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 / R_free (%)*	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

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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

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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

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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: Wed Jul 9 07:22:16 2025

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