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Magnesium in PDB 4g61: Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate

Enzymatic activity of Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate

All present enzymatic activity of Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate, PDB code: 4g61 was solved by S.Bhattacharyya, D.Dutta, A.K.Ghosh, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.67 / 2.30
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.709, 63.054, 141.617, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 25.5

Other elements in 4g61:

The structure of Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate (pdb code 4g61). 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate, PDB code: 4g61:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4g61

Go back to Magnesium Binding Sites List in 4g61
Magnesium binding site 1 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:22.9
occ:1.00
 O2 A:PO4303 1.9 19.3 1.0
OD1 A:ASP91 2.0 15.1 1.0
OD1 A:ASP209 2.1 12.5 1.0
O4 A:PO4303 2.1 15.4 1.0
OD2 A:ASP88 2.3 19.2 1.0
P A:PO4303 2.5 20.9 1.0
O A:HOH405 3.1 14.7 1.0
CG A:ASP91 3.2 13.4 1.0
CG A:ASP209 3.3 12.5 1.0
CG A:ASP88 3.4 16.5 1.0
O1 A:PO4303 3.5 14.8 1.0
O1 A:GOL305 3.6 33.6 1.0
O2 A:GOL305 3.7 37.5 1.0
MG A:MG302 3.7 15.1 1.0
O3 A:PO4303 3.7 16.6 1.0
OD1 A:ASP88 3.8 12.2 1.0
CA A:ASP91 3.8 12.1 1.0
CB A:ASP91 3.8 10.5 1.0
C1 A:GOL305 4.0 34.6 1.0
OD2 A:ASP209 4.0 13.3 1.0
OD2 A:ASP91 4.2 13.2 1.0
OE2 A:GLU70 4.2 10.5 1.0
CB A:ASP209 4.3 13.2 1.0
C2 A:GOL305 4.3 36.3 1.0
N A:GLY92 4.4 12.3 1.0
CD1 A:TRP208 4.4 8.4 1.0
CA A:ASP209 4.5 13.7 1.0
O A:ILE90 4.6 11.0 1.0
C A:ASP91 4.6 12.1 1.0
O A:HOH403 4.7 2.6 1.0
CB A:ASP88 4.7 15.3 1.0
NE1 A:TRP208 4.8 10.2 1.0
N A:ASP91 4.9 10.4 1.0
N A:ASP209 4.9 15.1 1.0
CD A:GLU70 4.9 14.1 1.0

Magnesium binding site 2 out of 6 in 4g61

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Magnesium binding site 2 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:15.1
occ:1.00
 O4 A:PO4303 1.9 15.4 1.0
OD1 A:ASP88 2.0 12.2 1.0
O A:ILE90 2.0 11.0 1.0
OE2 A:GLU70 2.0 10.5 1.0
O A:HOH401 2.2 5.8 1.0
O A:HOH403 2.3 2.6 1.0
CG A:ASP88 3.0 16.5 1.0
C A:ILE90 3.1 11.2 1.0
CD A:GLU70 3.1 14.1 1.0
P A:PO4303 3.2 20.9 1.0
OD2 A:ASP88 3.3 19.2 1.0
OE1 A:GLU70 3.6 10.8 1.0
O1 A:PO4303 3.7 14.8 1.0
MG A:MG301 3.7 22.9 1.0
N A:ASP91 3.8 10.4 1.0
O3 A:PO4303 3.8 16.6 1.0
CA A:ASP91 3.8 12.1 1.0
N A:ILE90 4.0 13.1 1.0
MG A:MG304 4.0 16.6 1.0
OE2 A:GLU71 4.1 14.8 1.0
OG1 A:THR93 4.1 12.9 1.0
CA A:ILE90 4.1 10.9 1.0
OD2 A:ASP47 4.2 13.9 1.0
CB A:ASP88 4.3 15.3 1.0
O A:HOH402 4.3 3.4 1.0
O2 A:PO4303 4.3 19.3 1.0
CG A:GLU70 4.4 14.1 1.0
CD A:PRO89 4.4 15.2 1.0
CB A:GLU70 4.5 15.2 1.0
N A:PRO89 4.5 16.0 1.0
CA A:ASP88 4.6 16.1 1.0
O A:HOH405 4.6 14.7 1.0
C A:ASP88 4.6 15.9 1.0
OD1 A:ASP91 4.7 15.1 1.0
CB A:ASP91 4.7 10.5 1.0
CB A:ILE90 4.8 11.1 1.0
C A:ASP91 4.9 12.1 1.0
CD1 A:TRP208 4.9 8.4 1.0
N A:GLY92 4.9 12.3 1.0
CG A:PRO89 4.9 15.3 1.0

Magnesium binding site 3 out of 6 in 4g61

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Magnesium binding site 3 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:16.6
occ:1.00
 O1 A:PO4303 1.9 14.8 1.0
O A:HOH407 2.1 18.6 1.0
O A:HOH402 2.1 3.4 1.0
O A:HOH404 2.2 13.1 1.0
OE1 A:GLU70 2.2 10.8 1.0
O A:HOH403 2.4 2.6 1.0
P A:PO4303 3.1 20.9 1.0
CD A:GLU70 3.3 14.1 1.0
O3 A:PO4303 3.5 16.6 1.0
OE2 A:GLU70 3.7 10.5 1.0
O4 A:PO4303 3.7 15.4 1.0
NZ A:LYS36 3.8 18.3 1.0
O A:LEU42 3.8 15.2 1.0
MG A:MG302 4.0 15.1 1.0
CE A:LYS36 4.1 21.6 1.0
OE2 A:GLU71 4.1 14.8 1.0
O A:HOH405 4.1 14.7 1.0
OG1 A:THR93 4.2 12.9 1.0
O A:HOH443 4.2 13.1 1.0
OD1 A:ASP41 4.2 18.1 1.0
O2 A:PO4303 4.3 19.3 1.0
CG A:GLU70 4.6 14.1 1.0
O A:HOH406 4.7 6.8 1.0
O A:HOH401 4.7 5.8 1.0
CB A:THR93 4.8 10.9 1.0

Magnesium binding site 4 out of 6 in 4g61

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Magnesium binding site 4 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:24.4
occ:1.00
 O1 B:PO4301 1.9 24.3 1.0
OD1 B:ASP209 1.9 16.1 1.0
OD1 B:ASP91 2.1 13.4 1.0
OD2 B:ASP88 2.2 17.5 1.0
O4 B:PO4301 2.6 24.9 1.0
P B:PO4301 2.8 25.1 1.0
O B:HOH473 3.1 17.5 1.0
CG B:ASP209 3.1 15.2 1.0
CG B:ASP91 3.2 11.2 1.0
O2 B:GOL305 3.3 38.4 1.0
CG B:ASP88 3.4 14.2 1.0
CB B:ASP91 3.7 11.6 1.0
CA B:ASP91 3.8 12.6 1.0
O1 B:GOL305 3.8 28.4 1.0
O3 B:PO4301 3.8 22.8 1.0
OD1 B:ASP88 3.8 14.3 1.0
MG B:MG303 3.9 19.4 1.0
OD2 B:ASP209 3.9 17.9 1.0
O2 B:PO4301 4.0 21.0 1.0
CB B:ASP209 4.1 13.4 1.0
OE2 B:GLU70 4.2 12.5 1.0
CA B:ASP209 4.3 13.5 1.0
OD2 B:ASP91 4.3 10.2 1.0
CD1 B:TRP208 4.3 12.2 1.0
C2 B:GOL305 4.4 38.0 1.0
N B:GLY92 4.6 12.1 1.0
CB B:ASP88 4.6 13.2 1.0
C B:ASP91 4.6 12.2 1.0
C1 B:GOL305 4.6 33.9 1.0
NE1 B:TRP208 4.6 11.4 1.0
O B:ILE90 4.7 12.0 1.0
O B:HOH406 4.7 6.0 1.0
N B:ASP209 4.8 14.1 1.0
O B:HOH474 4.8 24.1 1.0
N B:ASP91 4.8 12.7 1.0

Magnesium binding site 5 out of 6 in 4g61

Go back to Magnesium Binding Sites List in 4g61
Magnesium binding site 5 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:19.4
occ:1.00
 O4 B:PO4301 1.7 24.9 1.0
O B:ILE90 1.9 12.0 1.0
OE2 B:GLU70 2.0 12.5 1.0
OD1 B:ASP88 2.0 14.3 1.0
O B:HOH406 2.2 6.0 1.0
O B:HOH401 2.2 10.0 1.0
C B:ILE90 2.9 12.2 1.0
CG B:ASP88 3.1 14.2 1.0
P B:PO4301 3.1 25.1 1.0
CD B:GLU70 3.1 16.7 1.0
OD2 B:ASP88 3.4 17.5 1.0
N B:ASP91 3.7 12.7 1.0
O3 B:PO4301 3.7 22.8 1.0
OE1 B:GLU70 3.7 17.2 1.0
CA B:ASP91 3.7 12.6 1.0
O2 B:PO4301 3.8 21.0 1.0
N B:ILE90 3.9 12.1 1.0
MG B:MG304 3.9 22.0 1.0
MG B:MG302 3.9 24.4 1.0
CA B:ILE90 4.0 11.7 1.0
OG1 B:THR93 4.0 14.1 1.0
O1 B:PO4301 4.1 24.3 1.0
OD2 B:ASP47 4.2 19.4 1.0
CG B:GLU70 4.3 15.8 1.0
OE2 B:GLU71 4.3 18.0 1.0
CD B:PRO89 4.3 13.1 1.0
O B:HOH473 4.3 17.5 1.0
CB B:ASP88 4.4 13.2 1.0
N B:PRO89 4.5 13.2 1.0
O B:HOH405 4.5 8.9 1.0
CB B:GLU70 4.5 16.3 1.0
C B:ASP88 4.6 13.6 1.0
CB B:ASP91 4.6 11.6 1.0
CA B:ASP88 4.7 14.3 1.0
CB B:ILE90 4.7 11.2 1.0
C B:ASP91 4.9 12.2 1.0
CG B:PRO89 4.9 14.2 1.0
CD1 B:TRP208 5.0 12.2 1.0
N B:GLY92 5.0 12.1 1.0
OD1 B:ASP91 5.0 13.4 1.0

Magnesium binding site 6 out of 6 in 4g61

Go back to Magnesium Binding Sites List in 4g61
Magnesium binding site 6 out of 6 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with MG2+ 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 Impase/Nadp Phosphatase Complexed with MG2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:22.0
occ:1.00
 O3 B:PO4301 1.8 22.8 1.0
O B:HOH404 2.0 13.2 1.0
O B:HOH403 2.1 9.6 1.0
O B:HOH405 2.1 8.9 1.0
OE1 B:GLU70 2.1 17.2 1.0
O B:HOH406 2.2 6.0 1.0
P B:PO4301 3.0 25.1 1.0
CD B:GLU70 3.1 16.7 1.0
O4 B:PO4301 3.4 24.9 1.0
OE2 B:GLU70 3.4 12.5 1.0
O2 B:PO4301 3.6 21.0 1.0
O B:HOH473 3.7 17.5 1.0
NZ B:LYS36 3.8 24.8 1.0
O B:HOH474 3.9 24.1 1.0
MG B:MG303 3.9 19.4 1.0
O B:LEU42 3.9 17.3 1.0
OD1 B:ASP41 4.0 19.9 1.0
OE2 B:GLU71 4.1 18.0 1.0
OG1 B:THR93 4.3 14.1 1.0
O1 B:PO4301 4.3 24.3 1.0
O B:HOH401 4.3 10.0 1.0
CE B:LYS36 4.3 25.8 1.0
CG B:GLU70 4.4 15.8 1.0
O B:HOH402 4.7 9.7 1.0
CB B:THR93 4.7 10.5 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 15:23:13 2024

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