Atomistry » Magnesium » PDB 5kfu-5ktd » 5kny
Atomistry »
  Magnesium »
    PDB 5kfu-5ktd »
      5kny »

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

Go back to Magnesium Binding Sites List in 5kny
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy