Manganese in PDB 4z73: Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate:
3.6.1.1;

The structure of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate, PDB code: 4z73 was solved by A.C.Pratt, T.Biswas, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.620, 105.112, 254.729, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate (pdb code 4z73). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 27 binding sites of Manganese where determined in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate, PDB code: 4z73:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:82.9 occ:1.00 O A:GLU130 2.3 67.4 1.0 O A:LYS133 2.5 74.4 1.0 O A:ASP128 2.8 61.5 1.0 O A:LYS127 3.1 61.1 1.0 C A:GLU130 3.6 67.1 1.0 C A:LYS133 3.6 75.0 1.0 C A:ASP128 3.6 61.2 1.0 N A:LYS133 4.0 73.0 1.0 CA A:ASP128 4.1 60.6 1.0 C A:LYS127 4.2 60.7 1.0 CA A:LYS133 4.3 73.9 1.0 N A:GLU130 4.3 65.1 1.0 CA A:PRO131 4.4 69.1 1.0 N A:PRO131 4.4 68.5 1.0 CA A:GLU130 4.5 65.9 1.0 N A:GLY132 4.6 70.9 1.0 N A:PHE134 4.6 77.1 1.0 N A:ASP128 4.6 60.6 1.0 CB A:LYS133 4.7 73.9 1.0 N A:LEU129 4.7 61.8 1.0 C A:PRO131 4.8 69.8 1.0 C A:LEU129 4.8 63.8 1.0 CA A:PHE134 4.8 78.8 1.0 CB A:PHE134 4.9 79.8 1.0 CB A:GLU130 5.0 65.8 1.0

Manganese binding site 2 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:0.7 occ:1.00 OD1 A:ASP57 2.1 72.7 1.0 OD2 A:ASP89 3.0 76.3 1.0 OD2 A:ASP52 3.2 85.2 1.0 CG A:ASP57 3.2 72.4 1.0 OD1 A:ASP89 3.6 75.8 1.0 OD2 A:ASP57 3.6 72.7 1.0 CG A:ASP89 3.7 75.9 1.0 O A:PRO55 3.7 76.0 1.0 CG A:ASP52 4.3 85.4 1.0 CB A:ASP57 4.4 71.9 1.0 N A:ASP57 4.4 73.0 1.0 MN A:MN204 4.5 0.6 1.0 CB A:ASP54 4.8 80.8 1.0 C A:PRO55 4.9 76.5 1.0 CB A:ASP52 4.9 85.3 1.0

Manganese binding site 3 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:0.6 occ:1.00 OD2 A:ASP57 3.0 72.7 1.0 OH A:TYR42 3.6 59.3 1.0 O A:HOH304 3.7 37.2 1.0 O1 A:PO4202 3.8 80.8 1.0 O3 A:PO4202 3.9 81.2 1.0 CG A:ASP57 4.0 72.4 1.0 OD1 A:ASP57 4.4 72.7 1.0 MN A:MN203 4.5 0.7 1.0 NZ A:LYS16 4.5 59.3 1.0 P A:PO4202 4.5 81.3 1.0 CZ A:TYR42 4.7 58.9 1.0 O A:HOH307 4.7 42.5 1.0 CE1 A:TYR42 4.8 58.8 1.0 OD2 A:ASP89 5.0 76.3 1.0

Manganese binding site 4 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:83.3 occ:1.00 O B:LYS133 2.3 74.9 1.0 O B:ASP128 2.8 61.1 1.0 O B:GLU130 2.8 66.5 1.0 O B:LYS127 3.1 61.3 1.0 C B:ASP128 3.4 60.9 1.0 C B:LYS133 3.5 74.9 1.0 CA B:ASP128 3.8 60.6 1.0 C B:GLU130 3.9 65.9 1.0 C B:LYS127 4.0 61.1 1.0 N B:GLU130 4.0 63.1 1.0 N B:LYS133 4.2 74.2 1.0 N B:ASP128 4.3 60.8 1.0 CA B:LYS133 4.4 74.6 1.0 N B:LEU129 4.5 61.1 1.0 N B:PHE134 4.5 75.4 1.0 CA B:GLU130 4.5 64.1 1.0 CA B:PHE134 4.6 76.0 1.0 CB B:LYS133 4.7 74.7 1.0 CB B:PHE134 4.7 76.6 1.0 N B:PRO131 4.8 67.7 1.0 CA B:PRO131 5.0 68.8 1.0 C B:LEU129 5.0 62.0 1.0 CB B:GLU130 5.0 63.6 1.0

Manganese binding site 5 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:0.6 occ:1.00 OD1 B:ASP57 1.9 71.2 1.0 CG B:ASP57 3.1 70.2 1.0 OE1 B:GLU8 3.2 55.9 1.0 O B:GLY43 3.3 59.8 1.0 OH B:TYR42 3.4 55.2 1.0 CZ B:TYR42 3.8 55.1 1.0 CB B:ASP57 3.8 69.1 1.0 CE2 B:TYR42 3.8 55.3 1.0 CA B:ASP57 4.0 68.5 1.0 O3 B:POP201 4.1 91.0 1.0 OD2 B:ASP57 4.1 70.8 1.0 C B:GLY43 4.1 59.6 1.0 CB B:PHE44 4.2 60.9 1.0 CD B:GLU8 4.3 56.3 1.0 OE2 B:GLU8 4.7 56.3 1.0 N B:PHE44 4.7 60.5 1.0 CE1 B:TYR42 4.7 55.2 1.0 CD2 B:PHE44 4.7 60.6 1.0 O B:HOH306 4.8 31.2 1.0 CA B:PHE44 4.8 61.1 1.0 N B:ASP57 4.8 70.1 1.0 CD2 B:TYR42 4.8 55.4 1.0 CA B:GLY43 4.9 58.9 1.0 CG B:PHE44 5.0 60.7 1.0

Manganese binding site 6 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn204 b:0.5 occ:1.00 OD2 B:ASP57 2.2 70.8 1.0 CB B:ASP89 3.3 81.7 1.0 CG B:ASP57 3.4 70.2 1.0 OD2 B:ASP52 3.5 93.5 1.0 OD2 B:ASP89 3.7 83.3 1.0 OD1 B:ASP57 4.0 71.2 1.0 CG B:ASP89 4.0 82.4 1.0 NZ B:LYS91 4.1 65.5 1.0 O1 B:POP201 4.3 91.9 1.0 CB B:ASP57 4.5 69.1 1.0 CA B:ASP89 4.6 80.8 1.0 CG B:ASP52 4.7 93.2 1.0 O B:ASP90 4.7 70.9 1.0 O B:HOH301 4.9 63.2 1.0 N B:ASP90 5.0 76.5 1.0

Manganese binding site 7 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn202 b:82.2 occ:1.00 O C:GLU130 2.6 67.3 1.0 O C:ASP128 2.7 64.6 1.0 O C:LYS133 2.9 73.0 1.0 O C:LYS127 3.5 63.2 1.0 C C:ASP128 3.6 63.9 1.0 C C:GLU130 3.6 67.0 1.0 C C:LYS133 4.0 73.2 1.0 N C:LYS133 4.0 72.7 1.0 CA C:ASP128 4.1 63.4 1.0 CA C:PRO131 4.2 68.6 1.0 N C:GLY132 4.3 70.2 1.0 N C:GLU130 4.3 65.2 1.0 N C:PRO131 4.3 68.0 1.0 O C:HOH308 4.4 30.7 1.0 CA C:LYS133 4.5 72.8 1.0 C C:PRO131 4.5 69.3 1.0 C C:LYS127 4.6 62.8 1.0 N C:LEU129 4.6 64.0 1.0 CA C:GLU130 4.6 66.0 1.0 C C:LEU129 4.7 64.5 1.0 N C:ASP128 4.8 63.1 1.0 CB C:LYS133 4.9 72.9 1.0 CA C:LEU129 5.0 64.1 1.0

Manganese binding site 8 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn203 b:0.7 occ:1.00 OD1 C:ASP57 2.3 68.3 1.0 OD2 C:ASP52 3.2 78.2 1.0 OD1 C:ASP89 3.2 72.0 1.0 CG C:ASP57 3.3 67.7 1.0 OD2 C:ASP57 3.5 67.5 1.0 CB C:ASP54 3.8 76.7 1.0 OD2 C:ASP54 3.9 77.5 1.0 MN C:MN204 4.0 0.2 1.0 O C:PRO55 4.0 72.8 1.0 CG C:ASP89 4.1 72.0 1.0 CG C:ASP52 4.2 78.7 1.0 OD2 C:ASP89 4.2 71.9 1.0 CG C:ASP54 4.4 77.1 1.0 OD1 C:ASP52 4.4 79.1 1.0 CB C:ASP57 4.6 67.4 1.0 N C:ASP57 4.9 68.6 1.0

Manganese binding site 9 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn204 b:0.2 occ:1.00 OH C:TYR42 2.9 66.9 1.0 OD2 C:ASP57 2.9 67.5 1.0 O C:HOH307 3.0 37.8 1.0 O3 C:PO4201 3.5 64.6 1.0 MN C:MN203 4.0 0.7 1.0 CG C:ASP57 4.0 67.7 1.0 CZ C:TYR42 4.2 66.2 1.0 OD1 C:ASP57 4.3 68.3 1.0 OE2 C:GLU18 4.4 65.5 1.0 NZ C:LYS16 4.4 60.2 1.0 CE2 C:TYR42 4.7 66.1 1.0 O C:HOH301 4.8 54.1 1.0 OD2 C:ASP89 4.8 71.9 1.0 P C:PO4201 4.9 64.7 1.0 NZ C:LYS91 4.9 65.0 1.0

Manganese binding site 10 out of 27 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with A Phosphate Ion and An Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:0.2 occ:1.00 O D:ASP128 2.5 60.2 1.0 O D:LYS133 2.6 68.7 1.0 O D:GLU130 2.8 65.4 1.0 O D:LYS127 3.4 60.0 1.0 C D:ASP128 3.5 60.1 1.0 C D:LYS133 3.9 68.2 1.0 C D:GLU130 4.0 65.0 1.0 O D:PRO131 4.0 68.0 1.0 CA D:ASP128 4.2 59.9 1.0 N D:GLU130 4.3 62.8 1.0 N D:LYS133 4.3 67.6 1.0 C D:LYS127 4.5 59.7 1.0 N D:LEU129 4.6 60.3 1.0 C D:LEU129 4.6 61.6 1.0 C D:PRO131 4.6 67.3 1.0 CA D:GLU130 4.7 63.6 1.0 CA D:LYS133 4.7 67.7 1.0 N D:PHE134 4.8 68.4 1.0 CA D:LEU129 4.9 60.7 1.0 CA D:PHE134 4.9 68.7 1.0 N D:ASP128 4.9 60.0 1.0 CB D:PHE134 4.9 69.0 1.0

A.C.Pratt, S.W.Dewage, A.H.Pang, T.Biswas, S.Barnard-Britson, G.A.Cisneros, O.V.Tsodikov. Structural and Computational Dissection of the Catalytic Mechanism of the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis. J.Struct.Biol. V. 192 76 2015.
ISSN: ESSN 1095-8657
PubMed: 26296329
DOI: 10.1016/J.JSB.2015.08.010