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Sodium in PDB 6of5: The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

Enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

All present enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase:
3.1.3.2;

Protein crystallography data

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5 was solved by D.Feder, G.Schenk, L.W.Guddat, W.M.Hussein, R.P.Mcgeary, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.808, 126.808, 298.211, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 23.1

Other elements in 6of5:

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6of5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6of5

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Sodium binding site 1 out of 5 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na521

b:19.9
occ:1.00
 O D:HOH659 2.8 28.5 1.0
O D:HOH705 3.0 26.6 1.0
N A:ARG258 3.3 30.9 1.0
NZ A:LYS306 3.3 32.8 1.0
CE A:LYS306 3.4 32.5 1.0
O D:GLU299 3.6 30.2 1.0
CA A:GLY257 3.7 30.6 1.0
C A:GLY257 4.0 33.3 1.0
CB A:ARG258 4.0 34.6 1.0
O D:HOH738 4.0 30.3 1.0
CE1 D:TYR253 4.1 23.0 1.0
CA A:ARG258 4.2 30.3 1.0
CB D:GLU299 4.4 30.4 1.0
C D:GLU299 4.4 27.8 1.0
OE1 D:GLU299 4.7 33.8 1.0
CD1 D:TYR253 4.7 25.3 1.0
O A:ARG258 4.8 28.8 1.0
CA D:GLU299 4.8 24.3 1.0
OG D:SER287 4.8 32.0 1.0
CD A:LYS306 4.9 30.5 1.0
O D:SER252 5.0 27.1 1.0

Sodium binding site 2 out of 5 in 6of5

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Sodium binding site 2 out of 5 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na522

b:35.1
occ:1.00
 O4 A:SO4519 2.6 41.0 1.0
O A:ARG66 2.7 33.9 1.0
N A:SER61 2.9 28.6 1.0
N A:ARG66 3.0 39.0 1.0
OG A:SER61 3.3 38.0 1.0
CA A:TRP60 3.4 32.9 1.0
C A:ARG66 3.5 35.5 1.0
CA A:ARG66 3.6 34.9 1.0
CB A:TRP60 3.6 33.3 1.0
C A:TRP60 3.7 32.5 1.0
CB A:ARG66 3.7 45.6 1.0
NH1 A:ARG68 3.8 54.2 1.0
S A:SO4519 3.8 48.4 1.0
N A:GLY65 3.9 38.4 1.0
CA A:SER61 3.9 31.8 1.0
O3 A:SO4519 3.9 37.2 1.0
CB A:SER61 4.0 32.1 1.0
C A:GLY65 4.0 37.8 1.0
O A:SER61 4.2 37.0 1.0
CA A:GLY65 4.3 29.2 1.0
CB A:ASN64 4.3 35.5 1.0
C A:ASN64 4.4 34.7 1.0
C A:SER61 4.5 37.3 1.0
O2 A:SO4519 4.5 41.0 1.0
N A:LYS67 4.7 34.1 1.0
CZ A:ARG68 4.7 57.0 1.0
O A:TYR59 4.7 30.4 1.0
N A:TRP60 4.8 27.3 1.0
CA A:ASN64 4.8 35.0 1.0
CG A:ARG66 4.8 47.5 1.0
O A:TRP60 4.9 30.1 1.0
CG A:ARG68 4.9 39.5 1.0
O1 A:SO4519 4.9 53.5 1.0
CG A:TRP60 5.0 31.8 1.0
CE2 A:TYR101 5.0 24.3 1.0

Sodium binding site 3 out of 5 in 6of5

Go back to Sodium Binding Sites List in 6of5
Sodium binding site 3 out of 5 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na514

b:21.4
occ:1.00
 O A:HOH743 2.7 28.7 1.0
NZ D:LYS306 2.9 29.3 1.0
O A:HOH665 3.2 25.3 1.0
N D:ARG258 3.4 28.8 1.0
O A:GLU299 3.4 30.5 1.0
CE D:LYS306 3.5 30.3 1.0
CA D:GLY257 3.8 26.4 1.0
O A:HOH733 3.9 23.3 1.0
CB D:ARG258 4.0 31.3 1.0
C D:GLY257 4.1 30.9 1.0
CE1 A:TYR253 4.2 21.7 1.0
CA D:ARG258 4.3 28.3 1.0
C A:GLU299 4.3 26.4 1.0
CB A:GLU299 4.4 30.2 1.0
O4 D:SO4511 4.5 35.1 0.6
CD1 A:TYR253 4.7 20.6 1.0
OE1 A:GLU299 4.8 35.1 1.0
CA A:GLU299 4.8 31.9 1.0
OG A:SER287 4.8 26.8 1.0
O A:SER252 4.8 25.7 1.0
O D:ARG258 4.8 26.6 1.0
CD D:LYS306 5.0 29.6 1.0

Sodium binding site 4 out of 5 in 6of5

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Sodium binding site 4 out of 5 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na516

b:33.6
occ:1.00
 O2 B:SO4516 2.2 28.9 0.5
OG C:SER287 2.8 26.8 1.0
OE1 C:GLU299 2.9 37.8 1.0
S B:SO4516 3.0 20.3 0.5
O4 B:SO4516 3.0 29.2 0.5
OH C:TYR253 3.1 33.3 1.0
O3 B:SO4516 3.3 33.9 0.5
CB C:SER287 3.5 29.8 1.0
CE1 C:TYR253 3.5 27.4 1.0
NE2 C:HIS323 3.6 30.5 1.0
CB C:GLU299 3.7 30.0 1.0
CZ C:TYR253 3.7 30.1 1.0
CD C:GLU299 3.8 41.3 1.0
CD2 C:HIS323 3.9 29.1 1.0
CG C:GLU299 4.0 38.9 1.0
O1 B:SO4516 4.3 27.8 0.5
CE1 C:HIS323 4.4 36.8 1.0
O C:GLU299 4.5 29.2 1.0
CB B:ARG258 4.5 32.1 0.5
CB B:ARG258 4.5 31.7 0.5
O C:HOH748 4.5 31.1 1.0
C C:GLU299 4.7 29.2 1.0
CD1 C:TYR253 4.7 27.4 1.0
CA C:GLU299 4.8 30.2 1.0
CA C:SER287 4.8 26.9 1.0
CG C:HIS323 4.9 30.7 1.0
OE2 C:GLU299 5.0 37.8 1.0
N B:ARG258 5.0 30.5 1.0

Sodium binding site 5 out of 5 in 6of5

Go back to Sodium Binding Sites List in 6of5
Sodium binding site 5 out of 5 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na517

b:17.4
occ:1.00
 NZ C:LYS306 2.9 28.4 1.0
O B:HOH643 3.0 29.7 1.0
N C:ARG258 3.2 27.5 1.0
O B:HOH667 3.2 24.8 1.0
CE C:LYS306 3.5 28.3 1.0
O B:GLU299 3.7 29.1 1.0
CA C:GLY257 3.7 23.6 1.0
CB C:ARG258 3.9 31.9 1.0
C C:GLY257 3.9 29.6 1.0
CE1 B:TYR253 4.1 30.1 1.0
CA C:ARG258 4.1 30.9 1.0
O B:HOH703 4.2 32.8 1.0
CB B:GLU299 4.3 29.5 1.0
C B:GLU299 4.4 36.1 1.0
CD1 B:TYR253 4.7 26.0 1.0
CA B:GLU299 4.8 29.1 1.0
CD C:LYS306 4.8 30.1 1.0
OE1 B:GLU299 4.8 38.1 1.0
OG B:SER287 4.8 24.5 1.0
O C:ARG258 4.8 25.4 1.0
CG B:GLU299 4.9 34.2 1.0
CZ B:TYR253 5.0 32.4 1.0

Reference:

D.Feder, M.W.Kan, W.M.Hussein, L.W.Guddat, G.Schenk, R.P.Mcgeary. Synthesis, Evaluation and Structural Investigations of Potent Purple Acid Phosphatase Inhibitors As Drug Leads For Osteoporosis. Eur.J.Med.Chem. V. 182 11611 2019.
ISSN: ISSN 0223-5234
PubMed: 31445230
DOI: 10.1016/J.EJMECH.2019.111611
Page generated: Tue Oct 8 12:30:36 2024

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