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Sodium in PDB 4hxv: Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions

Enzymatic activity of Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions

All present enzymatic activity of Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions:
3.1.3.7;

Protein crystallography data

The structure of Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions, PDB code: 4hxv was solved by K.F.Tarique, S.A.Abdul Rehman, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.31 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.618, 63.877, 117.845, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28.3

Other elements in 4hxv:

The structure of Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions (pdb code 4hxv). 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 Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions, PDB code: 4hxv:

Sodium binding site 1 out of 1 in 4hxv

Go back to Sodium Binding Sites List in 4hxv
Sodium binding site 1 out of 1 in the Crystal Structure of 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions


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 3'(2'),5'-Bisphosphate NUCLEOTIDASE1 From Entamoeba Histolytica in Complex with Amp and Metal Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:21.9
occ:1.00
 O3' A:AMP402 2.1 19.8 1.0
OD2 A:ASP118 2.5 19.6 1.0
O A:HOH501 2.8 13.4 1.0
OD1 A:ASP257 2.9 18.4 1.0
MG A:MG401 3.2 21.6 1.0
OD2 A:ASP121 3.4 20.5 1.0
C3' A:AMP402 3.4 19.8 1.0
CG A:ASP118 3.5 19.6 1.0
OD1 A:ASP118 3.7 19.6 1.0
OE1 A:GLU69 3.7 21.3 1.0
CG A:ASP257 3.9 18.3 1.0
CG A:ASP121 4.0 20.5 1.0
N A:GLY122 4.0 20.2 1.0
CA A:ASP121 4.0 20.3 1.0
O A:ILE120 4.1 20.2 1.0
C4' A:AMP402 4.1 19.7 1.0
O2' A:AMP402 4.3 19.5 1.0
OD2 A:ASP257 4.3 18.2 1.0
CD A:GLU69 4.3 21.6 1.0
OE2 A:GLU69 4.3 21.9 1.0
C2' A:AMP402 4.4 19.8 1.0
CD1 A:TRP256 4.4 19.4 1.0
CB A:ASP121 4.5 20.2 1.0
C A:ASP121 4.5 20.2 1.0
OD1 A:ASP121 4.6 20.7 1.0
C5' A:AMP402 4.7 19.8 1.0
NE1 A:TRP256 4.7 19.9 1.0
CB A:ASP118 4.8 19.4 1.0
N A:ASP121 5.0 20.3 1.0
C A:ILE120 5.0 20.2 1.0

Reference:

K.Faisal Tarique, S.Arif Abdul Rehman, S.Gourinath. Structural Elucidation of A Dual-Activity Pap Phosphatase-1 From Entamoeba Histolytica Capable of Hydrolysing Both 3'-Phosphoadenosine 5'-Phosphate and Inositol 1,4-Bisphosphate Acta Crystallogr.,Sect.D V. 70 2019 2014.
ISSN: ISSN 0907-4449
PubMed: 25004978
DOI: 10.1107/S1399004714010268
Page generated: Mon Oct 7 15:54:40 2024

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