Sodium in PDB 8eya: Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide

Enzymatic activity of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide

All present enzymatic activity of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide:
2.7.10.2; 3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide, PDB code: 8eya was solved by R.Morris, N.J.Kershaw, J.J.Babon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.42 / 2.10
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	88.833, 88.833, 197.456, 90, 90, 120
*R / R_free (%)*	22.1 / 26

Other elements in 8eya:

The structure of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide (pdb code 8eya). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide, PDB code: 8eya:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8eya

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Sodium Binding Sites List in 8eya

Sodium binding site 1 out of 3 in the Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na406 b:70.3 occ:1.00	OE2	A:GLU167	2.3	67.5	1.0
	OG1	A:THR165	2.3	64.9	1.0
	CB	A:GLU167	3.0	57.2	1.0
	CB	A:THR165	3.2	66.4	1.0
	CD	A:GLU167	3.3	69.8	1.0
	CG2	A:THR165	3.5	69.2	1.0
	CZ2	A:TRP100	3.6	59.9	1.0
	CG	A:GLU167	3.7	60.6	1.0
	OD1	A:ASN162	4.2	67.7	1.0
	OE1	A:GLU167	4.3	69.8	1.0
	CA	A:GLU167	4.3	60.9	1.0
	CH2	A:TRP100	4.4	57.2	1.0
	N	A:GLU167	4.5	59.0	1.0
	CE2	A:TRP100	4.6	58.4	1.0
	CB	A:ASN162	4.6	58.7	1.0
	CA	A:THR165	4.6	62.0	1.0
	CG	A:ASN162	4.7	62.3	1.0
	NE1	A:TRP100	4.8	52.0	1.0
	C	A:THR165	5.0	66.3	1.0

Sodium binding site 2 out of 3 in 8eya

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Sodium Binding Sites List in 8eya

Sodium binding site 2 out of 3 in the Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na407 b:55.0 occ:1.00	OE1	A:GLU159	2.4	51.2	1.0
	OE1	A:GLU161	2.6	56.5	1.0
	O	A:HOH544	2.6	42.0	1.0
	CE	A:LYS141	3.3	57.0	1.0
	CD	A:GLU159	3.4	57.0	1.0
	CB	A:GLU161	3.4	48.9	1.0
	CD	A:GLU161	3.7	61.3	1.0
	NZ	A:LYS141	3.8	66.6	1.0
	CG	A:GLU159	3.9	46.5	1.0
	CG	A:GLU161	4.1	52.9	1.0
	OG1	A:THR143	4.4	41.5	1.0
	CG2	A:THR168	4.4	49.2	1.0
	OE2	A:GLU159	4.5	51.9	1.0
	CD	A:LYS141	4.6	53.3	1.0
	CA	A:GLU161	4.7	48.7	1.0
	OE2	A:GLU161	4.7	57.1	1.0
	CB	A:GLU159	4.8	47.8	1.0
	N	A:GLU161	4.8	41.7	1.0
	CG	A:LYS141	4.9	48.2	1.0

Sodium binding site 3 out of 3 in 8eya

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Sodium Binding Sites List in 8eya

Sodium binding site 3 out of 3 in the Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of PTP1B D181A/Q262A/C215A Phosphatase Domain with A JAK2 Activation Loop Phosphopeptide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na403 b:54.6 occ:1.00	OE2	B:GLU129	2.3	46.5	1.0
	O	B:ILE145	2.8	52.7	1.0
	CD	B:GLU129	3.2	43.8	1.0
	CG	B:GLU129	3.4	46.6	1.0
	C	B:ILE145	3.9	53.1	1.0
	CA	B:SER146	3.9	51.6	1.0
	CB	B:SER146	4.1	47.2	1.0
	N	B:SER146	4.3	49.4	1.0
	OE1	B:GLU129	4.4	47.4	1.0
	CB	B:GLU129	4.8	42.5	1.0

Reference:

R.Morris, N.Keating, C.Tan, H.Chen, A.Laktyushin, T.Saiyed, N.P.D.Liau, N.A.Nicola, T.Tiganis, N.J.Kershaw, J.J.Babon. Structure Guided Studies of the Interaction Between PTP1B and Jak. Commun Biol V. 6 641 2023.
ISSN: ESSN 2399-3642
PubMed: 37316570
DOI: 10.1038/S42003-023-05020-9

Page generated: Wed Oct 9 11:44:46 2024

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