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Magnesium in PDB 4i3y: Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex

Enzymatic activity of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex

All present enzymatic activity of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex, PDB code: 4i3y was solved by A.Dutta, S.Bhattacharyya, D.Dutta, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 2.04
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.136, 62.819, 141.580, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex (pdb code 4i3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex, PDB code: 4i3y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4i3y

Go back to Magnesium Binding Sites List in 4i3y
Magnesium binding site 1 out of 4 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex


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 Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:20.0
occ:1.00
 OD1 A:ASP88 2.0 12.0 1.0
OE2 A:GLU70 2.1 13.4 1.0
O A:ILE90 2.2 10.7 1.0
O4 A:PO4301 2.2 17.9 1.0
O A:HOH402 2.3 13.8 1.0
O3 A:PO4301 2.3 20.2 1.0
P A:PO4301 2.7 21.7 1.0
CG A:ASP88 2.9 13.3 1.0
C A:ILE90 3.2 11.3 1.0
CD A:GLU70 3.2 14.7 1.0
OD2 A:ASP88 3.2 12.7 1.0
O1 A:PO4301 3.7 17.2 1.0
OE1 A:GLU70 3.7 16.4 1.0
CA A:ASP91 3.8 12.9 1.0
O2 A:PO4301 3.8 17.7 1.0
N A:ASP91 3.9 11.6 1.0
OG1 A:THR93 4.0 12.5 1.0
MG A:MG304 4.0 20.9 1.0
N A:ILE90 4.0 12.4 1.0
OE2 A:GLU71 4.1 17.9 1.0
CA A:ILE90 4.2 10.8 1.0
CB A:ASP88 4.3 15.1 1.0
OD2 A:ASP47 4.3 14.6 1.0
CG A:GLU70 4.4 14.0 1.0
O A:HOH405 4.5 18.7 1.0
CB A:GLU70 4.5 13.7 1.0
O A:HOH401 4.5 15.8 1.0
CD A:PRO89 4.6 13.1 1.0
CA A:ASP88 4.6 15.7 1.0
N A:PRO89 4.6 14.8 1.0
C A:ASP88 4.7 15.1 1.0
CB A:ASP91 4.7 12.7 1.0
CD1 A:TRP208 4.8 13.3 1.0
OD1 A:ASP91 4.8 15.0 1.0
C A:ASP91 4.8 12.1 1.0
CB A:ILE90 4.9 11.3 1.0
OD1 A:ASP209 4.9 15.3 1.0
N A:GLY92 4.9 13.5 1.0

Magnesium binding site 2 out of 4 in 4i3y

Go back to Magnesium Binding Sites List in 4i3y
Magnesium binding site 2 out of 4 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex


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 Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:20.9
occ:1.00
 O1 A:PO4301 2.1 17.2 1.0
O A:HOH405 2.1 18.7 1.0
O A:HOH406 2.2 20.2 1.0
OE1 A:GLU70 2.2 16.4 1.0
O A:HOH403 2.2 21.7 1.0
O4 A:PO4301 2.4 17.9 1.0
P A:PO4301 2.8 21.7 1.0
CD A:GLU70 3.2 14.7 1.0
OE2 A:GLU70 3.6 13.4 1.0
O A:LEU42 3.8 15.5 1.0
O2 A:PO4301 3.8 17.7 1.0
NZ A:LYS36 3.8 15.8 1.0
O3 A:PO4301 3.9 20.2 1.0
O A:HOH456 3.9 23.9 1.0
MG A:MG302 4.0 20.0 1.0
O A:HOH401 4.0 15.8 1.0
O A:HOH404 4.0 18.6 1.0
OE2 A:GLU71 4.1 17.9 1.0
O A:HOH450 4.1 26.9 1.0
OD1 A:ASP41 4.1 26.8 1.0
OG1 A:THR93 4.2 12.5 1.0
CE A:LYS36 4.2 18.9 1.0
CG A:GLU70 4.5 14.0 1.0
O A:HOH402 4.6 13.8 1.0
CB A:THR93 4.7 12.2 1.0
O A:HOH408 4.8 23.1 1.0
C A:LEU42 5.0 18.4 1.0

Magnesium binding site 3 out of 4 in 4i3y

Go back to Magnesium Binding Sites List in 4i3y
Magnesium binding site 3 out of 4 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex


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 Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:12.3
occ:1.00
 OE2 B:GLU70 1.9 20.1 1.0
OD1 B:ASP88 2.0 13.5 1.0
O B:ILE90 2.0 13.3 1.0
O2 B:PO4302 2.1 15.0 1.0
O4 B:PO4302 2.3 16.2 1.0
O B:HOH406 2.3 14.3 1.0
P B:PO4302 2.7 17.2 1.0
CG B:ASP88 3.0 15.4 1.0
CD B:GLU70 3.1 19.4 1.0
C B:ILE90 3.2 13.0 1.0
OD2 B:ASP88 3.2 15.4 1.0
OE1 B:GLU70 3.7 19.4 1.0
O1 B:PO4302 3.7 15.8 1.0
CA B:ASP91 3.8 12.9 1.0
MG B:MG304 3.9 18.1 1.0
N B:ASP91 3.9 13.4 1.0
O3 B:PO4302 3.9 15.0 1.0
OG1 B:THR93 4.1 14.6 1.0
N B:ILE90 4.1 12.3 1.0
O B:HOH401 4.2 20.0 1.0
OD2 B:ASP47 4.2 17.8 1.0
CA B:ILE90 4.3 12.2 1.0
OE2 B:GLU71 4.3 22.2 1.0
CG B:GLU70 4.3 19.1 1.0
CB B:ASP88 4.4 14.7 1.0
CB B:GLU70 4.4 18.7 1.0
CD B:PRO89 4.5 13.8 1.0
O B:HOH404 4.5 20.8 1.0
CD1 B:TRP208 4.6 17.0 1.0
CB B:ASP91 4.7 12.8 1.0
N B:PRO89 4.7 14.8 1.0
CA B:ASP88 4.7 14.7 1.0
C B:ASP88 4.8 14.6 1.0
OD1 B:ASP91 4.8 13.2 1.0
NE1 B:TRP208 4.8 16.4 1.0
OD1 B:ASP209 4.8 16.9 1.0
C B:ASP91 4.9 12.8 1.0
N B:GLY92 4.9 12.5 1.0
CB B:ILE90 5.0 13.1 1.0

Magnesium binding site 4 out of 4 in 4i3y

Go back to Magnesium Binding Sites List in 4i3y
Magnesium binding site 4 out of 4 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex


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 Staphylococcal Inositol Monophosphatase-1: 100 Mm Licl Soaked Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:18.1
occ:1.00
 O B:HOH407 1.9 18.6 1.0
O B:HOH403 2.0 17.3 1.0
O1 B:PO4302 2.1 15.8 1.0
OE1 B:GLU70 2.2 19.4 1.0
O B:HOH404 2.2 20.8 1.0
O4 B:PO4302 2.2 16.2 1.0
P B:PO4302 2.7 17.2 1.0
CD B:GLU70 3.1 19.4 1.0
OE2 B:GLU70 3.4 20.1 1.0
O B:LEU42 3.7 14.3 1.0
O3 B:PO4302 3.8 15.0 1.0
O B:HOH460 3.8 28.4 1.0
O2 B:PO4302 3.8 15.0 1.0
O B:HOH401 3.9 20.0 1.0
MG B:MG301 3.9 12.3 1.0
NZ B:LYS36 4.0 19.8 1.0
OD1 B:ASP41 4.0 20.7 1.0
O B:HOH458 4.0 22.8 1.0
OG1 B:THR93 4.1 14.6 1.0
CE B:LYS36 4.2 20.4 1.0
OE2 B:GLU71 4.2 22.2 1.0
O B:HOH402 4.2 19.4 1.0
CG B:GLU70 4.4 19.1 1.0
O B:HOH406 4.4 14.3 1.0
CB B:THR93 4.7 14.1 1.0
C B:LEU42 4.9 17.9 1.0
O B:HOH457 5.0 18.2 1.0

Reference:

A.Dutta, S.Bhattacharyya, D.Dutta, A.K.Das. Structural Elucidation of the Binding Site and Mode of Inhibition of Li(+) and Mg(2+) in Inositol Monophosphatase Febs J. 2014.
ISSN: ISSN 1742-464X
PubMed: 25263816
DOI: 10.1111/FEBS.13070
Page generated: Fri Aug 16 16:33:25 2024

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