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Magnesium in PDB 5kam: Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate

Enzymatic activity of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate

All present enzymatic activity of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate:
2.4.2.8;

Protein crystallography data

The structure of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate, PDB code: 5kam 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) 43.23 / 2.48
Space group P 2 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.054, 109.819, 45.292, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 28.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 5kam

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Magnesium binding site 1 out of 5 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate


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 Inosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3304

b:80.8
occ:1.00
 OE2 A:GLU113 2.6 64.2 1.0
OD1 A:ASP114 2.7 39.0 1.0
CG A:GLU113 3.1 50.8 1.0
CD A:GLU113 3.2 63.4 1.0
O2' A:IMP3301 3.7 73.2 1.0
CG A:ASP114 3.7 40.9 1.0
O A:ILE115 3.8 55.6 1.0
OD2 A:ASP114 4.1 42.3 1.0
O3 A:SO43303 4.1 75.0 1.0
CG2 A:ILE115 4.2 46.3 1.0
N A:ILE115 4.4 47.2 1.0
O4 A:SO43302 4.4 86.5 1.0
OE1 A:GLU113 4.4 71.9 1.0
N A:ASP114 4.6 41.2 1.0
CB A:GLU113 4.6 45.4 1.0
O3' A:IMP3301 4.6 77.8 1.0
O1 A:SO43302 4.7 89.2 1.0
C A:ILE115 4.8 49.9 1.0
CG1 A:VAL52 4.9 37.6 1.0
C2' A:IMP3301 5.0 73.1 1.0

Magnesium binding site 2 out of 5 in 5kam

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Magnesium binding site 2 out of 5 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate


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 Inosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3305

b:80.2
occ:1.00
 OD1 A:ASP173 2.5 54.6 1.0
O A:HOH3402 2.7 79.4 1.0
O3 A:SO43302 2.7 85.4 1.0
OD2 A:ASP173 3.0 60.0 1.0
CG A:ASP173 3.1 57.6 1.0
O1 A:SO43302 3.5 89.2 1.0
S A:SO43302 3.7 85.3 1.0
NH1 A:ARG179 4.3 52.8 1.0
O2 A:SO43302 4.4 83.5 1.0
O A:ASP173 4.5 66.5 1.0
CB A:ASP173 4.6 58.7 1.0
O4' A:IMP3301 4.6 73.4 1.0
O3' A:IMP3301 4.7 77.8 1.0
O4 A:SO43302 4.9 86.5 1.0
C1' A:IMP3301 4.9 69.8 1.0
C4' A:IMP3301 4.9 78.2 1.0
NE2 A:GLN176 4.9 63.4 1.0
C A:ASP173 4.9 66.5 1.0
NH2 A:ARG179 4.9 55.9 1.0
N3 A:IMP3301 5.0 59.1 1.0

Magnesium binding site 3 out of 5 in 5kam

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Magnesium binding site 3 out of 5 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate


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 Inosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:76.0
occ:1.00
 O1 C:SO4303 2.0 72.8 1.0
O3' C:IMP301 2.3 69.2 1.0
MG C:MG306 3.1 72.8 1.0
S C:SO4303 3.3 66.8 1.0
C3' C:IMP301 3.4 68.9 1.0
C4' C:IMP301 3.5 72.1 1.0
O3 C:SO4303 3.6 62.5 1.0
O2 C:SO4303 3.9 68.8 1.0
O4' C:IMP301 4.0 67.3 1.0
C1' C:IMP301 4.2 64.5 1.0
C2' C:IMP301 4.4 67.3 1.0
O4 C:SO4303 4.4 67.5 1.0
O2' C:IMP301 4.7 68.4 1.0
C5' C:IMP301 4.8 81.3 1.0

Magnesium binding site 4 out of 5 in 5kam

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Magnesium binding site 4 out of 5 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate


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 Inosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:63.2
occ:1.00
 OD1 C:ASP114 2.6 43.2 1.0
OE2 C:GLU113 2.9 63.2 1.0
O2' C:IMP301 3.3 68.4 1.0
CG C:GLU113 3.3 46.6 1.0
CD C:GLU113 3.5 60.1 1.0
CG C:ASP114 3.6 43.1 1.0
O C:ILE115 3.7 51.0 1.0
OD2 C:ASP114 3.8 47.2 1.0
CG2 C:ILE115 3.8 30.0 1.0
O3 C:SO4302 4.1 68.6 1.0
O4 C:SO4303 4.1 67.5 1.0
N C:ILE115 4.2 27.5 1.0
O3' C:IMP301 4.5 69.2 1.0
O1 C:SO4303 4.6 72.8 1.0
N C:ASP114 4.6 32.1 1.0
C C:ILE115 4.6 43.0 1.0
C2' C:IMP301 4.7 67.3 1.0
OE1 C:GLU113 4.8 65.9 1.0
CA C:ILE115 4.8 37.4 1.0
CB C:GLU113 4.8 37.1 1.0
CB C:ILE115 4.8 38.3 1.0
CB C:ASP114 4.9 37.8 1.0

Magnesium binding site 5 out of 5 in 5kam

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Magnesium binding site 5 out of 5 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Inosine 5' Monophosphate


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 Inosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg306

b:72.8
occ:1.00
 OD1 C:ASP173 2.1 36.7 1.0
O3 C:SO4303 2.5 62.5 1.0
CG C:ASP173 3.0 35.8 1.0
MG C:MG304 3.1 76.0 1.0
OD2 C:ASP173 3.1 35.4 1.0
O1 C:SO4303 3.3 72.8 1.0
S C:SO4303 3.5 66.8 1.0
NH1 C:ARG179 4.1 31.8 1.0
CB C:ASP173 4.4 32.7 1.0
O2 C:SO4303 4.5 68.8 1.0
O4 C:SO4303 4.5 67.5 1.0
O C:ASP173 4.6 45.1 1.0
NH2 C:ARG179 4.6 38.3 1.0
N3 C:IMP301 4.6 55.5 1.0
O3' C:IMP301 4.7 69.2 1.0
CZ C:ARG179 4.8 44.3 1.0
O4' C:IMP301 4.8 67.3 1.0
C1' C:IMP301 4.8 64.5 1.0
N C:ASP173 4.9 32.5 1.0
C C:ASP173 4.9 42.8 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 18:55:02 2024

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