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Magnesium in PDB 9mmi: Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis

Enzymatic activity of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis

All present enzymatic activity of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis:
3.1.3.11; 3.1.3.25;

Protein crystallography data

The structure of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis, PDB code: 9mmi was solved by Z.A.Hoffpauir, K.M.Meneely, A.L.Lamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.68 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.19, 72.914, 119.245, 90, 90.03, 90
R / Rfree (%) 18.2 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis (pdb code 9mmi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis, PDB code: 9mmi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9mmi

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Magnesium binding site 1 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:14.9
occ:1.00
 OE1 A:GLU70 2.3 24.7 1.0
OD1 A:ASP86 2.3 19.9 1.0
O4 A:PO4307 2.4 23.1 1.0
O A:HOH416 2.4 19.9 1.0
O3 A:PO4307 2.4 23.8 1.0
O A:LEU88 2.5 17.8 1.0
OD2 A:ASP86 2.9 18.8 1.0
P A:PO4307 2.9 32.5 1.0
CG A:ASP86 3.0 20.2 1.0
CD A:GLU70 3.3 28.2 1.0
C A:LEU88 3.4 19.9 1.0
HA A:ASP89 3.4 21.5 1.0
HG1 A:THR91 3.5 25.9 1.0
H A:LEU88 3.5 18.3 1.0
MG A:MG306 3.7 20.4 1.0
HD2 A:PRO87 3.8 21.5 1.0
OE2 A:GLU70 3.9 30.0 1.0
OG1 A:THR91 4.0 21.5 1.0
O2 A:PO4307 4.0 25.1 1.0
N A:ASP89 4.1 16.2 1.0
CA A:ASP89 4.1 17.9 1.0
O1 A:PO4307 4.1 31.8 1.0
O A:HOH454 4.1 30.5 1.0
HB3 A:LEU88 4.2 21.5 1.0
N A:LEU88 4.2 15.5 1.0
OE2 A:GLU71 4.2 26.3 1.0
CA A:LEU88 4.3 15.3 1.0
HB3 A:GLU70 4.3 27.2 1.0
CB A:ASP86 4.5 18.9 1.0
HG2 A:PRO87 4.5 24.1 1.0
CG A:GLU70 4.5 23.9 1.0
O A:HOH412 4.6 31.6 1.0
H A:GLY90 4.6 20.8 1.0
OD2 A:ASP47 4.6 25.7 1.0
HA A:ASP86 4.6 18.5 1.0
HB2 A:GLU70 4.6 27.2 1.0
CD A:PRO87 4.7 17.9 1.0
CB A:GLU70 4.7 22.6 1.0
CB A:LEU88 4.7 17.9 1.0
H A:THR91 4.7 20.5 1.0
HB2 A:ASP89 4.8 19.5 1.0
HG A:LEU88 4.8 26.0 1.0
H A:ASP89 4.8 19.5 1.0
HG2 A:GLU70 4.8 28.8 1.0
HB2 A:ASP86 4.9 22.7 1.0
HD1 A:TRP213 4.9 25.8 1.0
CA A:ASP86 5.0 15.6 1.0
HB3 A:ASP86 5.0 22.7 1.0

Magnesium binding site 2 out of 8 in 9mmi

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Magnesium binding site 2 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:20.4
occ:1.00
 O3 A:PO4307 2.1 23.8 1.0
OD1 A:ASP214 2.2 26.4 1.0
OD2 A:ASP86 2.3 18.8 1.0
OD1 A:ASP89 2.3 26.9 1.0
O A:HOH454 2.9 30.5 1.0
HA A:ASP89 3.2 21.5 1.0
CG A:ASP214 3.4 27.2 1.0
CG A:ASP89 3.4 20.3 1.0
CG A:ASP86 3.5 20.2 1.0
P A:PO4307 3.5 32.5 1.0
O A:HOH411 3.6 27.5 1.0
MG A:MG305 3.7 14.9 1.0
HB2 A:ASP89 3.8 19.5 1.0
HA A:ASP214 3.8 24.3 1.0
HD1 A:TRP213 3.9 25.8 1.0
CB A:ASP89 3.9 16.2 1.0
CA A:ASP89 4.0 17.9 1.0
O1 A:PO4307 4.1 31.8 1.0
O2 A:PO4307 4.1 25.1 1.0
OD2 A:ASP214 4.2 21.2 1.0
OD1 A:ASP86 4.2 19.9 1.0
H A:GLY90 4.2 20.8 1.0
OE1 A:GLU70 4.2 24.7 1.0
CB A:ASP214 4.3 23.1 1.0
HB3 A:ASP214 4.4 27.8 1.0
HB2 A:ASP86 4.4 22.7 1.0
OD2 A:ASP89 4.5 26.4 1.0
CA A:ASP214 4.5 20.2 1.0
CB A:ASP86 4.5 18.9 1.0
HE1 A:TRP213 4.6 28.3 1.0
O4 A:PO4307 4.7 23.1 1.0
CD1 A:TRP213 4.7 21.4 1.0
HB3 A:ALA190 4.8 27.4 1.0
HB3 A:ASP86 4.8 22.7 1.0
N A:GLY90 4.9 17.3 1.0
HB3 A:ASP89 4.9 19.5 1.0
O A:LEU88 4.9 17.8 1.0
C A:ASP89 5.0 19.1 1.0
H A:ALA190 5.0 21.8 1.0
N A:ASP89 5.0 16.2 1.0

Magnesium binding site 3 out of 8 in 9mmi

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Magnesium binding site 3 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:15.1
occ:1.00
 OE1 B:GLU70 2.3 24.4 1.0
OD1 B:ASP86 2.3 20.2 1.0
O B:LEU88 2.4 18.5 1.0
O4 B:PO4307 2.4 25.5 1.0
O3 B:PO4307 2.4 24.5 1.0
O B:HOH427 2.5 20.4 1.0
OD2 B:ASP86 2.9 19.3 1.0
P B:PO4307 3.0 32.0 1.0
CG B:ASP86 3.0 19.8 1.0
CD B:GLU70 3.3 29.4 1.0
C B:LEU88 3.4 19.3 1.0
HA B:ASP89 3.4 22.2 1.0
H B:LEU88 3.5 19.1 1.0
HD2 B:PRO87 3.7 23.6 1.0
MG B:MG306 3.7 20.7 1.0
HG1 B:THR91 3.9 25.3 1.0
OE2 B:GLU70 3.9 29.9 1.0
OG1 B:THR91 4.0 21.0 1.0
N B:ASP89 4.1 16.7 1.0
O2 B:PO4307 4.1 24.7 1.0
O B:HOH457 4.1 31.8 1.0
CA B:ASP89 4.1 18.5 1.0
O1 B:PO4307 4.2 32.0 1.0
N B:LEU88 4.2 15.8 1.0
OE2 B:GLU71 4.2 27.3 1.0
HB3 B:LEU88 4.3 21.7 1.0
HB3 B:GLU70 4.3 27.7 1.0
CA B:LEU88 4.3 16.5 1.0
CB B:ASP86 4.4 17.5 1.0
CG B:GLU70 4.5 22.7 1.0
HG2 B:PRO87 4.5 24.4 1.0
HA B:ASP86 4.5 20.0 1.0
H B:GLY90 4.5 20.7 1.0
OD2 B:ASP47 4.6 25.2 1.0
O B:HOH413 4.6 31.9 1.0
HB2 B:GLU70 4.6 27.7 1.0
CD B:PRO87 4.6 19.6 1.0
H B:THR91 4.7 19.5 1.0
CB B:GLU70 4.7 23.1 1.0
HG B:LEU88 4.7 28.1 1.0
HG2 B:GLU70 4.8 27.3 1.0
CB B:LEU88 4.8 18.1 1.0
H B:ASP89 4.8 20.1 1.0
HB2 B:ASP89 4.8 20.9 1.0
HB2 B:ASP86 4.9 21.1 1.0
CA B:ASP86 4.9 16.6 1.0
HD1 B:TRP213 4.9 26.1 1.0
HB3 B:ASP86 5.0 21.1 1.0
N B:PRO87 5.0 17.7 1.0

Magnesium binding site 4 out of 8 in 9mmi

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Magnesium binding site 4 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:20.7
occ:1.00
 O3 B:PO4307 2.1 24.5 1.0
OD1 B:ASP214 2.2 26.1 1.0
OD2 B:ASP86 2.3 19.3 1.0
OD1 B:ASP89 2.3 24.9 1.0
O B:HOH457 2.9 31.8 1.0
HA B:ASP89 3.2 22.2 1.0
CG B:ASP214 3.4 27.9 1.0
CG B:ASP89 3.4 20.8 1.0
CG B:ASP86 3.5 19.8 1.0
P B:PO4307 3.5 32.0 1.0
O B:HOH428 3.7 29.6 1.0
MG B:MG305 3.7 15.1 1.0
HA B:ASP214 3.8 24.2 1.0
HB2 B:ASP89 3.8 20.9 1.0
HD1 B:TRP213 3.9 26.1 1.0
CB B:ASP89 4.0 17.4 1.0
CA B:ASP89 4.0 18.5 1.0
O1 B:PO4307 4.1 32.0 1.0
O2 B:PO4307 4.1 24.7 1.0
OD2 B:ASP214 4.2 21.5 1.0
OD1 B:ASP86 4.2 20.2 1.0
H B:GLY90 4.2 20.7 1.0
OE1 B:GLU70 4.2 24.4 1.0
CB B:ASP214 4.3 22.8 1.0
HB3 B:ASP214 4.4 27.4 1.0
HB2 B:ASP86 4.4 21.1 1.0
OD2 B:ASP89 4.5 25.8 1.0
CA B:ASP214 4.5 20.1 1.0
CB B:ASP86 4.5 17.5 1.0
HE1 B:TRP213 4.6 28.6 1.0
O4 B:PO4307 4.6 25.5 1.0
CD1 B:TRP213 4.7 21.7 1.0
HB3 B:ALA190 4.7 28.4 1.0
HB3 B:ASP86 4.8 21.1 1.0
O B:LEU88 4.8 18.5 1.0
N B:GLY90 4.9 17.2 1.0
HB3 B:ASP89 4.9 20.9 1.0
C B:ASP89 5.0 19.4 1.0
H B:ALA190 5.0 22.4 1.0

Magnesium binding site 5 out of 8 in 9mmi

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Magnesium binding site 5 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.4
occ:1.00
 OD2 C:ASP86 2.4 46.1 1.0
OD1 C:ASP214 2.6 52.9 1.0
OD1 C:ASP89 2.6 47.4 1.0
O C:HOH426 2.6 41.5 1.0
HA C:ASP89 3.1 49.1 1.0
MG C:MG303 3.4 40.0 1.0
CG C:ASP86 3.6 45.8 1.0
CG C:ASP89 3.6 42.8 1.0
O C:HOH405 3.7 47.3 1.0
CG C:ASP214 3.7 48.0 1.0
OE1 C:GLU70 3.9 54.4 1.0
CA C:ASP89 3.9 40.9 1.0
HB2 C:ASP89 3.9 47.4 1.0
H C:GLY90 4.0 46.7 1.0
CB C:ASP89 4.1 39.4 1.0
HD1 C:TRP213 4.2 58.7 1.0
OD1 C:ASP86 4.2 39.1 1.0
OD2 C:ASP214 4.4 50.5 1.0
HA C:ASP214 4.4 57.2 1.0
O C:LEU88 4.5 40.8 1.0
HE1 C:TRP213 4.5 62.1 1.0
N C:GLY90 4.6 38.9 1.0
CD C:GLU70 4.6 55.4 1.0
OE2 C:GLU70 4.6 60.4 1.0
HB2 C:ASP86 4.7 52.6 1.0
OD2 C:ASP89 4.7 47.4 1.0
CB C:ASP86 4.8 43.8 1.0
C C:ASP89 4.8 40.7 1.0
CD1 C:TRP213 4.9 48.9 1.0
N C:ASP89 4.9 39.5 1.0
CB C:ASP214 4.9 47.7 1.0

Magnesium binding site 6 out of 8 in 9mmi

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Magnesium binding site 6 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:40.0
occ:1.00
 OE1 C:GLU70 2.1 54.4 1.0
O C:LEU88 2.3 40.8 1.0
OD1 C:ASP86 2.4 39.1 1.0
O C:HOH403 2.5 44.4 1.0
OD2 C:ASP86 2.9 46.1 1.0
CG C:ASP86 2.9 45.8 1.0
O C:HOH426 3.0 41.5 1.0
CD C:GLU70 3.2 55.4 1.0
HA C:ASP89 3.3 49.1 1.0
C C:LEU88 3.3 39.9 1.0
MG C:MG302 3.4 45.4 1.0
H C:LEU88 3.4 43.8 1.0
OE2 C:GLU70 3.6 60.4 1.0
HD2 C:PRO87 3.8 49.8 1.0
HG1 C:THR91 4.0 52.9 1.0
N C:ASP89 4.0 39.5 1.0
CA C:ASP89 4.1 40.9 1.0
N C:LEU88 4.1 36.4 1.0
OG1 C:THR91 4.1 44.0 1.0
OE2 C:GLU71 4.2 60.4 1.0
HB3 C:GLU70 4.3 64.1 1.0
HB3 C:LEU88 4.3 46.5 1.0
CA C:LEU88 4.3 34.6 1.0
CB C:ASP86 4.4 43.8 1.0
CG C:GLU70 4.4 55.3 1.0
HG2 C:PRO87 4.5 46.7 1.0
H C:GLY90 4.5 46.7 1.0
HB2 C:GLU70 4.5 64.1 1.0
HA C:ASP86 4.6 47.2 1.0
OD2 C:ASP47 4.6 50.6 1.0
CB C:GLU70 4.6 53.4 1.0
CD C:PRO87 4.7 41.4 1.0
HB2 C:ASP89 4.7 47.4 1.0
HG2 C:GLU70 4.7 66.5 1.0
H C:ASP89 4.8 47.5 1.0
CB C:LEU88 4.8 38.7 1.0
HB2 C:ASP86 4.8 52.6 1.0
HG C:LEU88 4.9 53.8 1.0
HD1 C:TRP213 4.9 58.7 1.0
HB3 C:ASP86 4.9 52.6 1.0
CA C:ASP86 4.9 39.3 1.0
H C:THR91 4.9 49.7 1.0
CB C:ASP89 4.9 39.4 1.0
N C:PRO87 5.0 39.6 1.0

Magnesium binding site 7 out of 8 in 9mmi

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Magnesium binding site 7 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:46.9
occ:1.00
 O D:HOH431 2.4 41.4 1.0
OD2 D:ASP86 2.6 47.2 1.0
OD1 D:ASP89 2.7 45.6 1.0
OD1 D:ASP214 2.8 56.2 1.0
HA D:ASP89 2.9 47.6 1.0
MG D:MG302 3.1 39.8 1.0
H D:GLY90 3.7 45.8 1.0
CG D:ASP89 3.7 45.6 1.0
CG D:ASP86 3.7 44.8 1.0
OE1 D:GLU70 3.8 55.6 1.0
CA D:ASP89 3.8 39.6 1.0
CG D:ASP214 3.9 50.0 1.0
HB2 D:ASP89 4.2 48.6 1.0
CB D:ASP89 4.2 40.4 1.0
OD1 D:ASP86 4.2 39.2 1.0
O D:LEU88 4.2 41.4 1.0
OD2 D:ASP214 4.3 59.7 1.0
N D:GLY90 4.4 38.1 1.0
HD1 D:TRP213 4.4 56.5 1.0
OE2 D:GLU70 4.6 63.2 1.0
HE1 D:TRP213 4.6 60.7 1.0
CD D:GLU70 4.6 57.4 1.0
C D:ASP89 4.7 41.2 1.0
HA D:ASP214 4.7 58.3 1.0
N D:ASP89 4.8 39.6 1.0
OD2 D:ASP89 4.8 49.0 1.0
C D:LEU88 4.9 40.4 1.0
HB2 D:ASP86 5.0 50.4 1.0
CB D:ASP86 5.0 41.9 1.0

Magnesium binding site 8 out of 8 in 9mmi

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Magnesium binding site 8 out of 8 in the Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Myo-Inositol-1(or 4)-Monophosphatase That Can Perform Essential Dephosphorylation Step to Facilitate Riboflavin Biosynthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.8
occ:1.00
 OD1 D:ASP86 2.3 39.2 1.0
O D:LEU88 2.3 41.4 1.0
O D:HOH410 2.5 44.3 1.0
OE1 D:GLU70 2.6 55.6 1.0
OD2 D:ASP86 2.8 47.2 1.0
CG D:ASP86 2.9 44.8 1.0
O D:HOH431 3.1 41.4 1.0
MG D:MG301 3.1 46.9 1.0
HA D:ASP89 3.3 47.6 1.0
C D:LEU88 3.3 40.4 1.0
CD D:GLU70 3.4 57.4 1.0
H D:LEU88 3.4 42.5 1.0
OE2 D:GLU70 3.7 63.2 1.0
HD2 D:PRO87 3.8 48.6 1.0
HG1 D:THR91 3.9 54.8 1.0
N D:ASP89 4.0 39.6 1.0
CA D:ASP89 4.1 39.6 1.0
OG1 D:THR91 4.1 45.6 1.0
N D:LEU88 4.1 35.4 1.0
CA D:LEU88 4.3 37.0 1.0
OE2 D:GLU71 4.3 55.5 1.0
HB3 D:LEU88 4.3 45.5 1.0
CB D:ASP86 4.4 41.9 1.0
HB3 D:GLU70 4.5 63.2 1.0
OD2 D:ASP47 4.5 50.5 1.0
HG2 D:PRO87 4.5 47.1 1.0
H D:GLY90 4.5 45.8 1.0
HA D:ASP86 4.5 47.1 1.0
CG D:GLU70 4.6 59.0 1.0
CD D:PRO87 4.7 40.4 1.0
HB2 D:ASP89 4.7 48.6 1.0
HB2 D:GLU70 4.8 63.2 1.0
H D:ASP89 4.8 47.6 1.0
HB2 D:ASP86 4.8 50.4 1.0
CB D:LEU88 4.8 37.9 1.0
HD1 D:TRP213 4.8 56.5 1.0
HG D:LEU88 4.9 54.1 1.0
H D:THR91 4.9 50.2 1.0
CB D:GLU70 4.9 52.6 1.0
HG2 D:GLU70 4.9 70.9 1.0
CA D:ASP86 4.9 39.2 1.0
HB3 D:ASP86 4.9 50.4 1.0
CB D:ASP89 4.9 40.4 1.0
HE1 D:TRP213 4.9 60.7 1.0
OD1 D:ASP89 5.0 45.6 1.0
N D:PRO87 5.0 37.7 1.0

Reference:

Z.A.Hoffpauir, A.L.Lamb. Identification of the Phosphatase Essential For Riboflavin Biosynthesis in Aquifex Aeolicus. J.Biol.Chem. 08443 2025.
ISSN: ESSN 1083-351X
PubMed: 40147773
DOI: 10.1016/J.JBC.2025.108443
Page generated: Sat Aug 16 06:28:47 2025

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