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Magnesium in PDB 8qqt: Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed

Enzymatic activity of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed

All present enzymatic activity of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed:
1.1.1.205;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed (pdb code 8qqt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed, PDB code: 8qqt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 8qqt

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Magnesium binding site 1 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:45.4
occ:1.00
 OE2 A:GLU200 2.0 47.7 1.0
O3D A:G4P601 2.1 57.7 1.0
O2G A:ATP600 2.1 51.1 1.0
O3G E:ATP600 2.3 48.8 1.0
CD A:GLU200 2.8 41.9 1.0
OE1 A:GLU200 3.0 41.4 1.0
MG A:MG603 3.1 41.5 1.0
PG A:ATP600 3.3 38.4 1.0
PG E:ATP600 3.4 43.1 1.0
PD A:G4P601 3.6 49.7 1.0
O3G A:ATP600 3.7 46.2 1.0
O2G E:ATP600 3.8 52.9 1.0
O3B A:ATP600 3.9 37.3 1.0
O1G E:ATP600 3.9 38.7 1.0
O2C A:G4P601 4.0 54.6 1.0
NH2 E:ARG157 4.1 38.1 1.0
O1D A:G4P601 4.1 45.9 1.0
CG A:GLU200 4.2 40.0 1.0
O2D A:G4P601 4.3 58.9 1.0
MG E:MG602 4.4 39.1 1.0
NE E:ARG157 4.5 30.5 1.0
O1B A:ATP600 4.5 50.4 1.0
O3C A:G4P601 4.6 52.9 1.0
O1G A:ATP600 4.6 40.8 1.0
NH1 E:ARG160 4.7 55.9 1.0
CZ E:ARG157 4.8 34.7 1.0
O3B E:ATP600 4.8 32.9 1.0
PB A:ATP600 4.9 41.8 1.0
PC A:G4P601 5.0 50.0 1.0

Magnesium binding site 2 out of 16 in 8qqt

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Magnesium binding site 2 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:41.5
occ:1.00
 O2C A:G4P601 1.9 54.6 1.0
O2G A:ATP600 2.1 51.1 1.0
O1B A:ATP600 2.4 50.4 1.0
OE1 A:GLU200 2.6 41.4 1.0
O3D A:G4P601 2.9 57.7 1.0
PG A:ATP600 3.1 38.4 1.0
MG A:MG602 3.1 45.4 1.0
O3B A:ATP600 3.1 37.3 1.0
PB A:ATP600 3.2 41.8 1.0
PC A:G4P601 3.3 50.0 1.0
OG A:SER139 3.5 52.6 1.0
CD A:GLU200 3.5 41.9 1.0
O1G A:ATP600 3.6 40.8 1.0
O3' A:G4P601 3.8 60.5 1.0
OE2 A:GLU200 3.8 47.7 1.0
PD A:G4P601 3.8 49.7 1.0
O3C A:G4P601 3.9 52.9 1.0
O2B A:ATP600 4.0 43.3 1.0
O1D A:G4P601 4.0 45.9 1.0
CB A:SER139 4.1 45.5 1.0
O3G A:ATP600 4.4 46.2 1.0
O1C A:G4P601 4.4 52.7 1.0
O3A A:ATP600 4.6 41.3 1.0
NZ A:LYS201 4.6 40.8 1.0
O2' A:G4P601 4.8 54.8 1.0
CG A:GLU200 4.9 40.0 1.0
NH2 E:ARG157 5.0 38.1 1.0
O3G E:ATP600 5.0 48.8 1.0

Magnesium binding site 3 out of 16 in 8qqt

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Magnesium binding site 3 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:42.0
occ:1.00
 O3D B:G4P601 2.0 59.1 1.0
MG B:MG603 2.2 55.0 1.0
O3G F:ATP600 2.3 49.2 1.0
OE2 B:GLU200 2.5 49.0 1.0
O2G B:ATP600 3.0 61.8 1.0
PG F:ATP600 3.1 43.2 1.0
O3G B:ATP600 3.2 43.9 1.0
PD B:G4P601 3.4 52.0 1.0
CD B:GLU200 3.4 45.0 1.0
O2G F:ATP600 3.4 53.2 1.0
OE1 B:GLU200 3.6 46.5 1.0
O1G F:ATP600 3.6 40.6 1.0
PG B:ATP600 3.6 45.6 1.0
O1D B:G4P601 3.9 56.4 1.0
O2D B:G4P601 4.0 70.7 1.0
O2C B:G4P601 4.2 59.3 1.0
MG F:MG602 4.3 45.9 1.0
O3B B:ATP600 4.3 40.3 1.0
NH2 F:ARG157 4.5 39.4 1.0
O3C B:G4P601 4.5 53.7 1.0
O3B F:ATP600 4.6 43.2 1.0
NE F:ARG157 4.8 34.2 1.0
CG B:GLU200 4.8 44.4 1.0
NH1 F:ARG160 4.8 61.8 1.0

Magnesium binding site 4 out of 16 in 8qqt

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Magnesium binding site 4 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:55.0
occ:1.00
 OE1 B:GLU200 1.9 46.5 1.0
O2G B:ATP600 2.0 61.8 1.0
O3D B:G4P601 2.0 59.1 1.0
MG B:MG602 2.2 42.0 1.0
O2C B:G4P601 2.3 59.3 1.0
CD B:GLU200 2.6 45.0 1.0
OE2 B:GLU200 2.6 49.0 1.0
PG B:ATP600 3.1 45.6 1.0
O1B B:ATP600 3.2 56.0 1.0
PD B:G4P601 3.3 52.0 1.0
O3B B:ATP600 3.4 40.3 1.0
PC B:G4P601 3.5 59.8 1.0
O3G B:ATP600 3.7 43.9 1.0
O3C B:G4P601 3.7 53.7 1.0
O3G F:ATP600 3.9 49.2 1.0
PB B:ATP600 4.0 46.5 1.0
O1D B:G4P601 4.0 56.4 1.0
CG B:GLU200 4.1 44.4 1.0
O3' B:G4P601 4.4 64.2 1.0
NH2 F:ARG157 4.4 39.4 1.0
O1G B:ATP600 4.4 47.0 1.0
O2D B:G4P601 4.5 70.7 1.0
O1C B:G4P601 4.6 53.2 1.0
CB B:GLU200 4.6 49.2 1.0
OG B:SER139 4.7 57.1 1.0
O3A B:ATP600 4.9 50.0 1.0
O2A B:ATP600 5.0 45.2 1.0

Magnesium binding site 5 out of 16 in 8qqt

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Magnesium binding site 5 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:49.2
occ:1.00
 O3G G:ATP600 2.1 49.9 1.0
O3D C:G4P601 2.2 60.2 1.0
OE2 C:GLU200 2.4 51.0 1.0
O2G C:ATP600 2.6 60.0 1.0
MG C:MG603 3.0 51.2 1.0
PG G:ATP600 3.1 51.7 1.0
O1G G:ATP600 3.3 52.9 1.0
CD C:GLU200 3.4 47.1 1.0
PD C:G4P601 3.5 54.7 1.0
OE1 C:GLU200 3.7 48.6 1.0
PG C:ATP600 3.7 47.8 1.0
O3G C:ATP600 3.8 50.2 1.0
O2G G:ATP600 3.9 60.4 1.0
O2D C:G4P601 4.1 73.3 1.0
O1D C:G4P601 4.1 56.1 1.0
MG G:MG602 4.2 45.2 1.0
O2C C:G4P601 4.3 62.8 1.0
O3B G:ATP600 4.4 45.1 1.0
O3B C:ATP600 4.5 42.2 1.0
NH2 G:ARG157 4.5 42.6 1.0
O3C C:G4P601 4.7 53.5 1.0
NE G:ARG157 4.7 38.6 1.0
CG C:GLU200 4.7 45.0 1.0
NH1 G:ARG160 4.9 58.6 1.0
O1G C:ATP600 5.0 46.5 1.0

Magnesium binding site 6 out of 16 in 8qqt

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Magnesium binding site 6 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:51.2
occ:1.00
 O2C C:G4P601 1.9 62.8 1.0
O2G C:ATP600 1.9 60.0 1.0
OE1 C:GLU200 1.9 48.6 1.0
O3D C:G4P601 2.5 60.2 1.0
O1B C:ATP600 2.6 60.0 1.0
CD C:GLU200 2.8 47.1 1.0
OE2 C:GLU200 3.0 51.0 1.0
MG C:MG602 3.0 49.2 1.0
PG C:ATP600 3.1 47.8 1.0
O3B C:ATP600 3.1 42.2 1.0
PC C:G4P601 3.3 59.0 1.0
PB C:ATP600 3.4 45.4 1.0
PD C:G4P601 3.7 54.7 1.0
O3C C:G4P601 3.8 53.5 1.0
O1G C:ATP600 4.0 46.5 1.0
OG C:SER139 4.0 51.9 1.0
O3' C:G4P601 4.1 61.8 1.0
CG C:GLU200 4.2 45.0 1.0
O3G C:ATP600 4.2 50.2 1.0
O1D C:G4P601 4.3 56.1 1.0
O1C C:G4P601 4.3 54.3 1.0
O3G G:ATP600 4.3 49.9 1.0
NH2 G:ARG157 4.5 42.6 1.0
O2B C:ATP600 4.5 45.1 1.0
O3A C:ATP600 4.5 50.2 1.0
CB C:GLU200 4.6 51.2 1.0
CB C:SER139 4.8 50.9 1.0
NZ C:LYS201 4.8 42.9 1.0
O2A C:ATP600 4.8 49.0 1.0
O2D C:G4P601 5.0 73.3 1.0

Magnesium binding site 7 out of 16 in 8qqt

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Magnesium binding site 7 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:44.9
occ:1.00
 O3D D:G4P601 2.0 59.6 1.0
OE2 D:GLU200 2.3 52.3 1.0
O3G H:ATP600 2.5 55.7 1.0
O2G D:ATP600 2.7 57.3 1.0
MG D:MG603 2.9 47.3 1.0
CD D:GLU200 3.1 47.3 1.0
OE1 D:GLU200 3.2 48.0 1.0
PG H:ATP600 3.3 46.8 1.0
PD D:G4P601 3.4 52.1 1.0
O1G H:ATP600 3.6 47.2 1.0
PG D:ATP600 3.7 50.4 1.0
O2G H:ATP600 3.7 51.5 1.0
O3G D:ATP600 3.8 49.3 1.0
O1D D:G4P601 3.9 50.7 1.0
O2C D:G4P601 4.1 59.6 1.0
O2D D:G4P601 4.1 68.1 1.0
O3B D:ATP600 4.3 45.5 1.0
NH2 H:ARG157 4.4 38.1 1.0
NH1 H:ARG160 4.5 56.9 1.0
O3C D:G4P601 4.5 56.0 1.0
CG D:GLU200 4.5 44.1 1.0
MG H:MG602 4.6 49.1 1.0
NE H:ARG157 4.7 33.4 1.0
O3B H:ATP600 4.8 40.6 1.0
O1B D:ATP600 4.9 57.8 1.0
PC D:G4P601 5.0 54.5 1.0

Magnesium binding site 8 out of 16 in 8qqt

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Magnesium binding site 8 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:47.3
occ:1.00
 O2C D:G4P601 1.9 59.6 1.0
OE1 D:GLU200 2.0 48.0 1.0
O2G D:ATP600 2.0 57.3 1.0
O1B D:ATP600 2.4 57.8 1.0
O3D D:G4P601 2.7 59.6 1.0
MG D:MG602 2.9 44.9 1.0
CD D:GLU200 3.0 47.3 1.0
O3B D:ATP600 3.1 45.5 1.0
PG D:ATP600 3.1 50.4 1.0
PB D:ATP600 3.3 47.5 1.0
PC D:G4P601 3.3 54.5 1.0
OE2 D:GLU200 3.4 52.3 1.0
PD D:G4P601 3.8 52.1 1.0
O3C D:G4P601 3.9 56.0 1.0
OG D:SER139 3.9 53.7 1.0
O1G D:ATP600 4.1 50.0 1.0
O3' D:G4P601 4.1 58.7 1.0
O1D D:G4P601 4.2 50.7 1.0
O3G D:ATP600 4.2 49.3 1.0
O2B D:ATP600 4.3 44.0 1.0
CG D:GLU200 4.3 44.1 1.0
O1C D:G4P601 4.4 54.3 1.0
O3A D:ATP600 4.5 47.8 1.0
NH2 H:ARG157 4.5 38.1 1.0
CB D:SER139 4.5 48.7 1.0
O3G H:ATP600 4.5 55.7 1.0
CB D:GLU200 4.6 47.8 1.0
NZ D:LYS201 4.6 44.6 1.0

Magnesium binding site 9 out of 16 in 8qqt

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Magnesium binding site 9 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:39.1
occ:1.00
 O3D E:G4P601 2.0 57.0 1.0
O2G E:ATP600 2.2 52.9 1.0
OE2 E:GLU200 2.3 43.4 1.0
O3G A:ATP600 2.4 46.2 1.0
MG E:MG603 3.0 43.1 1.0
CD E:GLU200 3.2 42.1 1.0
PG A:ATP600 3.3 38.4 1.0
PD E:G4P601 3.4 48.9 1.0
OE1 E:GLU200 3.4 43.9 1.0
PG E:ATP600 3.5 43.1 1.0
O2G A:ATP600 3.6 51.1 1.0
O1G A:ATP600 3.6 40.8 1.0
O3G E:ATP600 3.8 48.8 1.0
O1D E:G4P601 4.0 40.3 1.0
O2D E:G4P601 4.0 63.1 1.0
O3B E:ATP600 4.2 32.9 1.0
O2C E:G4P601 4.3 58.2 1.0
NH2 A:ARG157 4.4 35.3 1.0
MG A:MG602 4.4 45.4 1.0
O3C E:G4P601 4.5 51.1 1.0
CG E:GLU200 4.6 39.8 1.0
O1G E:ATP600 4.6 38.7 1.0
NE A:ARG157 4.6 27.9 1.0
O3B A:ATP600 4.8 37.3 1.0
NH1 A:ARG160 4.8 62.8 1.0
O1B E:ATP600 4.9 51.3 1.0

Magnesium binding site 10 out of 16 in 8qqt

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Magnesium binding site 10 out of 16 in the Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Atp+Ppgpp-Bound Form, Compressed within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:43.1
occ:1.00
 O2C E:G4P601 1.9 58.2 1.0
OE1 E:GLU200 2.0 43.9 1.0
O2G E:ATP600 2.1 52.9 1.0
O1B E:ATP600 2.4 51.3 1.0
O3D E:G4P601 2.5 57.0 1.0
CD E:GLU200 2.9 42.1 1.0
MG E:MG602 3.0 39.1 1.0
PG E:ATP600 3.1 43.1 1.0
O3B E:ATP600 3.2 32.9 1.0
OE2 E:GLU200 3.2 43.4 1.0
PC E:G4P601 3.3 57.7 1.0
PB E:ATP600 3.3 35.9 1.0
PD E:G4P601 3.6 48.9 1.0
O1G E:ATP600 3.7 38.7 1.0
O3C E:G4P601 3.7 51.1 1.0
OG E:SER139 3.9 52.7 1.0
O3' E:G4P601 4.0 57.4 1.0
O1D E:G4P601 4.1 40.3 1.0
O2B E:ATP600 4.3 43.2 1.0
CG E:GLU200 4.3 39.8 1.0
O1C E:G4P601 4.4 53.5 1.0
CB E:SER139 4.4 49.7 1.0
O3G E:ATP600 4.4 48.8 1.0
NH2 A:ARG157 4.5 35.3 1.0
O3A E:ATP600 4.6 39.9 1.0
CB E:GLU200 4.6 44.2 1.0
O3G A:ATP600 4.6 46.2 1.0
NZ E:LYS201 4.7 38.7 1.0
O2A E:ATP600 4.9 41.9 1.0
O2D E:G4P601 5.0 63.1 1.0

Reference:

O.Bulvas, T.Kouba, I.Pichova. Mycobacterium Smegmatis Inosine Monophosphate Dehydrogenase (Impdh) Apo Form To Be Published.
DOI: 10.1038/S41467-024-50933-6
Page generated: Fri Oct 4 16:47:41 2024

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