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Magnesium in PDB 5knp: Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid, PDB code: 5knp 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) 46.44 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.264, 85.678, 154.586, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 29.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid (pdb code 5knp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid, PDB code: 5knp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5knp

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic 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 [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:43.9
occ:1.00
 O A:HOH407 2.1 35.1 1.0
O A:HOH419 2.1 23.5 1.0
O A:HOH406 2.1 27.5 1.0
OD2 A:ASP182 2.1 31.0 1.0
O4 A:POP304 2.2 56.9 0.5
O1 A:POP304 2.2 53.1 0.5
O1 A:POP304 2.6 53.0 0.5
O3 A:POP304 2.8 55.2 0.5
CG A:ASP182 3.1 31.1 1.0
P2 A:POP304 3.2 57.1 0.5
P1 A:POP304 3.2 53.1 0.5
P1 A:POP304 3.3 53.1 0.5
O A:POP304 3.3 56.9 0.5
OD1 A:ASP182 3.4 31.9 1.0
O4 A:POP304 3.8 58.4 0.5
O5 A:POP304 3.8 57.7 0.5
NH2 A:ARG188 3.9 37.3 1.0
O2 A:POP304 4.0 53.2 0.5
O A:HOH413 4.0 46.7 1.0
O A:POP304 4.3 53.2 0.5
O2 A:POP304 4.4 53.2 0.5
O A:ASP182 4.4 31.6 1.0
CB A:ASP182 4.4 31.1 1.0
O6 A:POP304 4.5 57.2 0.5
O3 A:POP304 4.5 53.1 0.5
NH1 A:ARG188 4.5 33.6 1.0
CZ A:ARG188 4.6 35.5 1.0
O A:HOH447 4.6 29.8 1.0
N3 A:6W7301 4.6 37.5 1.0
P2 A:POP304 4.7 58.6 0.5
N A:ASP182 4.8 27.9 1.0
C A:ASP182 4.9 31.4 1.0
CA A:ASP182 4.9 29.5 1.0

Magnesium binding site 2 out of 8 in 5knp

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic 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 [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:43.5
occ:1.00
 O A:HOH445 2.1 48.1 1.0
O A:HOH402 2.1 30.6 1.0
O A:HOH410 2.1 63.1 1.0
O A:HOH428 2.1 23.8 1.0
OD1 A:ASP123 2.1 30.5 1.0
OE1 A:GLU122 2.1 42.5 1.0
CG A:ASP123 3.1 30.4 1.0
CD A:GLU122 3.1 40.7 1.0
OE2 A:GLU122 3.6 43.2 1.0
OD2 A:ASP123 3.6 31.5 1.0
N A:ASP123 3.9 25.9 1.0
O2 A:POP304 4.0 53.2 0.5
O A:HOH423 4.2 35.9 1.0
O3 A:POP304 4.2 53.1 0.5
O A:VAL64 4.3 23.1 1.0
CB A:ASP123 4.4 29.2 1.0
O A:HOH424 4.4 27.2 1.0
CG A:GLU122 4.4 34.9 1.0
CB A:ALA68 4.5 30.3 1.0
CB A:GLU122 4.6 30.7 1.0
CA A:GLU122 4.6 28.1 1.0
CA A:ASP123 4.7 27.9 1.0
N A:VAL124 4.7 30.0 1.0
CB A:VAL64 4.8 26.9 1.0
C A:GLU122 4.8 27.9 1.0
O A:VAL124 4.8 30.8 1.0
O A:HOH413 4.8 46.7 1.0
N A:ALA68 4.9 30.2 1.0
O A:POP304 5.0 56.9 0.5

Magnesium binding site 3 out of 8 in 5knp

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic 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 [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.0
occ:1.00
 O B:HOH412 2.1 23.8 1.0
O B:HOH409 2.1 29.0 1.0
O B:HOH424 2.1 45.3 1.0
OD2 B:ASP182 2.1 29.2 1.0
O4 B:POP304 2.2 63.9 0.4
O1 B:POP304 2.3 60.0 0.4
O1 B:POP304 2.3 60.1 0.6
O3 B:POP304 2.8 63.3 0.6
P1 B:POP304 3.0 59.9 0.4
O B:POP304 3.0 64.2 0.4
P1 B:POP304 3.1 60.5 0.6
CG B:ASP182 3.1 35.5 1.0
P2 B:POP304 3.2 64.0 0.4
O2 B:POP304 3.3 60.5 0.4
OD1 B:ASP182 3.5 30.7 1.0
NH2 B:ARG188 3.7 17.9 1.0
O B:HOH404 3.7 62.3 1.0
O4 B:POP304 3.8 64.6 0.6
O5 B:POP304 4.1 64.6 0.4
O2 B:POP304 4.1 60.0 0.6
O B:POP304 4.3 60.6 0.6
O B:HOH420 4.3 39.9 1.0
O6 B:POP304 4.3 63.8 0.4
NH1 B:ARG188 4.4 15.5 1.0
O3 B:POP304 4.4 59.8 0.4
CB B:ASP182 4.4 33.7 1.0
CZ B:ARG188 4.4 24.0 1.0
O B:ASP182 4.5 35.2 1.0
N B:ASP182 4.7 29.6 1.0
N3 B:6W7301 4.7 37.1 1.0
O B:HOH442 4.7 40.6 1.0
P2 B:POP304 4.7 64.2 0.6
CA B:ASP182 4.9 31.6 1.0
C B:ASP182 4.9 33.9 1.0
O B:HOH439 4.9 32.9 1.0

Magnesium binding site 4 out of 8 in 5knp

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic 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 [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:66.8
occ:1.00
 OD1 B:ASP123 2.1 54.6 1.0
O B:HOH417 2.1 30.8 1.0
O B:HOH427 2.1 61.0 1.0
O B:HOH401 2.1 31.2 1.0
OE1 B:GLU122 2.1 44.7 1.0
OD2 B:ASP123 2.1 59.5 1.0
CG B:ASP123 2.1 54.8 1.0
CD B:GLU122 3.1 42.5 1.0
N B:ASP123 3.2 41.3 1.0
CB B:ASP123 3.4 50.7 1.0
OE2 B:GLU122 3.5 44.9 1.0
CA B:ASP123 3.8 45.1 1.0
CB B:ALA68 4.0 35.6 1.0
N B:VAL124 4.1 42.0 1.0
C B:GLU122 4.2 35.2 1.0
CA B:GLU122 4.3 32.1 1.0
O2 B:POP304 4.3 60.0 0.6
CG B:GLU122 4.3 37.8 1.0
N B:ALA68 4.4 38.4 1.0
O B:HOH404 4.4 62.3 1.0
CB B:GLU122 4.5 31.3 1.0
C B:ASP123 4.6 45.1 1.0
O3 B:POP304 4.6 59.8 0.4
O B:VAL64 4.6 27.1 1.0
O B:VAL124 4.6 43.8 1.0
C B:GLY67 4.7 41.3 1.0
CA B:ALA68 4.7 37.6 1.0
CA B:GLY67 4.9 42.2 1.0

Magnesium binding site 5 out of 8 in 5knp

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:49.1
occ:1.00
 O C:HOH401 2.1 51.2 1.0
O C:HOH414 2.1 53.8 1.0
O C:HOH427 2.1 24.4 1.0
OD2 C:ASP182 2.1 27.3 1.0
O2 C:POP304 2.1 78.7 0.5
O5 C:POP304 2.2 80.7 0.5
O2 C:POP304 2.3 78.8 0.6
O3 C:POP304 3.0 79.7 0.6
CG C:ASP182 3.0 29.6 1.0
P1 C:POP304 3.2 78.5 0.6
P2 C:POP304 3.3 80.7 0.5
OD1 C:ASP182 3.3 30.2 1.0
P1 C:POP304 3.3 78.5 0.5
O4 C:POP304 3.5 81.1 0.5
O3 C:POP304 3.7 78.0 0.5
O C:POP304 3.8 80.3 0.5
NH2 C:ARG188 3.9 35.9 1.0
O1 C:POP304 4.1 78.1 0.6
O5 C:POP304 4.1 95.4 0.6
O C:ASP182 4.3 30.1 1.0
O C:POP304 4.4 78.8 0.6
O C:HOH431 4.4 44.4 1.0
CB C:ASP182 4.4 29.6 1.0
O C:HOH413 4.5 55.9 1.0
O1 C:POP304 4.6 78.6 0.5
O6 C:POP304 4.6 80.6 0.5
CZ C:ARG188 4.7 36.0 1.0
N3 C:6W7301 4.7 36.6 1.0
C C:ASP182 4.7 31.5 1.0
NH1 C:ARG188 4.7 34.9 1.0
N C:ASP182 4.8 31.8 1.0
CA C:ASP182 4.9 30.6 1.0
P2 C:POP304 4.9 95.4 0.6

Magnesium binding site 6 out of 8 in 5knp

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:48.9
occ:1.00
 O C:HOH429 2.1 38.8 1.0
O C:HOH438 2.1 61.7 1.0
O C:HOH419 2.1 26.7 1.0
O C:HOH430 2.1 44.1 1.0
OE1 C:GLU122 2.1 40.6 1.0
OD1 C:ASP123 2.1 41.1 1.0
CD C:GLU122 3.1 41.0 1.0
CG C:ASP123 3.2 40.0 1.0
OE2 C:GLU122 3.6 42.2 1.0
OD2 C:ASP123 3.7 41.8 1.0
N C:ASP123 3.9 34.2 1.0
O C:HOH428 4.0 35.7 1.0
O C:HOH432 4.1 49.0 1.0
O C:HOH413 4.1 55.9 1.0
O C:HOH434 4.2 42.0 1.0
CG C:GLU122 4.4 39.2 1.0
CB C:ASP123 4.4 37.3 1.0
O C:VAL64 4.5 26.1 1.0
CA C:GLU122 4.5 35.9 1.0
CB C:GLU122 4.5 37.2 1.0
O C:VAL124 4.5 36.2 1.0
CB C:ALA68 4.6 37.0 1.0
N C:VAL124 4.6 34.5 1.0
CA C:ASP123 4.7 36.0 1.0
C C:GLU122 4.7 34.5 1.0
CB C:VAL64 4.8 32.4 1.0
O1 C:POP304 4.9 78.1 0.6
N C:ALA68 5.0 36.1 1.0

Magnesium binding site 7 out of 8 in 5knp

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:46.0
occ:1.00
 OD2 D:ASP182 2.1 33.1 1.0
O D:HOH417 2.1 28.8 1.0
O D:HOH409 2.1 28.3 1.0
O D:HOH411 2.1 27.3 1.0
O2 D:POP304 2.2 0.9 0.5
O2 D:POP304 2.3 0.9 0.5
O5 D:POP304 2.3 0.3 0.5
CG D:ASP182 3.0 34.8 1.0
O3 D:POP304 3.1 0.5 0.5
P1 D:POP304 3.2 0.0 0.5
OD1 D:ASP182 3.3 31.1 1.0
P1 D:POP304 3.3 1.0 0.5
P2 D:POP304 3.4 0.5 0.5
O D:POP304 3.5 0.1 0.5
NH2 D:ARG188 3.8 35.3 1.0
O D:HOH403 3.9 86.0 1.0
O1 D:POP304 4.0 0.5 0.5
O4 D:POP304 4.0 0.8 0.5
O1 D:POP304 4.0 0.8 0.5
O D:ASP182 4.3 37.8 1.0
CB D:ASP182 4.4 34.8 1.0
O5 D:POP304 4.4 0.1 0.5
O D:POP304 4.5 0.7 0.5
O3 D:POP304 4.5 0.7 0.5
CZ D:ARG188 4.6 35.7 1.0
N D:ASP182 4.6 34.0 1.0
O6 D:POP304 4.6 0.4 0.5
N3 D:6W7301 4.7 38.0 1.0
NH1 D:ARG188 4.7 35.8 1.0
C D:ASP182 4.7 37.2 1.0
CA D:ASP182 4.8 34.8 1.0

Magnesium binding site 8 out of 8 in 5knp

Go back to Magnesium Binding Sites List in 5knp
Magnesium binding site 8 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Hypoxanthin-9- Yl)Pyrrolidin-3-Yl)-Oxymethanephosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:39.6
occ:1.00
 O D:HOH431 2.1 50.2 1.0
O D:HOH405 2.1 28.3 1.0
O D:HOH418 2.1 50.6 1.0
O D:HOH429 2.1 46.0 1.0
OD1 D:ASP123 2.1 40.2 1.0
OE1 D:GLU122 2.1 42.9 1.0
CG D:ASP123 3.1 43.2 1.0
CD D:GLU122 3.1 40.3 1.0
OE2 D:GLU122 3.5 41.5 1.0
OD2 D:ASP123 3.5 46.9 1.0
N D:ASP123 3.9 38.2 1.0
CB D:ASP123 4.3 43.6 1.0
CG D:GLU122 4.4 36.3 1.0
O D:VAL64 4.5 25.9 1.0
O D:VAL124 4.5 43.1 1.0
O1 D:POP304 4.5 0.8 0.5
CB D:GLU122 4.6 35.2 1.0
CA D:GLU122 4.6 34.5 1.0
O D:HOH403 4.6 86.0 1.0
N D:VAL124 4.7 42.0 1.0
CB D:ALA68 4.7 36.6 1.0
CA D:ASP123 4.7 41.3 1.0
O3 D:POP304 4.8 0.7 0.5
C D:GLU122 4.8 36.6 1.0
N D:ALA68 4.9 37.8 1.0
CB D:VAL64 4.9 28.3 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: Mon Dec 14 20:37:56 2020

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