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Calcium in PDB 5kdf: Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate

Enzymatic activity of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate

All present enzymatic activity of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate:
3.6.1.1;

Protein crystallography data

The structure of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate, PDB code: 5kdf was solved by A.H.Pang, A.Garzan, S.Garneau-Tsodikova, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.45
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.972, 98.972, 97.571, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate (pdb code 5kdf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate, PDB code: 5kdf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5kdf

Go back to Calcium Binding Sites List in 5kdf
Calcium binding site 1 out of 3 in the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:88.2
occ:1.00
OE2 A:GLU18 3.1 64.8 1.0
OD2 A:ASP29 3.2 48.4 1.0
O1 A:POP205 3.4 87.3 1.0
O A:POP205 3.8 0.5 1.0
CD A:GLU18 3.9 57.6 1.0
CG A:ASP29 4.0 44.0 1.0
OD1 A:ASP29 4.3 45.2 1.0
P1 A:POP205 4.3 97.4 1.0
NZ A:LYS16 4.5 41.4 1.0
CG A:GLU18 4.6 54.3 1.0
OE1 A:GLU18 4.7 56.0 1.0
NH1 A:ARG30 4.8 53.7 1.0
O2 A:POP205 5.0 91.9 1.0

Calcium binding site 2 out of 3 in 5kdf

Go back to Calcium Binding Sites List in 5kdf
Calcium binding site 2 out of 3 in the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:77.3
occ:1.00
O A:LYS133 2.6 78.6 1.0
O A:GLU130 2.8 58.1 1.0
O A:LYS127 3.0 35.0 1.0
O A:ASP128 3.5 39.6 1.0
C A:ASP128 3.7 37.5 1.0
C A:LYS133 3.8 74.6 1.0
CA A:ASP128 3.8 35.8 1.0
C A:LYS127 3.9 37.5 1.0
C A:GLU130 3.9 57.6 1.0
N A:ASP128 4.2 36.3 1.0
N A:GLU130 4.3 47.6 1.0
N A:LYS133 4.4 76.1 1.0
CA A:LYS133 4.6 73.7 1.0
N A:LEU129 4.6 39.1 1.0
CA A:PRO131 4.7 67.5 1.0
CA A:GLU130 4.7 52.7 1.0
CB A:LYS133 4.7 70.0 1.0
N A:PRO131 4.8 66.9 1.0
N A:PHE134 4.8 78.8 1.0
CA A:PHE134 4.9 81.5 1.0

Calcium binding site 3 out of 3 in 5kdf

Go back to Calcium Binding Sites List in 5kdf
Calcium binding site 3 out of 3 in the Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis in Complex with Inhibitor 6 and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:78.7
occ:1.00
O A:HOH301 2.5 60.5 1.0
O A:HOH307 2.5 57.5 1.0
O A:HOH302 3.0 37.7 1.0
OE1 A:GLU8 3.7 54.5 1.0
O A:HOH320 3.8 49.2 1.0
OE2 A:GLU8 4.0 47.0 1.0
O5 A:POP205 4.1 96.0 1.0
O A:HOH321 4.1 62.9 1.0
NZ A:LYS16 4.1 41.4 1.0
CD A:GLU8 4.3 47.0 1.0
CG A:GLU18 4.3 54.3 1.0
OD1 A:ASP57 4.3 47.3 1.0
CB A:GLU18 4.8 49.0 1.0
CE2 A:TYR42 4.8 40.4 1.0
OH A:TYR42 4.9 45.3 1.0
CA A:GLU18 4.9 45.2 1.0

Reference:

A.H.Pang, A.Garzan, M.J.Larsen, T.J.Mcquade, S.Garneau-Tsodikova, O.V.Tsodikov. Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase From Mycobacterium Tuberculosis. Acs Chem. Biol. V. 11 3084 2016.
ISSN: ESSN 1554-8937
PubMed: 27622287
DOI: 10.1021/ACSCHEMBIO.6B00510
Page generated: Sat Dec 12 05:33:14 2020

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