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Magnesium in PDB 5kap: Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine

Enzymatic activity of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine

All present enzymatic activity of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine:
2.4.2.8;

Protein crystallography data

The structure of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine, PDB code: 5kap 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) 45.11 / 2.95
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 45.106, 93.893, 109.784, 90.00, 90.00, 90.00
R / Rfree (%) 27.5 / 30.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine (pdb code 5kap). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine, PDB code: 5kap:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5kap

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Magnesium binding site 1 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:73.4
occ:1.00
 OD2 A:ASP114 2.5 67.2 1.0
OE1 A:GLU113 2.9 68.8 1.0
CG A:ASP114 3.4 63.5 1.0
OD1 A:ASP114 3.5 61.5 1.0
CD A:GLU113 3.7 62.6 1.0
OE2 A:GLU113 3.8 56.8 1.0
O2 A:SO4302 3.8 80.6 1.0
CG2 A:ILE115 3.9 53.8 1.0
O A:ILE115 4.2 58.3 1.0
O3 A:SO4303 4.4 56.5 1.0
N A:ILE115 4.5 52.3 1.0
O4 A:SO4302 4.6 80.0 1.0
S A:SO4302 4.8 79.0 1.0
N A:ASP114 4.8 58.9 1.0
CB A:ASP114 4.8 52.4 1.0

Magnesium binding site 2 out of 6 in 5kap

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Magnesium binding site 2 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:69.9
occ:1.00
 O4 A:SO4302 2.5 80.0 1.0
OD1 A:ASP173 2.6 66.9 1.0
CG A:ASP173 3.4 59.4 1.0
OD2 A:ASP173 3.5 54.9 1.0
O3 A:SO4302 3.5 75.6 1.0
S A:SO4302 3.6 79.0 1.0
C12 A:6RH301 3.9 92.0 1.0
N05 A:6RH301 4.0 78.6 1.0
O A:ASP173 4.2 68.5 1.0
C13 A:6RH301 4.2 97.8 1.0
O2 A:SO4302 4.2 80.6 1.0
C11 A:6RH301 4.6 89.4 1.0
O1 A:SO4302 4.8 79.0 1.0
C04 A:6RH301 4.8 80.2 1.0
CB A:ASP173 4.8 56.8 1.0
C A:ASP173 4.8 71.8 1.0

Magnesium binding site 3 out of 6 in 5kap

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Magnesium binding site 3 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:70.2
occ:0.50
 OE1 A:GLU17 3.9 0.6 1.0
OD1 A:ASP62 4.0 65.7 1.0
NH1 A:ARG65 4.1 99.4 1.0
NE2 A:HIS21 4.6 89.6 1.0
CG A:ASP62 4.8 65.4 1.0
CZ A:ARG65 4.9 93.9 1.0

Magnesium binding site 4 out of 6 in 5kap

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Magnesium binding site 4 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:62.0
occ:1.00
 OD1 B:ASP114 2.7 45.6 1.0
OE2 B:GLU113 2.7 64.4 1.0
CG B:GLU113 3.4 48.3 1.0
CD B:GLU113 3.4 62.8 1.0
CG B:ASP114 3.6 41.8 1.0
OD2 B:ASP114 3.7 44.2 1.0
C14 B:6RH301 3.8 39.3 0.6
C12 B:6RH301 3.9 46.3 0.6
O2 B:SO4302 4.0 75.7 1.0
CG2 B:ILE115 4.1 34.8 1.0
O B:ILE115 4.2 51.5 1.0
C13 B:6RH301 4.2 45.2 0.6
N B:ILE115 4.5 41.7 1.0
OE1 B:GLU113 4.6 69.1 1.0
O1 B:SO4302 4.7 76.3 1.0
N B:ASP114 4.7 35.5 1.0
S B:SO4302 4.8 75.9 1.0
CB B:GLU113 4.9 37.6 1.0
O4 B:SO4302 4.9 82.4 1.0
CB B:ASP114 5.0 34.4 1.0

Magnesium binding site 5 out of 6 in 5kap

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Magnesium binding site 5 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:55.9
occ:1.00
 O4 B:SO4302 2.1 82.4 1.0
OD1 B:ASP173 2.3 65.6 1.0
CG B:ASP173 3.1 54.8 1.0
OD2 B:ASP173 3.3 46.0 1.0
S B:SO4302 3.5 75.9 1.0
O3 B:SO4302 3.8 70.2 1.0
N05 B:6RH301 4.2 54.2 0.6
O B:ASP173 4.2 64.5 1.0
O2 B:SO4302 4.2 75.7 1.0
N05 B:6RH301 4.3 54.4 0.4
C11 B:6RH301 4.4 50.5 0.4
O1 B:SO4302 4.4 76.3 1.0
CB B:ASP173 4.6 50.1 1.0
NH1 B:ARG179 4.7 55.6 1.0
C B:ASP173 4.8 56.3 1.0
C11 B:6RH301 4.8 50.4 0.6
C04 B:6RH301 4.9 53.5 0.6
N B:ASP173 5.0 44.6 1.0
C13 B:6RH301 5.0 51.7 0.4

Magnesium binding site 6 out of 6 in 5kap

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Magnesium binding site 6 out of 6 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with A 9-(4-(Phosphonobutil)Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:58.1
occ:1.00
 OG B:SER177 2.3 35.6 1.0
O B:GLN176 2.7 47.5 1.0
O B:ASP175 3.2 62.9 1.0
C B:GLN176 3.3 38.9 1.0
CB B:SER177 3.6 47.7 1.0
N B:SER177 3.9 39.8 1.0
CA B:SER177 4.0 45.7 1.0
CB B:GLN176 4.0 34.4 1.0
CA B:GLN176 4.2 39.6 1.0
C B:ASP175 4.3 57.1 1.0
N B:GLN176 4.7 53.2 1.0

Reference:

D.Teran, D.Hockova, M.Cesnek, A.Zikova, L.Naesens, D.T.Keough, L.W.Guddat. Crystal Structures and Inhibition of Trypanosoma Brucei Hypoxanthine-Guanine Phosphoribosyltransferase. Sci Rep V. 6 35894 2016.
ISSN: ESSN 2045-2322
PubMed: 27786284
DOI: 10.1038/SREP35894
Page generated: Sun Sep 29 18:55:16 2024

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