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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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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