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Magnesium in PDB 4qxd: Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica

Enzymatic activity of Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica

All present enzymatic activity of Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica:
3.1.3.57;

Protein crystallography data

The structure of Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica, PDB code: 4qxd was solved by K.F.Tarique, S.A.Abdul Rehman, C.Betzel, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.741, 76.289, 101.067, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica (pdb code 4qxd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica, PDB code: 4qxd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qxd

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Magnesium binding site 1 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:26.6
occ:1.00
 O A:LEU108 2.0 38.0 1.0
OE1 A:GLU68 2.0 38.6 1.0
OD1 A:ASP106 2.2 32.9 1.0
O4 A:PO4301 2.4 37.7 1.0
O3 A:PO4301 2.5 44.3 1.0
C A:LEU108 3.0 38.6 1.0
CG A:ASP106 3.0 35.4 1.0
P A:PO4301 3.0 44.1 1.0
CD A:GLU68 3.1 39.7 1.0
OD2 A:ASP106 3.1 41.5 1.0
OE2 A:GLU68 3.5 42.6 1.0
N A:ASP109 3.7 37.9 1.0
OG1 A:THR111 3.7 40.7 1.0
N A:LEU108 3.8 37.2 1.0
CA A:ASP109 3.9 37.5 1.0
CA A:LEU108 3.9 37.9 1.0
OE2 A:GLU69 4.0 45.4 1.0
OD2 A:ASP45 4.0 43.7 1.0
O2 A:PO4301 4.0 34.1 1.0
O1 A:PO4301 4.1 37.1 1.0
MG A:MG304 4.2 25.6 1.0
CG A:GLU68 4.3 38.4 1.0
CD A:PRO107 4.4 38.3 1.0
CB A:ASP106 4.4 32.3 1.0
CB A:LEU108 4.5 39.3 1.0
O A:HOH402 4.5 28.6 1.0
CB A:GLU68 4.5 36.2 1.0
O A:HOH401 4.7 30.4 1.0
N A:GLY110 4.8 39.6 1.0
C A:ASP109 4.8 37.7 1.0
N A:PRO107 4.8 36.9 1.0
CG A:PRO107 4.8 40.3 1.0
CA A:ASP106 4.9 33.2 1.0
CB A:ASP109 4.9 36.6 1.0
C A:ASP106 4.9 34.9 1.0
OD1 A:ASP109 5.0 37.7 1.0
MG A:MG303 5.0 29.3 1.0

Magnesium binding site 2 out of 6 in 4qxd

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Magnesium binding site 2 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:29.3
occ:1.00
 OE2 A:GLU68 2.2 42.6 1.0
O A:HOH401 2.4 30.4 1.0
O1 A:PO4301 2.5 37.1 1.0
O4 A:PO4301 3.2 37.7 1.0
P A:PO4301 3.4 44.1 1.0
CD A:GLU68 3.5 39.7 1.0
NZ A:LYS35 4.0 58.7 1.0
O A:GLU40 4.2 54.9 1.0
CB A:SER39 4.2 58.3 1.0
OE1 A:GLU68 4.2 38.6 1.0
O A:HOH402 4.4 28.6 1.0
O2 A:PO4301 4.5 34.1 1.0
CG A:GLU68 4.5 38.4 1.0
O3 A:PO4301 4.5 44.3 1.0
OG A:SER39 4.5 60.9 1.0
O A:HOH404 4.6 46.5 1.0
OE2 A:GLU69 4.6 45.4 1.0
CE A:LYS35 4.7 59.4 1.0
O A:HOH403 4.8 45.7 1.0
MG A:MG302 5.0 26.6 1.0
OG1 A:THR111 5.0 40.7 1.0

Magnesium binding site 3 out of 6 in 4qxd

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Magnesium binding site 3 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:25.6
occ:1.00
 OD2 A:ASP223 2.0 32.6 1.0
OD1 A:ASP109 2.2 37.7 1.0
O3 A:PO4301 2.2 44.3 1.0
O A:HOH402 2.2 28.6 1.0
OD2 A:ASP106 2.5 41.5 1.0
CG A:ASP223 3.1 33.0 1.0
CG A:ASP109 3.4 38.1 1.0
P A:PO4301 3.4 44.1 1.0
OD1 A:ASP223 3.5 36.2 1.0
O1 A:PO4301 3.6 37.1 1.0
CG A:ASP106 3.7 35.4 1.0
OE1 A:GLU68 3.9 38.6 1.0
CB A:ASP109 4.1 36.6 1.0
O2 A:PO4301 4.1 34.1 1.0
CA A:ASP109 4.2 37.5 1.0
MG A:MG302 4.2 26.6 1.0
NE1 A:TRP222 4.3 36.4 1.0
CD1 A:TRP222 4.3 34.1 1.0
CB A:ASP223 4.3 33.2 1.0
OD1 A:ASP106 4.4 32.9 1.0
O A:HOH403 4.4 45.7 1.0
OD2 A:ASP109 4.4 37.5 1.0
OG A:SER197 4.5 54.3 1.0
O4 A:PO4301 4.6 37.7 1.0
CD A:GLU68 4.6 39.7 1.0
CB A:ASP106 4.8 32.3 1.0
N A:GLY110 4.8 39.6 1.0
CA A:ASP223 4.9 32.8 1.0
OE2 A:GLU68 4.9 42.6 1.0

Magnesium binding site 4 out of 6 in 4qxd

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Magnesium binding site 4 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:29.2
occ:1.00
 OE1 B:GLU68 2.0 31.7 1.0
O4 B:PO4303 2.0 46.3 1.0
O B:LEU108 2.1 32.9 1.0
OD2 B:ASP106 2.2 34.0 1.0
O B:HOH401 2.2 28.8 1.0
O2 B:PO4303 2.8 40.3 1.0
P B:PO4303 2.9 47.4 1.0
CG B:ASP106 2.9 34.0 1.0
CD B:GLU68 3.0 35.7 1.0
C B:LEU108 3.0 35.0 1.0
OD1 B:ASP106 3.0 36.7 1.0
OE2 B:GLU68 3.5 38.1 1.0
N B:ASP109 3.7 36.6 1.0
CA B:ASP109 3.7 39.4 1.0
MG B:MG302 3.8 26.9 1.0
OG1 B:THR111 3.8 49.7 1.0
O3 B:PO4303 3.8 45.0 1.0
O1 B:PO4303 4.0 37.3 1.0
N B:LEU108 4.0 33.3 1.0
CA B:LEU108 4.1 34.3 1.0
OE2 B:GLU69 4.1 44.9 1.0
OD2 B:ASP45 4.2 42.8 1.0
CG B:GLU68 4.3 35.2 1.0
CB B:ASP106 4.4 32.4 1.0
CB B:GLU68 4.5 34.8 1.0
CD B:PRO107 4.6 34.0 1.0
O B:HOH411 4.6 40.1 1.0
N B:GLY110 4.6 41.1 1.0
OD1 B:ASP109 4.7 38.8 1.0
CB B:LEU108 4.7 35.4 1.0
C B:ASP109 4.7 40.3 1.0
CB B:ASP109 4.7 38.4 1.0
MG B:MG304 4.9 40.6 1.0
CA B:ASP106 4.9 32.0 1.0
N B:PRO107 5.0 32.6 1.0

Magnesium binding site 5 out of 6 in 4qxd

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Magnesium binding site 5 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.9
occ:1.00
 O2 B:PO4303 1.9 40.3 1.0
OD2 B:ASP223 2.1 37.3 1.0
OD1 B:ASP109 2.1 38.8 1.0
OD1 B:ASP106 2.3 36.7 1.0
CG B:ASP223 3.2 38.2 1.0
CG B:ASP109 3.3 40.5 1.0
P B:PO4303 3.3 47.4 1.0
CG B:ASP106 3.5 34.0 1.0
OD1 B:ASP223 3.7 39.8 1.0
OE1 B:GLU68 3.7 31.7 1.0
MG B:MG301 3.8 29.2 1.0
O3 B:PO4303 3.8 45.0 1.0
CB B:ASP109 4.0 38.4 1.0
CA B:ASP109 4.1 39.4 1.0
OD2 B:ASP106 4.1 34.0 1.0
O4 B:PO4303 4.2 46.3 1.0
O1 B:PO4303 4.2 37.3 1.0
CD1 B:TRP222 4.3 32.2 1.0
OD2 B:ASP109 4.3 41.1 1.0
NE1 B:TRP222 4.3 32.8 1.0
CB B:ASP223 4.4 36.9 1.0
CD B:GLU68 4.5 35.7 1.0
OG B:SER197 4.5 53.0 1.0
CB B:ASP106 4.6 32.4 1.0
OE2 B:GLU68 4.8 38.1 1.0
N B:GLY110 4.8 41.1 1.0
CA B:ASP223 4.9 35.9 1.0
C B:ASP109 5.0 40.3 1.0

Magnesium binding site 6 out of 6 in 4qxd

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Magnesium binding site 6 out of 6 in the Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica


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 Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:40.6
occ:1.00
 O B:HOH412 2.0 47.1 1.0
O B:HOH411 2.3 40.1 1.0
OE2 B:GLU68 2.3 38.1 1.0
O3 B:PO4303 2.3 45.0 1.0
P B:PO4303 3.5 47.4 1.0
O4 B:PO4303 3.5 46.3 1.0
CD B:GLU68 3.5 35.7 1.0
O B:GLU40 3.9 59.7 1.0
NZ B:LYS35 4.0 55.1 1.0
CB B:SER39 4.1 74.4 1.0
OE1 B:GLU68 4.3 31.7 1.0
O1 B:PO4303 4.4 37.3 1.0
OE2 B:GLU69 4.5 44.9 1.0
OG B:SER39 4.5 77.3 1.0
CG B:GLU68 4.5 35.2 1.0
O2 B:PO4303 4.6 40.3 1.0
O B:HOH402 4.6 31.6 1.0
CE B:LYS35 4.6 56.6 1.0
OG1 B:THR111 4.8 49.7 1.0
MG B:MG301 4.9 29.2 1.0

Reference:

K.F.Tarique, S.A.Abdul Rehman, C.Betze, S.Gourinath. Crystal Structure of Inositol Polyphosphate 1-Phosphatase From Entamoeba Histolytica To Be Published.
Page generated: Mon Dec 14 19:27:40 2020

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