Sodium in PDB 5z5o: Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K

Enzymatic activity of Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K

All present enzymatic activity of Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K:
3.4.22.38;

Protein crystallography data

The structure of Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K, PDB code: 5z5o was solved by S.Biswas, S.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	52.22 / 1.92
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.100, 67.270, 82.870, 90.00, 91.83, 90.00
*R / R_free (%)*	16.2 / 20.4

Other elements in 5z5o:

The structure of Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K (pdb code 5z5o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K, PDB code: 5z5o:

Sodium binding site 1 out of 1 in 5z5o

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Sodium Binding Sites List in 5z5o

Sodium binding site 1 out of 1 in the Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Pycnonodysostosis Disease Related I249T Mutant of Human Cathepsin K within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na429 b:58.3 occ:1.00	OE1	A:GLU193	2.5	43.9	1.0
	OD2	A:ASP154	2.7	35.6	1.0
	CG	A:GLN150	3.5	32.4	1.0
	CD	A:GLU193	3.6	61.9	1.0
	CB	A:GLU193	3.6	56.8	1.0
	CG	A:ASP154	3.7	48.1	1.0
	CE1	A:TYR186	3.8	40.2	1.0
	NE2	A:GLN150	3.9	35.0	1.0
	CD	A:GLN150	4.0	42.0	1.0
	CG	A:GLU193	4.0	73.2	1.0
	OD1	A:ASP154	4.1	37.1	1.0
	CG2	A:VAL189	4.1	46.4	0.9
	OH	A:TYR186	4.4	43.3	1.0
	CZ	A:TYR186	4.6	39.3	1.0
	CG2	A:VAL189	4.6	60.4	0.1
	OE2	A:GLU193	4.6	60.8	1.0
	CD1	A:TYR186	4.7	35.4	1.0
	CB	A:GLN150	4.8	28.3	1.0
	CA	A:GLU193	4.8	42.6	1.0
	O	A:SER194	4.9	37.3	1.0
	O	A:PRO187	4.9	38.0	1.0
	OE1	A:GLN150	4.9	32.6	1.0
	N	A:GLU193	5.0	49.7	1.0

Reference:

S.Roy, S.Das Chakraborty, S.Biswas. Not All Pycnodysostosis-Related Mutants of Human Cathepsin K Are Inactive - Crystal Structure and Biochemical Studies of An Active Mutant I249T. Febs J. V. 285 4265 2018.
ISSN: ISSN 1742-4658
PubMed: 30199612
DOI: 10.1111/FEBS.14655

Page generated: Tue Oct 8 01:28:59 2024

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