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

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: Mon Jul 15 06:49:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy