Atomistry » Magnesium » PDB 5kfv-5ktj » 5knq
Atomistry »
  Magnesium »
    PDB 5kfv-5ktj »
      5knq »

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

Go back to Magnesium Binding Sites List in 5knq
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

Last articles

Al in 8SHL
Al in 8SHE
Al in 8SHG
Al in 8SHF
Al in 8SHD
Al in 8SHA
Al in 8SGL
Al in 8SH9
Al in 8SGC
Al in 8SG9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy