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Magnesium in PDB 4ptk: Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate, PDB code: 4ptk 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) 46.72 / 2.50
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.428, 62.455, 140.497, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate (pdb code 4ptk). 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 Staphylococcal Impase-I Complex with 3MG2+ and Phosphate, PDB code: 4ptk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4ptk

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Magnesium binding site 1 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:20.0
occ:1.00
 O1 A:PO4301 1.7 24.7 1.0
OD1 A:ASP209 2.0 20.0 1.0
OD2 A:ASP88 2.0 15.5 1.0
OD1 A:ASP91 2.0 17.9 1.0
O2 A:GOL305 2.7 36.0 1.0
O A:HOH442 2.9 29.9 1.0
P A:PO4301 3.1 26.8 1.0
CG A:ASP88 3.2 18.0 1.0
CG A:ASP209 3.2 19.0 1.0
CG A:ASP91 3.2 17.2 1.0
MG A:MG303 3.4 18.7 1.0
O2 A:PO4301 3.4 25.8 1.0
OD1 A:ASP88 3.7 20.0 1.0
O3 A:GOL305 3.7 31.0 1.0
C2 A:GOL305 3.8 35.2 1.0
CA A:ASP91 3.8 15.9 1.0
CB A:ASP91 3.9 16.2 1.0
OD2 A:ASP209 3.9 19.8 1.0
O3 A:PO4301 4.0 24.9 1.0
O4 A:PO4301 4.1 23.9 1.0
CB A:ASP209 4.2 18.8 1.0
C3 A:GOL305 4.2 32.2 1.0
OD2 A:ASP91 4.3 16.2 1.0
OE2 A:GLU70 4.3 16.1 1.0
CD1 A:TRP208 4.3 19.1 1.0
CA A:ASP209 4.4 18.5 1.0
CB A:ASP88 4.4 17.5 1.0
N A:GLY92 4.5 15.2 1.0
NE1 A:TRP208 4.6 19.8 1.0
O A:ILE90 4.6 16.1 1.0
C A:ASP91 4.7 15.3 1.0
N A:ASP91 4.9 16.2 1.0
N A:ASP209 4.9 17.9 1.0
CD A:GLU70 5.0 15.9 1.0

Magnesium binding site 2 out of 6 in 4ptk

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Magnesium binding site 2 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:18.7
occ:1.00
 OD1 A:ASP88 2.0 20.0 1.0
O4 A:PO4301 2.2 23.9 1.0
OE2 A:GLU70 2.2 16.1 1.0
O A:ILE90 2.3 16.1 1.0
O A:HOH401 2.4 11.9 1.0
O1 A:PO4301 2.6 24.7 1.0
P A:PO4301 2.7 26.8 1.0
CG A:ASP88 2.8 18.0 1.0
OD2 A:ASP88 3.0 15.5 1.0
CD A:GLU70 3.1 15.9 1.0
C A:ILE90 3.3 16.6 1.0
MG A:MG302 3.4 20.0 1.0
OE1 A:GLU70 3.5 14.9 1.0
O2 A:PO4301 3.5 25.8 1.0
CA A:ASP91 3.8 15.9 1.0
N A:ASP91 3.9 16.2 1.0
MG A:MG304 4.0 25.6 1.0
O3 A:PO4301 4.0 24.9 1.0
O A:HOH442 4.1 29.9 1.0
OG1 A:THR93 4.2 12.5 1.0
CB A:ASP88 4.2 17.5 1.0
N A:ILE90 4.3 18.8 1.0
CA A:ILE90 4.4 17.5 1.0
OE2 A:GLU71 4.4 23.2 1.0
CG A:GLU70 4.5 17.0 1.0
OD1 A:ASP91 4.5 17.9 1.0
CA A:ASP88 4.6 17.9 1.0
OD2 A:ASP47 4.6 20.8 1.0
O A:HOH440 4.7 26.2 1.0
CB A:GLU70 4.7 18.2 1.0
N A:GLY92 4.8 15.2 1.0
CB A:ASP91 4.8 16.2 1.0
C A:ASP88 4.8 19.3 1.0
C A:ASP91 4.8 15.3 1.0
CD A:PRO89 4.8 19.2 1.0
CD1 A:TRP208 4.9 19.1 1.0
N A:PRO89 4.9 18.9 1.0
CB A:ILE90 5.0 17.7 1.0
NE1 A:TRP208 5.0 19.8 1.0

Magnesium binding site 3 out of 6 in 4ptk

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Magnesium binding site 3 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:25.6
occ:1.00
 O A:HOH418 2.0 42.0 1.0
O2 A:PO4301 2.2 25.8 1.0
OE1 A:GLU70 2.2 14.9 1.0
O A:HOH440 2.5 26.2 1.0
O4 A:PO4301 2.6 23.9 1.0
P A:PO4301 2.9 26.8 1.0
CD A:GLU70 3.4 15.9 1.0
O3 A:PO4301 3.8 24.9 1.0
OE2 A:GLU70 3.9 16.1 1.0
O A:LEU42 3.9 25.9 1.0
MG A:MG303 4.0 18.7 1.0
OD1 A:ASP41 4.0 32.0 1.0
O A:HOH431 4.1 26.0 1.0
NZ A:LYS36 4.1 27.3 1.0
O1 A:PO4301 4.2 24.7 1.0
OE2 A:GLU71 4.2 23.2 1.0
O A:HOH442 4.3 29.9 1.0
OG1 A:THR93 4.3 12.5 1.0
CE A:LYS36 4.4 29.8 1.0
CG A:GLU70 4.5 17.0 1.0
O A:HOH401 4.7 11.9 1.0
CB A:THR93 4.9 12.9 1.0

Magnesium binding site 4 out of 6 in 4ptk

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Magnesium binding site 4 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:25.9
occ:1.00
 OE2 B:GLU70 1.9 20.3 1.0
OD1 B:ASP88 2.0 21.2 1.0
O B:ILE90 2.1 15.8 1.0
O B:HOH427 2.2 22.5 1.0
O4 B:PO4303 2.3 26.1 1.0
O3 B:PO4303 2.3 26.0 1.0
P B:PO4303 2.8 25.6 1.0
CD B:GLU70 2.9 20.4 1.0
CG B:ASP88 3.0 22.7 1.0
C B:ILE90 3.1 17.8 1.0
OD2 B:ASP88 3.3 22.8 1.0
MG B:MG304 3.3 33.0 1.0
OE1 B:GLU70 3.4 22.2 1.0
O1 B:PO4303 3.7 23.3 1.0
N B:ASP91 3.7 18.6 1.0
CA B:ASP91 3.8 19.3 1.0
O2 B:PO4303 3.9 21.4 1.0
MG B:MG302 4.1 27.3 1.0
OG1 B:THR93 4.1 16.3 1.0
CG B:GLU70 4.2 20.0 1.0
N B:ILE90 4.3 20.0 1.0
CA B:ILE90 4.3 17.6 1.0
CB B:ASP88 4.3 22.8 1.0
OD2 B:ASP47 4.4 22.9 1.0
OE2 B:GLU71 4.4 22.1 1.0
CB B:GLU70 4.4 21.0 1.0
CD B:PRO89 4.6 21.2 1.0
CA B:ASP88 4.6 22.7 1.0
O B:HOH428 4.6 25.9 1.0
CB B:ASP91 4.7 20.4 1.0
OD1 B:ASP91 4.7 21.3 1.0
N B:PRO89 4.7 20.5 1.0
C B:ASP88 4.7 22.3 1.0
C B:ASP91 4.9 19.7 1.0
CD1 B:TRP208 4.9 23.3 1.0
N B:GLY92 4.9 20.8 1.0
CB B:ILE90 4.9 18.1 1.0
CG B:PRO89 5.0 21.2 1.0
O1 B:GOL305 5.0 39.3 1.0

Magnesium binding site 5 out of 6 in 4ptk

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Magnesium binding site 5 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:27.3
occ:1.00
 O B:HOH429 1.8 21.8 1.0
OE1 B:GLU70 2.1 22.2 1.0
O B:HOH430 2.1 33.2 1.0
O B:HOH428 2.3 25.9 1.0
O1 B:PO4303 2.4 23.3 1.0
O4 B:PO4303 2.5 26.1 1.0
P B:PO4303 2.9 25.6 1.0
CD B:GLU70 3.2 20.4 1.0
O B:HOH424 3.4 32.0 1.0
OE2 B:GLU70 3.7 20.3 1.0
O B:LEU42 3.8 22.8 1.0
OD1 B:ASP41 3.9 27.4 1.0
O2 B:PO4303 3.9 21.4 1.0
NZ B:LYS36 4.1 28.1 1.0
MG B:MG301 4.1 25.9 1.0
O3 B:PO4303 4.1 26.0 1.0
OG1 B:THR93 4.4 16.3 1.0
O B:HOH427 4.4 22.5 1.0
OE2 B:GLU71 4.4 22.1 1.0
CE B:LYS36 4.4 29.1 1.0
CG B:GLU70 4.4 20.0 1.0
CB B:THR93 4.9 15.8 1.0
MG B:MG304 4.9 33.0 1.0
C B:LEU42 5.0 24.5 1.0

Magnesium binding site 6 out of 6 in 4ptk

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Magnesium binding site 6 out of 6 in the Crystal Structure of Staphylococcal Impase-I Complex with 3MG2+ and Phosphate


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 Staphylococcal Impase-I Complex with 3MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:33.0
occ:1.00
 O3 B:PO4303 1.6 26.0 1.0
OD1 B:ASP209 2.1 20.8 1.0
OD2 B:ASP88 2.3 22.8 1.0
O1 B:GOL305 2.3 39.3 1.0
OD1 B:ASP91 2.4 21.3 1.0
P B:PO4303 2.8 25.6 1.0
O1 B:PO4303 3.0 23.3 1.0
CG B:ASP88 3.3 22.7 1.0
CG B:ASP209 3.3 19.4 1.0
MG B:MG301 3.3 25.9 1.0
CG B:ASP91 3.5 20.6 1.0
OD1 B:ASP88 3.6 21.2 1.0
C1 B:GOL305 3.6 37.8 1.0
O2 B:PO4303 3.7 21.4 1.0
OE2 B:GLU70 3.8 20.3 1.0
CA B:ASP91 3.9 19.3 1.0
O4 B:PO4303 3.9 26.1 1.0
OD2 B:ASP209 4.0 19.0 1.0
O2 B:GOL305 4.0 33.5 1.0
CB B:ASP91 4.0 20.4 1.0
CD1 B:TRP208 4.1 23.3 1.0
NE1 B:TRP208 4.4 23.8 1.0
C2 B:GOL305 4.4 37.6 1.0
CB B:ASP209 4.4 19.6 1.0
CD B:GLU70 4.5 20.4 1.0
O B:ILE90 4.5 15.8 1.0
OD2 B:ASP91 4.6 20.0 1.0
CB B:ASP88 4.6 22.8 1.0
N B:GLY92 4.6 20.8 1.0
OE1 B:GLU70 4.6 22.2 1.0
CA B:ASP209 4.6 19.3 1.0
C B:ASP91 4.8 19.7 1.0
N B:ASP91 4.9 18.6 1.0
MG B:MG302 4.9 27.3 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 Aug 11 22:08:38 2025

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