Atomistry » Magnesium » PDB 6alf-6asx » 6apu
Atomistry »
  Magnesium »
    PDB 6alf-6asx »
      6apu »

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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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

Go back to Magnesium Binding Sites List in 6apu
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: Wed Aug 13 02:17:08 2025

Last articles

Mg in 6LY6
Mg in 6LY3
Mg in 6LX1
Mg in 6LTW
Mg in 6LVW
Mg in 6LUH
Mg in 6LTS
Mg in 6LTU
Mg in 6LTV
Mg in 6LTR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy