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Magnesium in PDB 5jv5: Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 5' Monophosphate

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

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

Protein crystallography data

The structure of Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 5' Monophosphate, PDB code: 5jv5 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) 48.01 / 2.73
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.944, 111.711, 45.226, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 5' Monophosphate (pdb code 5jv5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 5' Monophosphate, PDB code: 5jv5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5jv5

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Magnesium binding site 1 out of 4 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 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 Guanosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:64.2
occ:1.00
 O1 A:SO4303 2.0 58.2 1.0
O3' A:5GP301 2.5 55.1 1.0
MG A:MG305 3.1 34.1 1.0
S A:SO4303 3.4 53.7 1.0
C3' A:5GP301 3.6 55.4 1.0
C4' A:5GP301 3.6 58.1 1.0
O3 A:SO4303 3.8 53.8 1.0
O A:HOH420 4.0 35.0 1.0
O4' A:5GP301 4.0 55.6 1.0
O2 A:SO4303 4.1 52.6 1.0
C1' A:5GP301 4.3 52.2 1.0
O4 A:SO4303 4.3 52.5 1.0
C2' A:5GP301 4.5 52.5 1.0
O2' A:5GP301 4.9 49.5 1.0
C5' A:5GP301 4.9 63.7 1.0
O A:HOH406 5.0 20.7 1.0

Magnesium binding site 2 out of 4 in 5jv5

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Magnesium binding site 2 out of 4 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 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 Guanosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:34.1
occ:1.00
 O A:HOH420 2.2 35.0 1.0
OD1 A:ASP173 2.2 31.6 1.0
O3 A:SO4303 2.7 53.8 1.0
CG A:ASP173 3.0 30.3 1.0
OD2 A:ASP173 3.1 32.0 1.0
MG A:MG304 3.1 64.2 1.0
O1 A:SO4303 3.3 58.2 1.0
S A:SO4303 3.6 53.7 1.0
NH1 A:ARG179 4.1 20.3 1.0
CB A:ASP173 4.4 26.6 1.0
O2 A:SO4303 4.4 52.6 1.0
NH2 A:ARG179 4.5 18.8 1.0
O A:ASP173 4.6 24.1 1.0
O4 A:SO4303 4.7 52.5 1.0
CZ A:ARG179 4.7 19.0 1.0
O A:HOH406 4.8 20.7 1.0
N A:ASP173 4.8 24.3 1.0
NE2 A:GLN176 4.9 28.8 1.0
O4' A:5GP301 4.9 55.6 1.0
C A:ASP173 4.9 25.9 1.0
CA A:ASP173 5.0 24.9 1.0

Magnesium binding site 3 out of 4 in 5jv5

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Magnesium binding site 3 out of 4 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 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 Guanosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:53.4
occ:1.00
 OD1 B:ASP173 2.3 35.7 1.0
CG B:ASP173 3.1 32.7 1.0
O2 B:SO4303 3.2 52.3 1.0
OD2 B:ASP173 3.4 32.5 1.0
MG B:MG305 3.4 53.1 1.0
O B:ASP173 3.5 27.3 1.0
N3 B:5GP301 3.7 45.0 1.0
O B:HOH405 3.9 40.2 1.0
O4' B:5GP301 4.1 53.4 1.0
N2 B:5GP301 4.2 42.7 1.0
O4 B:SO4303 4.2 53.2 1.0
N B:ASP173 4.2 28.8 1.0
S B:SO4303 4.3 52.9 1.0
C1' B:5GP301 4.3 51.2 1.0
C B:ASP173 4.3 28.2 1.0
CB B:ASP173 4.3 29.4 1.0
C2 B:5GP301 4.4 44.1 1.0
CA B:ASP173 4.5 28.0 1.0
C4 B:5GP301 4.7 46.9 1.0
C4' B:5GP301 4.8 55.8 1.0
O3' B:5GP301 4.8 54.2 1.0
NH2 B:ARG179 4.8 16.4 1.0
N9 B:5GP301 4.9 48.9 1.0

Magnesium binding site 4 out of 4 in 5jv5

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Magnesium binding site 4 out of 4 in the Trypanosome Brucei Hypoxanthine-Guanine Phosphoribosyltranferase in Complex with Guanosine 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 Guanosine 5' Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:53.1
occ:1.00
 O2 B:SO4303 1.9 52.3 1.0
O3' B:5GP301 2.3 54.2 1.0
S B:SO4303 3.3 52.9 1.0
C3' B:5GP301 3.4 54.6 1.0
C4' B:5GP301 3.4 55.8 1.0
MG B:MG304 3.4 53.4 1.0
O1 B:SO4303 3.7 53.9 1.0
O4' B:5GP301 3.8 53.4 1.0
O3 B:SO4303 4.0 51.8 1.0
C1' B:5GP301 4.1 51.2 1.0
O4 B:SO4303 4.3 53.2 1.0
C2' B:5GP301 4.3 52.4 1.0
O2' B:5GP301 4.7 51.0 1.0
C5' B:5GP301 4.8 59.6 1.0
OD1 B:ASP173 4.9 35.7 1.0
O B:HOH416 4.9 17.4 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 17:57:23 2024

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