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Magnesium in PDB 5kny: Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid, PDB code: 5kny was solved by W.S.Eng, D.Rejman, D.T.Keough, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.77 / 2.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.523, 86.075, 79.824, 90.00, 105.95, 90.00
R / Rfree (%) 20.1 / 26.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid (pdb code 5kny). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid, PDB code: 5kny:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5kny

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) 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 Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:33.8
occ:1.00
 OAB A:YPG301 2.1 30.7 0.3
OD1 A:ASP182 2.1 35.5 1.0
O A:HOH401 2.1 36.6 1.0
O A:HOH402 2.1 54.9 1.0
O A:HOH404 2.1 40.5 1.0
OAI A:YPG301 2.1 33.7 0.7
OAH A:YPG301 2.7 33.7 0.3
CAN A:YPG301 3.1 36.0 0.7
CAU A:YPG301 3.1 33.7 0.3
CG A:ASP182 3.2 34.9 1.0
PBF A:YPG301 3.3 33.4 0.7
CAZ A:YPG301 3.6 34.5 0.7
OD2 A:ASP182 3.6 26.8 1.0
CAP A:YPG301 3.7 41.9 0.3
NBC A:YPG301 3.8 39.8 0.3
OAF A:YPG301 3.8 34.2 0.7
NH2 A:ARG188 3.9 39.2 1.0
N3 A:YPG301 3.9 36.9 0.7
OAT A:YPG301 3.9 38.9 0.7
PBE A:YPG301 3.9 33.4 0.3
OAE A:YPG301 4.1 33.0 0.7
N3 A:YPG301 4.1 36.9 0.3
N2 A:YPG301 4.1 37.4 0.3
N2 A:YPG301 4.2 38.8 0.7
OAD A:YPG301 4.3 33.4 0.3
CAL A:YPG301 4.3 33.8 0.3
O A:ASP182 4.4 44.4 1.0
CBB A:YPG301 4.4 43.3 0.7
OAJ A:YPG301 4.4 32.8 0.7
CB A:ASP182 4.4 35.1 1.0
N A:ASP182 4.5 23.9 1.0
C2 A:YPG301 4.5 39.6 0.7
C2 A:YPG301 4.6 41.5 0.3
CAM A:YPG301 4.7 34.6 0.3
CBA A:YPG301 4.7 41.6 0.7
CZ A:ARG188 4.8 40.7 1.0
C A:ASP182 4.8 40.7 1.0
CBB A:YPG301 4.8 45.7 0.3
CA A:ASP182 4.8 34.3 1.0
C4 A:YPG301 4.8 44.3 0.7

Magnesium binding site 2 out of 4 in 5kny

Go back to Magnesium Binding Sites List in 5kny
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) 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 Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:63.9
occ:1.00
 O B:HOH404 2.1 35.7 1.0
O B:HOH410 2.1 48.8 1.0
O B:HOH408 2.1 24.7 1.0
OD1 B:ASP182 2.1 35.2 1.0
OAI B:YPG301 2.1 28.8 1.0
CAN B:YPG301 2.7 26.7 1.0
PBF B:YPG301 3.3 34.3 1.0
CG B:ASP182 3.3 33.9 1.0
CAZ B:YPG301 3.4 19.8 1.0
N3 B:YPG301 3.7 34.1 1.0
OAF B:YPG301 3.8 12.8 1.0
OAT B:YPG301 3.8 36.6 1.0
OD2 B:ASP182 3.9 28.7 1.0
O B:ASP182 4.0 37.1 1.0
N2 B:YPG301 4.1 30.2 1.0
O B:HOH406 4.2 13.6 1.0
OAJ B:YPG301 4.2 34.0 1.0
CBB B:YPG301 4.2 40.0 1.0
NH1 B:ARG188 4.2 36.0 1.0
N B:ASP182 4.3 29.3 1.0
OAE B:YPG301 4.3 29.6 1.0
C2 B:YPG301 4.4 32.0 1.0
CB B:ASP182 4.5 32.4 1.0
C B:ASP182 4.6 34.0 1.0
CBA B:YPG301 4.6 43.6 1.0
C4 B:YPG301 4.7 34.9 1.0
CA B:ASP182 4.7 30.6 1.0
N9 B:YPG301 4.9 35.7 1.0

Magnesium binding site 3 out of 4 in 5kny

Go back to Magnesium Binding Sites List in 5kny
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) 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 Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:32.9
occ:1.00
 OD1 C:ASP182 2.0 56.2 1.0
O C:HOH404 2.1 25.3 1.0
OAI C:YPG301 2.4 48.9 1.0
CAN C:YPG301 2.6 53.3 1.0
CG C:ASP182 3.2 44.9 1.0
PBF C:YPG301 3.5 43.5 1.0
CAZ C:YPG301 3.5 48.6 1.0
N3 C:YPG301 3.6 49.0 1.0
OAT C:YPG301 3.7 54.9 1.0
OD2 C:ASP182 3.9 38.1 1.0
N2 C:YPG301 4.0 56.8 1.0
O C:ASP182 4.0 36.9 1.0
N C:ASP182 4.1 31.5 1.0
CBA C:YPG301 4.1 54.0 1.0
OAF C:YPG301 4.1 50.0 1.0
NH2 C:ARG188 4.1 27.9 1.0
CBB C:YPG301 4.2 50.8 1.0
C2 C:YPG301 4.3 51.5 1.0
CB C:ASP182 4.3 44.0 1.0
OAE C:YPG301 4.4 38.2 1.0
CA C:ASP182 4.5 43.6 1.0
OAJ C:YPG301 4.5 46.5 1.0
C C:ASP182 4.5 38.2 1.0
C4 C:YPG301 4.6 47.9 1.0
CZ C:ARG188 4.9 40.2 1.0
N9 C:YPG301 4.9 49.0 1.0
NH1 C:ARG188 5.0 38.1 1.0

Magnesium binding site 4 out of 4 in 5kny

Go back to Magnesium Binding Sites List in 5kny
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) 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 Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with (3-((3R,4R)-3-(Guanin-9- Yl)-4-((S)-2-Hydroxy-2-Phosphonoethoxy)Pyrrolidin-1-Yl)-3-Oxopropyl) Phosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:60.3
occ:1.00
 OD2 D:ASP182 2.1 70.1 1.0
OAI D:YPG301 2.2 56.6 0.8
CAN D:YPG301 2.8 51.5 1.0
CG D:ASP182 3.2 67.2 1.0
PBF D:YPG301 3.4 53.7 1.0
OD1 D:ASP182 3.7 63.9 1.0
CAZ D:YPG301 3.7 49.5 1.0
N3 D:YPG301 3.9 46.9 0.5
OAT D:YPG301 4.0 52.3 1.0
N2 D:YPG301 4.0 46.3 1.0
NH2 D:ARG188 4.1 46.4 1.0
O D:ASP182 4.2 69.0 1.0
OAJ D:YPG301 4.4 49.7 1.0
OAE D:YPG301 4.4 52.1 1.0
CBA D:YPG301 4.4 50.4 1.0
C2 D:YPG301 4.4 46.8 0.8
CB D:ASP182 4.5 65.8 1.0
N D:ASP182 4.5 62.7 1.0
OAF D:YPG301 4.6 51.9 0.6
C D:ASP182 4.7 67.2 1.0
CBB D:YPG301 4.7 49.3 0.9
CA D:ASP182 4.8 64.7 1.0
CZ D:ARG188 4.9 54.1 1.0
C4 D:YPG301 5.0 44.9 1.0

Reference:

W.S.Eng, D.Rejman, D.T.Keough, L.W.Guddat. Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with Pyrrolidine Nucleoside Phosphonate To Be Published.
Page generated: Sun Sep 29 19:10:12 2024

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