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

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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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

Go back to Magnesium Binding Sites List in 5knp
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: Sun Sep 29 19:09:04 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy