Manganese in PDB 9m2r: Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure

All present enzymatic activity of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure:
4.2.1.19;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Manganese atom in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure (pdb code 9m2r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 48 binding sites of Manganese where determined in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure, PDB code: 9m2r:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:85.2 occ:1.00 OE1 A:GLU77 2.2 100.2 1.0 O A:HOH404 2.2 86.8 1.0 NE2 A:HIS152 2.2 88.2 1.0 NE2 A:HIS73 2.2 80.3 1.0 NE2 D:HIS177 2.2 81.5 1.0 CE1 D:HIS177 3.1 84.7 1.0 CD A:GLU77 3.1 101.5 1.0 CE1 A:HIS73 3.1 81.5 1.0 CD2 A:HIS152 3.1 94.2 1.0 CE1 A:HIS152 3.2 92.2 1.0 CD2 A:HIS73 3.2 81.8 1.0 CD2 D:HIS177 3.3 79.4 1.0 OE2 A:GLU77 3.5 106.0 1.0 OD2 D:ASP108 4.1 115.1 1.0 ND1 D:HIS177 4.3 84.7 1.0 ND1 A:HIS73 4.3 81.1 1.0 CG A:HIS152 4.3 92.4 1.0 ND1 A:HIS152 4.3 99.5 1.0 CG A:HIS73 4.4 84.7 1.0 CG D:HIS177 4.4 82.7 1.0 CG A:GLU77 4.4 96.2 1.0 CB A:GLU77 4.8 90.2 1.0 CG D:ASP108 5.0 108.1 1.0

Manganese binding site 2 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:115.7 occ:1.00 O A:HOH429 2.2 125.6 1.0 NE2 A:HIS176 2.2 94.1 1.0 OE1 A:GLU180 2.2 110.5 1.0 NE2 A:HIS47 2.2 108.2 1.0 NE2 B:HIS74 2.3 110.1 1.0 CE1 B:HIS74 3.0 110.0 1.0 CE1 A:HIS47 3.1 113.5 1.0 CE1 A:HIS176 3.1 92.2 1.0 CD A:GLU180 3.2 107.4 1.0 CD2 A:HIS176 3.2 89.3 1.0 CD2 A:HIS47 3.3 108.4 1.0 CD2 B:HIS74 3.5 106.9 1.0 OE2 A:GLU180 3.6 113.0 1.0 ND1 B:HIS74 4.2 108.7 1.0 ND1 A:HIS176 4.3 88.8 1.0 ND1 A:HIS47 4.3 113.8 1.0 CG A:HIS176 4.4 87.9 1.0 CG A:HIS47 4.4 102.7 1.0 CG B:HIS74 4.5 103.9 1.0 CG A:GLU180 4.6 97.5 1.0 CE A:MET48 4.8 98.2 1.0 CE A:MET107 5.0 121.5 1.0

Manganese binding site 3 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:85.3 occ:1.00 OE1 B:GLU77 2.2 100.4 1.0 O B:HOH404 2.2 87.0 1.0 NE2 B:HIS152 2.2 88.1 1.0 NE2 B:HIS73 2.2 80.4 1.0 NE2 A:HIS177 2.2 81.6 1.0 CE1 A:HIS177 3.1 84.7 1.0 CD B:GLU77 3.1 101.6 1.0 CE1 B:HIS73 3.2 81.5 1.0 CD2 B:HIS152 3.2 94.2 1.0 CE1 B:HIS152 3.2 92.2 1.0 CD2 B:HIS73 3.2 81.9 1.0 CD2 A:HIS177 3.3 79.5 1.0 OE2 B:GLU77 3.5 106.2 1.0 OD2 A:ASP108 4.1 115.1 1.0 ND1 A:HIS177 4.3 84.8 1.0 ND1 B:HIS73 4.3 81.1 1.0 CG B:HIS152 4.3 92.4 1.0 ND1 B:HIS152 4.3 99.5 1.0 CG B:HIS73 4.4 84.7 1.0 CG A:HIS177 4.4 82.7 1.0 CG B:GLU77 4.4 96.2 1.0 CB B:GLU77 4.8 90.2 1.0 CG A:ASP108 5.0 108.1 1.0

Manganese binding site 4 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:115.9 occ:1.00 O B:HOH428 2.2 124.8 1.0 NE2 B:HIS176 2.2 94.0 1.0 OE1 B:GLU180 2.2 110.6 1.0 NE2 B:HIS47 2.2 108.2 1.0 NE2 C:HIS74 2.3 109.8 1.0 CE1 C:HIS74 3.0 110.0 1.0 CE1 B:HIS47 3.1 113.4 1.0 CE1 B:HIS176 3.1 92.2 1.0 CD B:GLU180 3.2 107.4 1.0 CD2 B:HIS176 3.2 89.2 1.0 CD2 B:HIS47 3.3 108.4 1.0 CD2 C:HIS74 3.5 106.5 1.0 OE2 B:GLU180 3.6 112.9 1.0 ND1 C:HIS74 4.2 108.7 1.0 ND1 B:HIS176 4.3 88.8 1.0 ND1 B:HIS47 4.3 113.8 1.0 CG B:HIS176 4.4 87.9 1.0 CG B:HIS47 4.4 102.6 1.0 CG C:HIS74 4.5 103.9 1.0 CG B:GLU180 4.6 97.5 1.0 CE B:MET48 4.8 98.3 1.0 CE B:MET107 5.0 121.6 1.0

Manganese binding site 5 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:85.3 occ:1.00 OE1 C:GLU77 2.2 100.6 1.0 O C:HOH404 2.2 87.0 1.0 NE2 C:HIS152 2.2 88.1 1.0 NE2 C:HIS73 2.2 80.3 1.0 NE2 B:HIS177 2.2 81.6 1.0 CE1 B:HIS177 3.1 84.7 1.0 CD C:GLU77 3.1 101.7 1.0 CD2 C:HIS152 3.1 94.2 1.0 CE1 C:HIS73 3.2 81.5 1.0 CE1 C:HIS152 3.2 92.2 1.0 CD2 C:HIS73 3.2 81.8 1.0 CD2 B:HIS177 3.3 79.5 1.0 OE2 C:GLU77 3.5 106.3 1.0 OD2 B:ASP108 4.1 115.1 1.0 ND1 B:HIS177 4.3 84.8 1.0 ND1 C:HIS73 4.3 81.1 1.0 CG C:HIS152 4.3 92.4 1.0 ND1 C:HIS152 4.3 99.4 1.0 CG C:HIS73 4.4 84.7 1.0 CG B:HIS177 4.4 82.7 1.0 CG C:GLU77 4.4 96.2 1.0 CB C:GLU77 4.8 90.2 1.0 CG B:ASP108 5.0 108.1 1.0

Manganese binding site 6 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:115.8 occ:1.00 O C:HOH429 2.2 125.0 1.0 NE2 C:HIS176 2.2 94.1 1.0 NE2 C:HIS47 2.2 108.2 1.0 OE1 C:GLU180 2.2 110.5 1.0 NE2 D:HIS74 2.3 110.0 1.0 CE1 D:HIS74 3.0 110.0 1.0 CE1 C:HIS47 3.1 113.5 1.0 CE1 C:HIS176 3.1 92.2 1.0 CD C:GLU180 3.2 107.5 1.0 CD2 C:HIS176 3.2 89.3 1.0 CD2 C:HIS47 3.3 108.4 1.0 CD2 D:HIS74 3.5 106.8 1.0 OE2 C:GLU180 3.6 112.8 1.0 ND1 D:HIS74 4.2 108.7 1.0 ND1 C:HIS176 4.3 88.8 1.0 ND1 C:HIS47 4.3 113.8 1.0 CG C:HIS176 4.4 87.9 1.0 CG C:HIS47 4.4 102.6 1.0 CG D:HIS74 4.5 103.9 1.0 CG C:GLU180 4.6 97.5 1.0 CE C:MET48 4.8 98.3 1.0 CE C:MET107 5.0 121.5 1.0

Manganese binding site 7 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:85.3 occ:1.00 OE1 D:GLU77 2.2 100.4 1.0 O D:HOH404 2.2 87.0 1.0 NE2 D:HIS152 2.2 88.1 1.0 NE2 D:HIS73 2.2 80.4 1.0 NE2 C:HIS177 2.2 81.6 1.0 CE1 C:HIS177 3.1 84.7 1.0 CD D:GLU77 3.1 101.6 1.0 CE1 D:HIS73 3.1 81.5 1.0 CD2 D:HIS152 3.2 94.2 1.0 CE1 D:HIS152 3.2 92.2 1.0 CD2 D:HIS73 3.2 81.9 1.0 CD2 C:HIS177 3.3 79.4 1.0 OE2 D:GLU77 3.5 106.2 1.0 OD2 C:ASP108 4.1 115.1 1.0 ND1 C:HIS177 4.3 84.8 1.0 ND1 D:HIS73 4.3 81.1 1.0 CG D:HIS152 4.3 92.4 1.0 ND1 D:HIS152 4.3 99.5 1.0 CG D:HIS73 4.4 84.7 1.0 CG C:HIS177 4.4 82.7 1.0 CG D:GLU77 4.4 96.2 1.0 CB D:GLU77 4.8 90.2 1.0 CG C:ASP108 5.0 108.1 1.0

Manganese binding site 8 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:116.0 occ:1.00 O D:HOH429 2.2 126.0 1.0 NE2 D:HIS176 2.2 94.0 1.0 NE2 D:HIS47 2.2 108.3 1.0 OE1 D:GLU180 2.2 110.3 1.0 NE2 A:HIS74 2.3 110.3 1.0 CE1 A:HIS74 3.0 110.0 1.0 CE1 D:HIS47 3.1 113.6 1.0 CE1 D:HIS176 3.1 92.2 1.0 CD D:GLU180 3.2 107.3 1.0 CD2 D:HIS176 3.2 89.2 1.0 CD2 D:HIS47 3.3 108.4 1.0 CD2 A:HIS74 3.5 107.1 1.0 OE2 D:GLU180 3.6 112.7 1.0 ND1 A:HIS74 4.2 108.8 1.0 ND1 D:HIS176 4.3 88.8 1.0 ND1 D:HIS47 4.3 113.9 1.0 CG D:HIS176 4.4 87.9 1.0 CG D:HIS47 4.4 102.7 1.0 CG A:HIS74 4.5 103.9 1.0 CG D:GLU180 4.6 97.5 1.0 CE D:MET48 4.8 98.3 1.0 CE D:MET107 5.0 121.8 1.0

Manganese binding site 9 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:85.1 occ:1.00 OE1 E:GLU77 2.2 101.2 1.0 O E:HOH404 2.2 87.5 1.0 NE2 E:HIS73 2.2 80.6 1.0 NE2 E:HIS152 2.2 87.9 1.0 NE2 O:HIS177 2.2 81.8 1.0 CE1 O:HIS177 3.1 84.6 1.0 CD E:GLU77 3.1 102.0 1.0 CE1 E:HIS73 3.2 81.8 1.0 CD2 E:HIS152 3.2 94.2 1.0 CE1 E:HIS152 3.2 92.2 1.0 CD2 E:HIS73 3.2 82.1 1.0 CD2 O:HIS177 3.3 79.6 1.0 OE2 E:GLU77 3.5 106.7 1.0 OD2 O:ASP108 4.1 115.2 1.0 ND1 O:HIS177 4.3 84.7 1.0 ND1 E:HIS73 4.3 81.2 1.0 CG E:HIS152 4.3 92.4 1.0 ND1 E:HIS152 4.3 99.4 1.0 CG E:HIS73 4.4 84.9 1.0 CG O:HIS177 4.4 82.6 1.0 CG E:GLU77 4.4 96.3 1.0 CB E:GLU77 4.8 90.3 1.0 CG O:ASP108 5.0 108.1 1.0

Manganese binding site 10 out of 48 in the Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Imidazole Glycerol Phosphate Dehydratase From Mycobacterium Tuberculosis, Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn302 b:115.9 occ:1.00 O E:HOH428 2.2 123.8 1.0 NE2 E:HIS176 2.2 94.1 1.0 OE1 E:GLU180 2.2 110.5 1.0 NE2 E:HIS47 2.2 108.1 1.0 NE2 J:HIS74 2.3 109.9 1.0 CE1 J:HIS74 3.0 110.1 1.0 CE1 E:HIS47 3.1 113.4 1.0 CE1 E:HIS176 3.1 92.2 1.0 CD E:GLU180 3.2 107.4 1.0 CD2 E:HIS176 3.2 89.3 1.0 CD2 E:HIS47 3.3 108.4 1.0 CD2 J:HIS74 3.5 106.6 1.0 OE2 E:GLU180 3.6 112.8 1.0 ND1 J:HIS74 4.2 108.8 1.0 ND1 E:HIS176 4.3 88.8 1.0 ND1 E:HIS47 4.3 113.8 1.0 CG E:HIS176 4.4 87.9 1.0 CG E:HIS47 4.4 102.6 1.0 CG J:HIS74 4.5 104.0 1.0 CG E:GLU180 4.6 97.5 1.0 CE E:MET48 4.8 98.3 1.0 CE E:MET107 5.0 121.7 1.0

R.Raina, D.Kar, M.Singla, S.Tiwari, S.Kumari, S.Aneja, V.Kumar, S.Banerjee, S.Goyal, R.K.Pal, K.R.Vinothkumar, B.Biswal. Cryo-Em Structures of Mycobacterium Tuberculosis Imidazole Glycerol Phosphate Dehydratase in the Apo State and in the Presence of Small Molecules. Acta Crystallogr.,Sect.F 2025.
ISSN: ESSN 2053-230X
PubMed: 40478632
DOI: 10.1107/S2053230X25004595