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Calcium in PDB 4z72: Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions

Enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions

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

Protein crystallography data

The structure of Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions, PDB code: 4z72 was solved by A.C.Pratt, T.Biswas, S.Barnard-Britson, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.35
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 99.319, 99.319, 96.732, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions (pdb code 4z72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions, PDB code: 4z72:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4z72

Go back to Calcium Binding Sites List in 4z72
Calcium binding site 1 out of 3 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions


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 Two Phosphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:63.0
occ:1.00
 O A:HOH305 2.3 47.6 1.0
O A:HOH327 2.3 62.8 1.0
O A:HOH314 2.3 44.1 1.0
OE1 A:GLU8 3.2 37.9 1.0
O A:HOH317 3.4 35.0 1.0
OD1 A:ASP57 3.5 39.7 1.0
OE2 A:GLU8 3.9 35.6 1.0
CD A:GLU8 4.0 35.9 1.0
O A:HOH306 4.1 22.4 1.0
OH A:TYR42 4.1 37.1 1.0
O2 A:PO4201 4.2 50.0 1.0
CG A:ASP57 4.3 37.4 1.0
CE2 A:TYR42 4.3 33.6 1.0
OD2 A:ASP57 4.4 37.4 1.0
O A:HOH315 4.5 39.0 1.0
CZ A:TYR42 4.7 34.0 1.0
CG A:GLU18 4.9 46.5 1.0

Calcium binding site 2 out of 3 in 4z72

Go back to Calcium Binding Sites List in 4z72
Calcium binding site 2 out of 3 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions


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 Two Phosphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:72.1
occ:1.00
 O A:HOH321 2.3 57.2 1.0
O A:HOH324 2.3 62.5 1.0
OE2 A:GLU18 2.3 60.3 1.0
OD2 A:ASP29 3.2 34.7 1.0
CD A:GLU18 3.4 49.1 1.0
CG A:ASP29 3.7 33.1 1.0
OD1 A:ASP29 3.8 34.6 1.0
OE1 A:GLU18 4.0 44.0 1.0
O A:HOH315 4.1 39.0 1.0
CG A:GLU18 4.5 46.5 1.0
O2 A:PO4202 4.6 58.7 1.0
O1 A:PO4202 4.7 63.5 1.0
NH1 A:ARG30 4.7 46.2 1.0
O A:HOH327 4.8 62.8 1.0
CB A:ASP29 4.8 31.9 1.0
NZ A:LYS16 4.9 31.6 1.0
O3 A:PO4202 4.9 58.6 1.0

Calcium binding site 3 out of 3 in 4z72

Go back to Calcium Binding Sites List in 4z72
Calcium binding site 3 out of 3 in the Crystal Structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Two Phosphate Ions


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 Two Phosphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:51.1
occ:1.00
 O A:HOH326 2.3 47.4 1.0
O A:LYS133 2.3 48.5 1.0
O A:GLU130 2.3 42.9 1.0
O A:LYS127 2.8 33.4 1.0
O A:ASP128 3.2 40.6 1.0
C A:GLU130 3.4 42.4 1.0
C A:LYS133 3.5 46.8 1.0
C A:ASP128 3.6 36.8 1.0
C A:LYS127 3.8 34.8 1.0
N A:GLU130 3.9 38.8 1.0
CA A:ASP128 4.0 34.8 1.0
N A:LYS133 4.1 47.2 1.0
CA A:GLU130 4.2 40.3 1.0
CA A:LYS133 4.3 45.7 1.0
N A:ASP128 4.3 35.3 1.0
N A:PRO131 4.3 46.2 1.0
N A:LEU129 4.4 36.8 1.0
CA A:PRO131 4.5 47.6 1.0
N A:PHE134 4.6 47.3 1.0
CB A:LYS133 4.6 45.9 1.0
C A:LEU129 4.7 37.6 1.0
N A:GLY132 4.7 47.4 1.0
CB A:GLU130 4.7 40.4 1.0
CA A:PHE134 4.8 48.6 1.0
C A:PRO131 4.8 47.1 1.0
CA A:LEU129 4.9 36.1 1.0
CB A:LYS127 4.9 39.5 1.0
CA A:LYS127 5.0 36.7 1.0

Reference:

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
Page generated: Sun Jul 14 15:32:58 2024

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