.2 1.0
N B:ILE115 4.8 13.2 1.0
N B:LEU53 4.9 22.4 1.0

Magnesium binding site 7 out of 7 in 6apu

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Magnesium binding site 7 out of 7 in the Crystal Structure of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid


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 Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with (2-{[2-(2-Amino-6-Oxo-1,6- Dihydro-9H-Purin-9-Yl)Ethyl](3-Aminopropyl)Amino}Ethyl)Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:34.4
occ:1.00
 OD1 B:ASP173 2.1 24.3 1.0
O B:HOH446 2.1 32.8 1.0
O B:HOH497 2.1 16.7 0.6
O4 B:SO4301 2.1 21.0 0.7
NAA B:3L6305 2.2 33.5 1.0
O B:HOH514 2.4 29.7 1.0
CAG B:3L6305 3.0 29.2 1.0
CG B:ASP173 3.1 17.4 1.0
S B:SO4301 3.4 27.1 0.7
OD2 B:ASP173 3.5 20.1 1.0
O B:HOH497 3.5 20.1 0.4
O2 B:SO4301 3.7 33.5 0.7
O B:HOH566 4.1 36.1 1.0
NH2 B:ARG179 4.2 14.5 1.0
CAI B:3L6305 4.3 36.6 1.0
O3 B:SO4301 4.4 21.9 0.7
NH1 B:ARG179 4.4 12.8 1.0
O B:ASP173 4.4 13.8 1.0
O1 B:SO4301 4.4 19.6 0.7
CB B:ASP173 4.5 10.9 1.0
N B:ASP173 4.6 9.6 1.0
N2 B:3L6305 4.6 15.8 1.0
N3 B:3L6305 4.6 14.3 1.0
CZ B:ARG179 4.7 13.9 1.0
O B:HOH413 4.7 36.4 1.0
O B:HOH472 4.8 31.5 1.0
CA B:ASP173 4.9 10.3 1.0
C B:ASP173 5.0 18.2 1.0

Reference:

E.Dolezelova, D.Teran, O.Gahura, Z.Kotrbova, M.Prochazkova, D.Keough, P.Spacek, D.Hockova, L.Guddat, A.Zikova. Evaluation of the Trypanosoma Brucei 6-Oxopurine Salvage Pathway As A Potential Target For Drug Discovery. Plos Negl Trop Dis V. 12 06301 2018.
ISSN: ESSN 1935-2735
PubMed: 29481567
DOI: 10.1371/JOURNAL.PNTD.0006301
Page generated: Mon Sep 30 19:16:17 2024

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