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Sodium in PDB 6g46: Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid

Enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid

All present enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid:
3.1.3.2;

Protein crystallography data

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 6g46 was solved by D.F.Feder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.26 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.208, 126.208, 297.119, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22.3

Other elements in 6g46:

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid (pdb code 6g46). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 6g46:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6g46

Go back to Sodium Binding Sites List in 6g46
Sodium binding site 1 out of 3 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na513

b:32.1
occ:1.00
 O4 C:SO4511 2.3 30.4 0.5
O1 C:SO4511 2.6 30.4 0.5
OE1 B:GLU299 2.7 34.8 1.0
OH B:TYR253 2.8 27.7 1.0
S C:SO4511 2.9 10.9 0.5
OG B:SER287 2.9 24.0 1.0
NE2 B:HIS323 3.4 34.6 1.0
CB B:SER287 3.4 26.4 1.0
O2 C:SO4511 3.4 30.1 0.5
CB B:GLU299 3.5 29.1 1.0
CE2 B:TYR253 3.6 27.7 1.0
CZ B:TYR253 3.6 31.1 1.0
CD B:GLU299 3.7 38.0 1.0
CD2 B:HIS323 3.8 34.1 1.0
O B:HOH621 4.0 24.2 1.0
CG B:GLU299 4.1 29.5 1.0
O3 C:SO4511 4.2 28.4 0.5
CE1 B:HIS323 4.2 33.3 1.0
O B:GLU299 4.4 27.7 1.0
C B:GLU299 4.5 31.5 1.0
CB C:ARG258 4.6 29.4 1.0
CA B:GLU299 4.6 29.8 1.0
CA B:SER287 4.6 28.6 1.0
CG B:HIS323 4.7 33.3 1.0
CD2 B:TYR253 4.8 28.3 1.0
O C:HOH745 4.9 36.3 1.0
OE2 B:GLU299 4.9 30.4 1.0
ND1 B:HIS323 4.9 30.4 1.0
CE1 B:TYR253 4.9 29.5 1.0
O C:HOH602 5.0 27.3 1.0

Sodium binding site 2 out of 3 in 6g46

Go back to Sodium Binding Sites List in 6g46
Sodium binding site 2 out of 3 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na514

b:16.7
occ:1.00
 O C:HOH683 2.9 28.1 1.0
NZ B:LYS306 3.0 31.8 1.0
O C:HOH646 3.1 20.1 1.0
N B:ARG258 3.1 34.6 1.0
O C:GLU299 3.5 25.9 1.0
CE B:LYS306 3.5 31.0 1.0
CA B:GLY257 3.6 30.9 1.0
CE2 C:TYR253 3.9 25.5 1.0
C B:GLY257 3.9 31.5 1.0
CB B:ARG258 3.9 31.1 1.0
CA B:ARG258 4.1 32.9 1.0
C C:GLU299 4.3 23.9 1.0
O C:HOH664 4.3 26.7 1.0
CB C:GLU299 4.4 27.8 1.0
CD2 C:TYR253 4.5 23.1 1.0
OE1 C:GLU299 4.6 31.1 1.0
OG C:SER287 4.7 28.2 1.0
O B:ARG258 4.7 29.0 1.0
CA C:GLU299 4.7 28.2 1.0
CD B:LYS306 4.8 30.9 1.0
CZ C:TYR253 4.9 26.6 1.0
OH C:TYR253 4.9 28.1 1.0
C B:ARG258 5.0 32.8 1.0
O C:SER252 5.0 26.9 1.0

Sodium binding site 3 out of 3 in 6g46

Go back to Sodium Binding Sites List in 6g46
Sodium binding site 3 out of 3 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na513

b:19.4
occ:1.00
 NZ D:LYS306 2.9 30.5 1.0
O A:HOH659 3.2 26.4 1.0
O A:HOH701 3.2 25.0 1.0
N D:ARG258 3.3 26.2 1.0
O A:GLU299 3.4 31.7 1.0
CE D:LYS306 3.4 27.4 1.0
CA D:GLY257 3.8 26.2 1.0
CB D:ARG258 4.0 30.0 1.0
O A:HOH741 4.0 29.9 1.0
C D:GLY257 4.1 27.4 1.0
CE2 A:TYR253 4.1 21.6 1.0
CA D:ARG258 4.3 26.1 1.0
C A:GLU299 4.3 29.8 1.0
CB A:GLU299 4.4 25.4 1.0
CD2 A:TYR253 4.7 24.9 1.0
OG A:SER287 4.7 28.3 1.0
CA A:GLU299 4.7 28.9 1.0
OE1 A:GLU299 4.7 27.9 1.0
O D:ARG258 4.8 24.7 1.0
O D:HOH835 4.9 32.8 1.0
CD D:LYS306 4.9 25.6 1.0
CG A:GLU299 5.0 24.5 1.0

Reference:

W.M.Hussein, D.Feder, G.Schenk, L.W.Guddat, R.P.Mcgeary. Purple Acid Phosphatase Inhibitors As Leads For Osteoporosis Chemotherapeutics. Eur J Med Chem V. 157 462 2018.
ISSN: ISSN 1768-3254
PubMed: 30107365
DOI: 10.1016/J.EJMECH.2018.08.004
Page generated: Tue Dec 15 12:16:40 2020

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