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Magnesium in PDB 4i40: Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex

Enzymatic activity of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex

All present enzymatic activity of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex, PDB code: 4i40 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) 19.74 / 2.50
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.977, 62.397, 140.638, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex (pdb code 4i40). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex, PDB code: 4i40:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4i40

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Magnesium binding site 1 out of 5 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited 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: 50MM Licl Inhibited Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:20.4
occ:1.00
 OE1 A:GLU70 2.1 14.0 1.0
O A:HOH402 2.1 29.2 1.0
O1 A:PO4303 2.2 18.8 1.0
O A:HOH401 2.4 15.1 1.0
O4 A:PO4303 2.9 19.7 1.0
P A:PO4303 3.1 21.1 1.0
CD A:GLU70 3.2 14.1 1.0
OE2 A:GLU70 3.7 13.9 1.0
NZ A:LYS36 3.7 25.4 1.0
O A:LEU42 3.8 23.4 1.0
OD1 A:ASP41 3.9 29.8 1.0
O A:HOH404 3.9 15.6 1.0
O A:HOH405 3.9 15.2 1.0
O3 A:PO4303 4.0 20.6 1.0
O2 A:PO4303 4.2 19.2 1.0
CE A:LYS36 4.2 26.4 1.0
MG A:MG302 4.3 8.5 1.0
OE2 A:GLU71 4.3 17.7 1.0
CG A:GLU70 4.3 14.7 1.0
OG1 A:THR93 4.6 11.0 1.0
O A:HOH403 4.7 7.9 1.0
O A:HOH458 4.7 8.7 1.0
CG A:ASP41 5.0 28.3 1.0
C A:LEU42 5.0 24.4 1.0

Magnesium binding site 2 out of 5 in 4i40

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Magnesium binding site 2 out of 5 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited 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: 50MM Licl Inhibited Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:8.5
occ:1.00
 OD1 A:ASP88 1.9 13.9 1.0
O A:ILE90 2.1 11.1 1.0
OE2 A:GLU70 2.1 13.9 1.0
O A:HOH403 2.2 7.9 1.0
O2 A:PO4303 2.3 19.2 1.0
O4 A:PO4303 2.4 19.7 1.0
P A:PO4303 2.8 21.1 1.0
CG A:ASP88 2.8 14.0 1.0
C A:ILE90 3.1 11.5 1.0
OD2 A:ASP88 3.1 13.3 1.0
CD A:GLU70 3.2 14.1 1.0
MG A:MG305 3.2 13.7 0.5
O1 A:PO4303 3.6 18.8 1.0
OE1 A:GLU70 3.7 14.0 1.0
N A:ASP91 3.7 11.4 1.0
CA A:ASP91 3.7 11.4 1.0
O3 A:PO4303 4.0 20.6 1.0
N A:ILE90 4.1 12.5 1.0
OG1 A:THR93 4.1 11.0 1.0
CA A:ILE90 4.2 12.0 1.0
CB A:ASP88 4.2 14.5 1.0
MG A:MG301 4.3 20.4 1.0
OE2 A:GLU71 4.3 17.7 1.0
OD2 A:ASP47 4.4 14.7 1.0
CG A:GLU70 4.4 14.7 1.0
O A:HOH405 4.5 15.2 1.0
CA A:ASP88 4.6 14.7 1.0
CB A:GLU70 4.6 14.7 1.0
CD A:PRO89 4.6 13.9 1.0
C A:ASP88 4.6 14.4 1.0
O A:HOH401 4.7 15.1 1.0
N A:PRO89 4.7 13.9 1.0
C A:ASP91 4.7 11.7 1.0
N A:GLY92 4.7 11.9 1.0
OD1 A:ASP91 4.7 10.5 1.0
CB A:ASP91 4.8 11.4 1.0
CD1 A:TRP208 4.8 12.7 1.0
CB A:ILE90 4.8 12.0 1.0
OD1 A:ASP209 4.8 11.7 1.0
NE1 A:TRP208 5.0 12.8 1.0

Magnesium binding site 3 out of 5 in 4i40

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Magnesium binding site 3 out of 5 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited 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: 50MM Licl Inhibited Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:13.7
occ:0.50
 O2 A:PO4303 1.7 19.2 1.0
OD2 A:ASP88 2.0 13.3 1.0
OD1 A:ASP209 2.0 11.7 1.0
OD1 A:ASP91 2.3 10.5 1.0
P A:PO4303 3.0 21.1 1.0
CG A:ASP88 3.1 14.0 1.0
CG A:ASP209 3.2 12.2 1.0
MG A:MG302 3.2 8.5 1.0
O A:HOH405 3.3 15.2 1.0
CG A:ASP91 3.4 11.2 1.0
O1 A:PO4303 3.4 18.8 1.0
OD1 A:ASP88 3.5 13.9 1.0
O2 A:GOL304 3.7 20.6 1.0
CA A:ASP91 3.7 11.4 1.0
O3 A:PO4303 3.8 20.6 1.0
OE2 A:GLU70 3.9 13.9 1.0
CB A:ASP91 3.9 11.4 1.0
CB A:ASP209 4.0 12.1 1.0
C1 A:GOL304 4.1 23.4 1.0
O4 A:PO4303 4.1 19.7 1.0
OD2 A:ASP209 4.1 12.6 1.0
CD1 A:TRP208 4.1 12.7 1.0
CA A:ASP209 4.1 12.3 1.0
N A:GLY92 4.4 11.9 1.0
CB A:ASP88 4.4 14.5 1.0
O A:ILE90 4.4 11.1 1.0
C2 A:GOL304 4.5 22.0 1.0
OD2 A:ASP91 4.5 11.0 1.0
NE1 A:TRP208 4.6 12.8 1.0
C A:ASP91 4.6 11.7 1.0
N A:ASP209 4.6 12.7 1.0
N A:ASP91 4.7 11.4 1.0
CD A:GLU70 4.7 14.1 1.0
O A:HOH404 4.8 15.6 1.0
OE1 A:GLU70 4.9 14.0 1.0
C A:ILE90 5.0 11.5 1.0

Magnesium binding site 4 out of 5 in 4i40

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Magnesium binding site 4 out of 5 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited 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: 50MM Licl Inhibited Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:25.4
occ:1.00
 O B:HOH403 1.7 23.9 1.0
O B:HOH402 2.2 20.0 1.0
OE1 B:GLU70 2.2 14.8 1.0
O4 B:PO4303 2.4 22.2 1.0
O1 B:PO4303 2.4 22.8 1.0
P B:PO4303 3.0 22.4 1.0
CD B:GLU70 3.3 15.5 1.0
O B:LEU42 3.5 25.3 1.0
OE2 B:GLU70 3.8 15.3 1.0
NZ B:LYS36 3.9 26.5 1.0
O2 B:PO4303 3.9 19.1 1.0
OD1 B:ASP41 4.0 20.4 1.0
MG B:MG302 4.1 16.1 1.0
OG1 B:THR93 4.1 11.9 1.0
O B:HOH408 4.1 19.7 1.0
O3 B:PO4303 4.2 23.3 1.0
CE B:LYS36 4.2 27.5 1.0
OE2 B:GLU71 4.3 16.4 1.0
O B:HOH407 4.3 20.3 1.0
O B:HOH401 4.5 11.5 1.0
CG B:GLU70 4.6 16.8 1.0
CB B:THR93 4.6 12.3 1.0
C B:LEU42 4.7 22.8 1.0
O B:HOH406 4.7 9.0 1.0

Magnesium binding site 5 out of 5 in 4i40

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Magnesium binding site 5 out of 5 in the Crystal Structure of Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex


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 Staphylococcal Inositol Monophosphatase-1: 50MM Licl Inhibited Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:16.1
occ:1.00
 OE2 B:GLU70 2.0 15.3 1.0
OD1 B:ASP88 2.1 17.2 1.0
O B:ILE90 2.1 14.6 1.0
O B:HOH401 2.1 11.5 1.0
O4 B:PO4303 2.2 22.2 1.0
O3 B:PO4303 2.2 23.3 1.0
P B:PO4303 2.7 22.4 1.0
CG B:ASP88 3.0 18.3 1.0
CD B:GLU70 3.1 15.5 1.0
C B:ILE90 3.1 14.9 1.0
OD2 B:ASP88 3.3 18.4 1.0
OE1 B:GLU70 3.5 14.8 1.0
O1 B:PO4303 3.6 22.8 1.0
N B:ASP91 3.8 15.2 1.0
O2 B:PO4303 3.8 19.1 1.0
CA B:ASP91 3.8 14.8 1.0
OG1 B:THR93 4.0 11.9 1.0
O B:HOH408 4.0 19.7 1.0
MG B:MG301 4.1 25.4 1.0
N B:ILE90 4.2 15.3 1.0
OD2 B:ASP47 4.2 21.8 1.0
OE2 B:GLU71 4.3 16.4 1.0
CA B:ILE90 4.3 14.4 1.0
CG B:GLU70 4.3 16.8 1.0
CB B:ASP88 4.4 18.5 1.0
CB B:GLU70 4.5 18.3 1.0
O B:HOH402 4.5 20.0 1.0
CD B:PRO89 4.6 16.6 1.0
CB B:ASP91 4.8 15.3 1.0
CA B:ASP88 4.8 18.5 1.0
CD1 B:TRP208 4.8 18.2 1.0
N B:PRO89 4.8 16.8 1.0
CB B:ILE90 4.9 14.3 1.0
C B:ASP88 4.9 17.9 1.0
C B:ASP91 4.9 15.0 1.0
OD1 B:ASP91 4.9 15.4 1.0
N B:GLY92 5.0 14.4 1.0
OD1 B:ASP209 5.0 14.0 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: Mon Dec 14 18:52:07 2020

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