Calcium in PDB 4z74: Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate:
3.6.1.1;

The structure of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate, PDB code: 4z74 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 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.011, 105.199, 255.872, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.9

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 - 44;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate (pdb code 4z74). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 44 binding sites of Calcium where determined in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate, PDB code: 4z74:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:38.2 occ:1.00 O A:GLU130 2.3 39.5 1.0 O A:LYS133 2.3 43.5 1.0 O A:ASP128 2.3 34.9 1.0 O A:LYS127 2.3 32.8 1.0 C A:ASP128 3.1 33.3 1.0 C A:GLU130 3.5 39.8 1.0 C A:LYS127 3.5 31.4 1.0 C A:LYS133 3.5 47.3 1.0 CA A:ASP128 3.5 32.2 1.0 O A:HOH367 3.7 43.0 1.0 N A:GLU130 3.8 36.8 1.0 O A:HOH372 3.8 43.7 1.0 N A:ASP128 4.0 31.8 1.0 N A:LEU129 4.1 34.1 1.0 CA A:GLU130 4.1 37.9 1.0 N A:LYS133 4.1 47.0 1.0 CA A:LYS133 4.2 47.2 1.0 C A:LEU129 4.4 35.5 1.0 CB A:LYS133 4.5 47.5 1.0 N A:PRO131 4.5 42.2 1.0 N A:PHE134 4.5 49.2 1.0 CB A:GLU130 4.6 37.5 1.0 CA A:LEU129 4.6 34.6 1.0 CA A:PRO131 4.8 43.1 1.0 CA A:LYS127 4.8 30.9 1.0 CA A:PHE134 4.8 51.8 1.0 CB A:LYS127 4.9 30.6 1.0 CB A:ASP128 4.9 31.5 1.0 N A:GLY132 4.9 45.0 1.0

Calcium binding site 2 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:59.9 occ:1.00 O3 A:POP201 2.3 58.2 1.0 O A:HOH301 2.3 58.0 1.0 O6 A:POP201 2.3 59.7 1.0 O5 A:POP201 2.3 60.7 1.0 P2 A:POP201 2.6 59.2 1.0 OD2 A:ASP89 3.0 51.7 1.0 P1 A:POP201 3.1 57.0 1.0 O A:POP201 3.1 57.9 1.0 O1 A:POP201 3.4 56.9 1.0 OD2 A:ASP84 3.4 55.3 1.0 CG A:ASP89 3.9 50.9 1.0 O4 A:POP201 4.1 59.1 1.0 NZ A:LYS127 4.2 30.4 1.0 OH A:TYR126 4.3 31.4 1.0 OD1 A:ASP89 4.4 52.2 1.0 NZ A:LYS91 4.4 38.0 1.0 O2 A:POP201 4.5 57.5 1.0 O A:HOH337 4.5 42.8 1.0 CG A:ASP84 4.6 55.8 1.0 CB A:ASP89 4.9 50.1 1.0

Calcium binding site 3 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:43.9 occ:1.00 O A:HOH357 2.3 43.2 1.0 OD1 A:ASP57 2.3 43.8 1.0 OE1 A:GLU8 2.3 35.5 1.0 O A:GLY43 3.4 29.8 1.0 CD A:GLU8 3.5 32.5 1.0 CE2 A:TYR42 3.5 29.7 1.0 OH A:TYR42 3.6 30.3 1.0 CG A:ASP57 3.6 42.6 1.0 O A:HOH354 3.8 51.0 1.0 CZ A:TYR42 3.8 30.0 1.0 C A:GLY43 3.8 29.9 1.0 O A:HOH317 3.8 33.8 1.0 OE2 A:GLU8 3.9 32.9 1.0 CB A:PHE44 4.2 31.1 1.0 O4 A:POP201 4.3 59.1 1.0 CA A:GLY43 4.3 29.3 1.0 OD2 A:ASP57 4.4 46.4 1.0 N A:PHE44 4.4 30.5 1.0 CD2 A:TYR42 4.5 29.7 1.0 CB A:ASP57 4.5 41.3 1.0 CD2 A:PHE44 4.6 31.0 1.0 CA A:ASP57 4.7 40.0 1.0 CA A:PHE44 4.7 31.3 1.0 CG A:GLU8 4.7 31.2 1.0 CG A:PHE44 4.9 31.1 1.0 CE1 A:TYR42 4.9 30.0 1.0

Calcium binding site 4 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:53.5 occ:1.00 O A:HOH365 2.3 52.5 1.0 O A:HOH313 2.3 50.9 1.0 OD2 A:ASP57 2.3 46.4 1.0 OD1 A:ASP89 2.3 52.2 1.0 CG A:ASP89 3.5 50.9 1.0 CG A:ASP57 3.5 42.6 1.0 O A:HOH354 3.6 51.0 1.0 O A:HOH301 3.9 58.0 1.0 O5 A:POP201 4.1 60.7 1.0 OD2 A:ASP89 4.2 51.7 1.0 OD2 A:ASP52 4.2 62.7 1.0 OD1 A:ASP57 4.3 43.8 1.0 CB A:ASP57 4.4 41.3 1.0 CA A:ASP89 4.5 49.1 1.0 CB A:ASP89 4.5 50.1 1.0 O A:HOH369 4.5 35.7 1.0 NZ A:LYS91 4.6 38.0 1.0 O A:ASP90 4.7 41.2 1.0 N A:ASP90 4.7 45.2 1.0 C A:ASP89 5.0 47.4 1.0

Calcium binding site 5 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:47.6 occ:1.00 O B:HOH363 2.3 46.9 1.0 OD1 B:ASP57 2.3 45.5 1.0 OE1 B:GLU8 2.3 38.4 1.0 O B:GLY43 3.4 33.0 1.0 CD B:GLU8 3.5 34.6 1.0 OH B:TYR42 3.5 31.5 1.0 CE2 B:TYR42 3.5 31.4 1.0 O B:HOH346 3.6 47.1 1.0 CG B:ASP57 3.6 43.8 1.0 O B:HOH302 3.7 30.0 1.0 CZ B:TYR42 3.7 31.5 1.0 OE2 B:GLU8 3.9 34.9 1.0 C B:GLY43 3.9 32.8 1.0 O2 B:POP201 4.3 54.7 1.0 OD2 B:ASP57 4.3 47.6 1.0 CB B:PHE44 4.4 33.1 1.0 CA B:GLY43 4.5 32.4 1.0 CD2 B:TYR42 4.5 31.1 1.0 CD2 B:PHE44 4.5 33.2 1.0 CB B:ASP57 4.6 42.4 1.0 N B:PHE44 4.6 33.1 1.0 CG B:GLU8 4.7 33.4 1.0 CE1 B:TYR42 4.8 31.5 1.0 CA B:ASP57 4.9 40.9 1.0 CA B:PHE44 4.9 33.3 1.0 CG B:PHE44 4.9 33.1 1.0

Calcium binding site 6 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:54.6 occ:1.00 OD2 B:ASP89 2.3 53.9 1.0 O1 B:POP201 2.3 54.8 1.0 OD2 B:ASP84 2.3 56.0 1.0 O B:HOH307 2.3 51.2 1.0 O4 B:POP201 2.3 54.9 1.0 CG B:ASP89 3.5 53.1 1.0 P1 B:POP201 3.5 54.6 1.0 CG B:ASP84 3.5 56.3 1.0 P2 B:POP201 3.7 54.5 1.0 O3 B:POP201 3.8 54.5 1.0 NZ B:LYS127 3.8 38.9 1.0 O B:POP201 3.9 54.7 1.0 OD1 B:ASP89 4.2 53.4 1.0 OH B:TYR126 4.3 33.5 1.0 OD1 B:ASP84 4.4 56.6 1.0 CB B:ASP84 4.4 56.2 1.0 CB B:ASP89 4.4 52.7 1.0 NZ B:LYS91 4.4 36.6 1.0 O5 B:POP201 4.6 54.6 1.0 CE B:MET82 4.6 54.1 1.0 O6 B:POP201 4.7 54.4 1.0 O2 B:POP201 4.8 54.7 1.0

Calcium binding site 7 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:43.8 occ:1.00 O B:LYS127 2.3 40.6 1.0 O B:GLU130 2.3 43.3 1.0 O B:LYS133 2.3 48.3 1.0 O B:ASP128 2.4 41.5 1.0 C B:ASP128 3.1 40.1 1.0 C B:GLU130 3.4 43.1 1.0 C B:LYS127 3.5 38.8 1.0 C B:LYS133 3.5 50.5 1.0 CA B:ASP128 3.6 39.8 1.0 N B:GLU130 3.7 41.3 1.0 N B:ASP128 4.0 39.4 1.0 N B:LEU129 4.1 40.3 1.0 CA B:GLU130 4.1 42.0 1.0 N B:LYS133 4.2 50.2 1.0 CA B:LYS133 4.3 50.1 1.0 N B:PRO131 4.5 44.3 1.0 CB B:LYS133 4.5 50.4 1.0 C B:LEU129 4.5 40.5 1.0 N B:PHE134 4.6 52.0 1.0 CB B:GLU130 4.6 42.0 1.0 CA B:LEU129 4.7 40.0 1.0 CA B:LYS127 4.7 37.9 1.0 CA B:PRO131 4.8 45.1 1.0 CA B:PHE134 4.9 53.8 1.0 CB B:LYS127 4.9 38.2 1.0 N B:GLY132 4.9 47.0 1.0 CB B:ASP128 5.0 39.8 1.0

Calcium binding site 8 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:54.2 occ:1.00 O B:HOH325 2.3 53.5 1.0 OD2 B:ASP57 2.3 47.6 1.0 OD1 B:ASP89 2.3 53.4 1.0 CG B:ASP89 3.4 53.1 1.0 CG B:ASP57 3.5 43.8 1.0 O B:HOH340 3.8 52.4 1.0 OD2 B:ASP89 4.1 53.9 1.0 O B:ASP90 4.1 42.7 1.0 CB B:ASP57 4.2 42.4 1.0 NZ B:LYS91 4.2 36.6 1.0 O B:HOH362 4.4 43.3 1.0 N B:ASP90 4.4 47.0 1.0 CA B:ASP89 4.4 51.9 1.0 OD1 B:ASP57 4.4 45.5 1.0 CB B:ASP89 4.5 52.7 1.0 C B:ASP89 4.8 49.7 1.0 O B:HOH346 4.9 47.1 1.0 N B:ASP57 4.9 41.5 1.0 OD2 B:ASP52 4.9 68.3 1.0 C B:ASP90 5.0 42.7 1.0

Calcium binding site 9 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:62.1 occ:1.00 O C:HOH301 2.5 49.6 1.0 OD2 C:ASP57 3.0 45.2 1.0 OD1 C:ASP89 3.2 45.3 1.0 CG C:ASP57 3.2 43.5 1.0 O C:PRO55 3.3 45.9 1.0 OD1 C:ASP57 3.5 45.0 1.0 CB C:ASP57 4.0 42.3 1.0 N C:ASP57 4.0 41.9 1.0 OD2 C:ASP52 4.2 70.7 1.0 CG C:ASP89 4.3 45.7 1.0 C C:PRO55 4.5 45.7 1.0 CB C:ASP54 4.6 54.0 1.0 CA C:ASP57 4.6 41.3 1.0 O C:HOH338 4.7 45.8 1.0 CA C:LEU56 4.8 43.9 1.0 C C:LEU56 4.8 42.9 1.0 OD2 C:ASP89 4.8 47.9 1.0 O2 C:POP201 4.9 53.9 1.0 O C:ASP90 5.0 41.3 1.0

Calcium binding site 10 out of 44 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:41.4 occ:1.00 O C:GLU130 2.3 40.9 1.0 O C:LYS133 2.3 42.1 1.0 O C:ASP128 2.3 38.0 1.0 O C:LYS127 3.1 34.4 1.0 C C:ASP128 3.2 36.2 1.0 O C:HOH317 3.4 42.5 1.0 C C:LYS133 3.4 42.8 1.0 C C:GLU130 3.5 40.2 1.0 CA C:ASP128 3.7 35.7 1.0 N C:LYS133 3.8 43.3 1.0 O C:HOH378 3.9 44.9 1.0 N C:GLU130 4.0 38.0 1.0 CA C:LYS133 4.0 42.8 1.0 C C:LYS127 4.1 34.0 1.0 N C:LEU129 4.2 36.7 1.0 CA C:GLU130 4.3 38.9 1.0 CB C:LYS133 4.4 42.6 1.0 N C:ASP128 4.4 34.9 1.0 N C:PRO131 4.4 41.4 1.0 CA C:PRO131 4.4 42.0 1.0 C C:LEU129 4.5 37.3 1.0 N C:GLY132 4.5 43.1 1.0 N C:PHE134 4.6 43.2 1.0 C C:PRO131 4.7 42.5 1.0 CA C:LEU129 4.7 37.0 1.0 CB C:GLU130 4.9 38.3 1.0 CA C:PHE134 5.0 44.0 1.0 C C:GLY132 5.0 43.6 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