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

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

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

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate, PDB code: 5knq 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) 42.75 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.262, 85.507, 81.468, 90.00, 107.22, 90.00
R / Rfree (%) 18.7 / 23.7

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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate (pdb code 5knq). 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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate, PDB code: 5knq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5knq

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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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:64.2
occ:1.00
 O A:HOH426 2.1 52.1 1.0
O A:HOH451 2.1 41.8 1.0
O A:HOH438 2.1 62.8 1.0
O A:HOH439 2.1 48.5 1.0
OE1 A:GLU122 2.1 64.5 1.0
OD1 A:ASP123 2.1 41.9 1.0
CD A:GLU122 3.1 58.5 1.0
CG A:ASP123 3.2 41.8 1.0
OE2 A:GLU122 3.4 64.8 1.0
OD2 A:ASP123 3.7 44.6 1.0
N A:ASP123 4.0 39.2 1.0
O A:HOH444 4.1 58.6 1.0
O A:HOH420 4.3 63.4 1.0
O A:VAL124 4.4 49.0 1.0
CG A:GLU122 4.4 42.6 1.0
CB A:ASP123 4.5 41.9 1.0
N A:VAL124 4.5 44.0 1.0
CB A:GLU122 4.7 35.8 1.0
CA A:GLU122 4.7 34.3 1.0
O5 A:POP304 4.7 0.6 1.0
CA A:ASP123 4.8 42.6 1.0
O A:VAL64 4.8 40.4 1.0
C A:GLU122 4.9 37.9 1.0

Magnesium binding site 2 out of 8 in 5knq

Go back to Magnesium Binding Sites List in 5knq
Magnesium binding site 2 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:82.0
occ:1.00
 O A:HOH415 2.1 64.5 1.0
OD2 A:ASP182 2.1 53.1 1.0
O6 A:POP304 2.2 0.7 1.0
O A:HOH445 2.9 46.3 1.0
CG A:ASP182 3.4 49.5 1.0
P2 A:POP304 3.4 0.8 1.0
O4 A:POP304 3.4 0.6 1.0
N2 A:6W8301 3.7 48.8 1.0
N3 A:6W8301 3.8 47.4 1.0
OD1 A:ASP182 4.1 49.2 1.0
N A:ASP182 4.1 37.4 1.0
C2 A:6W8301 4.2 49.0 1.0
O5 A:POP304 4.3 0.6 1.0
O A:ASP182 4.3 44.8 1.0
NH1 A:ARG188 4.4 38.8 1.0
CB A:ASP182 4.4 44.6 1.0
O A:POP304 4.5 0.6 1.0
NH2 A:ARG188 4.5 43.9 1.0
CA A:ASP182 4.6 38.7 1.0
C A:ASP182 4.7 41.7 1.0
CZ A:ARG188 4.8 47.2 1.0
CAT A:6W8301 4.9 54.1 1.0
C4 A:6W8301 5.0 47.8 1.0

Magnesium binding site 3 out of 8 in 5knq

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


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:61.4
occ:1.00
 O B:HOH436 2.1 40.2 1.0
O B:HOH414 2.1 70.3 1.0
OD1 B:ASP123 2.1 47.5 1.0
O B:HOH425 2.1 41.0 1.0
OE1 B:GLU122 2.1 62.1 1.0
CD B:GLU122 3.1 59.6 1.0
CG B:ASP123 3.2 41.6 1.0
OE2 B:GLU122 3.3 64.8 1.0
OD2 B:ASP123 3.6 41.1 1.0
N B:ASP123 4.0 34.4 1.0
O B:HOH423 4.3 37.5 1.0
O B:VAL124 4.4 54.5 1.0
CG B:GLU122 4.4 49.0 1.0
CB B:ASP123 4.5 36.7 1.0
N B:VAL124 4.5 36.3 1.0
CB B:GLU122 4.7 40.9 1.0
CA B:ASP123 4.8 36.2 1.0
CA B:GLU122 4.8 40.0 1.0
C B:GLU122 4.9 36.9 1.0

Magnesium binding site 4 out of 8 in 5knq

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


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:0.2
occ:1.00
 OD1 B:ASP182 2.0 58.4 1.0
O B:HOH401 2.1 61.4 1.0
OD2 B:ASP182 2.2 51.0 1.0
O5 B:POP304 2.3 0.3 1.0
CG B:ASP182 2.4 52.1 1.0
O B:HOH448 3.4 56.6 1.0
NH2 B:ARG188 3.6 47.3 1.0
O B:HOH446 3.7 47.5 1.0
P2 B:POP304 3.7 0.3 1.0
CB B:ASP182 3.9 45.2 1.0
O3 B:POP304 4.0 0.9 1.0
O4 B:POP304 4.3 0.0 1.0
CZ B:ARG188 4.4 45.9 1.0
O B:POP304 4.5 0.9 1.0
NH1 B:ARG188 4.5 40.3 1.0
O B:ASP182 4.6 47.7 1.0
C B:ASP182 4.7 46.0 1.0
CA B:ASP182 4.7 41.3 1.0
O6 B:POP304 4.7 0.8 1.0
OE1 B:GLU185 4.8 71.8 1.0
N B:ASP182 4.9 34.5 1.0
P1 B:POP304 4.9 0.0 1.0

Magnesium binding site 5 out of 8 in 5knq

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


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:0.5
occ:1.00
 OD1 C:ASP123 2.0 0.7 1.0
O C:HOH401 2.1 0.4 1.0
O C:HOH402 2.1 83.9 1.0
O C:HOH408 2.1 56.4 1.0
OE2 C:GLU122 2.1 0.5 1.0
OE1 C:GLU122 2.2 0.3 1.0
OD2 C:ASP123 2.2 0.5 1.0
CG C:ASP123 2.2 0.3 1.0
CD C:GLU122 2.3 0.0 1.0
N C:ASP123 3.3 92.4 1.0
CB C:ASP123 3.5 99.7 1.0
CG C:GLU122 3.7 97.4 1.0
O C:HOH419 3.8 0.1 1.0
CA C:ASP123 4.0 96.1 1.0
N C:VAL124 4.1 98.6 1.0
CB C:GLU122 4.2 92.9 1.0
C C:GLU122 4.3 91.2 1.0
CA C:GLU122 4.3 87.2 1.0
O C:VAL124 4.4 0.4 1.0
CB C:ALA68 4.6 73.1 1.0
C C:ASP123 4.6 99.1 1.0
O4 C:POP304 4.7 0.2 1.0
O C:VAL64 4.8 53.6 1.0
N C:ALA68 4.8 72.3 1.0
CA C:GLY67 5.0 64.8 1.0

Magnesium binding site 6 out of 8 in 5knq

Go back to Magnesium Binding Sites List in 5knq
Magnesium binding site 6 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:0.7
occ:1.00
 O C:HOH415 2.1 66.3 1.0
O C:HOH411 2.1 95.2 1.0
O5 C:POP304 2.1 0.1 1.0
OD2 C:ASP182 2.1 84.8 1.0
O1 C:POP304 2.3 0.9 1.0
CG C:ASP182 3.3 79.3 1.0
P2 C:POP304 3.3 0.2 1.0
P1 C:POP304 3.4 0.3 1.0
O C:HOH420 3.4 58.1 1.0
O2 C:POP304 3.6 0.2 1.0
O4 C:POP304 3.8 0.2 1.0
O C:POP304 3.8 0.3 1.0
NH2 C:ARG188 3.9 67.5 1.0
OD1 C:ASP182 4.0 71.8 1.0
N2 C:6W8301 4.0 0.5 1.0
O C:HOH416 4.1 56.2 1.0
N C:ASP182 4.2 82.5 1.0
O C:ASP182 4.3 77.8 1.0
NH1 C:ARG188 4.4 68.3 1.0
CB C:ASP182 4.4 80.4 1.0
N3 C:6W8301 4.5 0.8 1.0
O6 C:POP304 4.5 0.3 1.0
CZ C:ARG188 4.6 68.4 1.0
O C:HOH419 4.6 0.1 1.0
O3 C:POP304 4.7 0.4 1.0
CA C:ASP182 4.7 81.5 1.0
C C:ASP182 4.7 79.5 1.0
C2 C:6W8301 4.8 0.9 1.0

Magnesium binding site 7 out of 8 in 5knq

Go back to Magnesium Binding Sites List in 5knq
Magnesium binding site 7 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Hypoxanthine Guanine Phosphoribosyltransferase in Complex with [3S,4R]-(4-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:71.4
occ:1.00
 O D:HOH411 2.1 62.5 1.0
O D:HOH409 2.1 57.4 1.0
O D:HOH410 2.1 93.8 1.0
OE1 D:GLU122 2.1 89.0 1.0
OD1 D:ASP123 2.1 73.5 1.0
CD D:GLU122 3.0 82.8 1.0
CG D:ASP123 3.2 73.9 1.0
OE2 D:GLU122 3.3 83.8 1.0
OD2 D:ASP123 3.6 72.7 1.0
N D:ASP123 4.0 72.4 1.0
CG D:GLU122 4.3 76.0 1.0
CB D:ASP123 4.5 77.5 1.0
O D:VAL124 4.5 82.9 1.0
CA D:GLU122 4.6 68.0 1.0
CB D:GLU122 4.6 71.7 1.0
N D:VAL124 4.7 85.6 1.0
O D:VAL64 4.7 51.5 1.0
CA D:ASP123 4.8 77.8 1.0
C D:GLU122 4.8 71.1 1.0
CB D:VAL64 4.9 49.6 1.0

Magnesium binding site 8 out of 8 in 5knq

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


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-(Guanin-9-Yl) Pyrrolidin-3-Yl)Oxymethanephosphonic Acid and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:0.1
occ:1.00
 O1 D:POP304 1.9 0.2 1.0
OD1 D:ASP182 2.0 64.3 1.0
O D:HOH412 2.1 69.3 1.0
O D:HOH402 2.1 78.9 1.0
O6 D:POP304 2.2 0.4 1.0
CG D:ASP182 3.0 60.3 1.0
P1 D:POP304 3.3 0.1 1.0
OD2 D:ASP182 3.5 54.2 1.0
P2 D:POP304 3.5 98.7 1.0
NH2 D:ARG188 3.8 53.5 1.0
O2 D:POP304 3.8 0.2 1.0
O D:POP304 3.9 0.4 1.0
CB D:ASP182 4.3 59.3 1.0
O4 D:POP304 4.3 98.6 1.0
O3 D:POP304 4.4 0.7 1.0
NH1 D:ARG188 4.4 50.5 1.0
CZ D:ARG188 4.5 53.7 1.0
O5 D:POP304 4.5 97.0 1.0
N2 D:6W8301 4.6 79.3 1.0
O D:ASP182 4.6 68.0 1.0
N D:ASP182 4.7 64.7 1.0
CA D:ASP182 4.9 64.7 1.0
C D:ASP182 4.9 68.3 1.0
N3 D:6W8301 4.9 84.5 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 19:09:21 2024

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