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

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

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

Resolution Low / High (Å) 20.05 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.174, 126.174, 298.044, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 19.9

Other elements in 6ofd:

The structure of The Crystal Structure of Octadecyloxy(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
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6ofd). 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 Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6ofd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6ofd

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Sodium binding site 1 out of 5 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:Na518

b:16.3
occ:1.00
 O D:HOH693 2.9 18.6 1.0
O D:HOH675 3.0 20.9 1.0
N A:ARG258 3.2 22.0 1.0
NZ A:LYS306 3.2 24.9 1.0
CE A:LYS306 3.5 28.9 1.0
O D:GLU299 3.6 23.5 1.0
CA A:GLY257 3.7 21.4 1.0
CB A:ARG258 3.9 21.2 1.0
C A:GLY257 3.9 23.2 1.0
CE1 D:TYR253 4.0 20.6 1.0
CA A:ARG258 4.1 21.7 1.0
O D:HOH777 4.2 23.2 1.0
O2 A:SO4524 4.3 40.0 1.0
C D:GLU299 4.4 20.6 1.0
CB D:GLU299 4.4 25.9 1.0
CD1 D:TYR253 4.6 17.8 1.0
O A:ARG258 4.6 19.6 1.0
OG D:SER287 4.8 26.2 1.0
CA D:GLU299 4.8 23.4 1.0
OE1 D:GLU299 4.8 22.9 1.0
O D:SER252 4.9 21.3 1.0
C A:ARG258 4.9 26.1 1.0
CZ D:TYR253 4.9 26.6 1.0
CG D:GLU299 4.9 24.2 1.0
OH D:TYR253 5.0 22.0 1.0
CD A:LYS306 5.0 31.8 1.0

Sodium binding site 2 out of 5 in 6ofd

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Sodium binding site 2 out of 5 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:Na519

b:34.1
occ:1.00
 O4 A:SO4522 2.5 36.6 1.0
O A:ARG66 2.7 26.1 1.0
N A:SER61 2.9 28.3 1.0
N A:ARG66 3.0 30.4 1.0
C A:ARG66 3.4 31.7 1.0
CA A:ARG66 3.4 30.4 1.0
CA A:TRP60 3.5 28.3 1.0
OG A:SER61 3.5 34.4 1.0
CB A:ARG66 3.6 34.5 1.0
CB A:TRP60 3.6 27.8 1.0
C A:TRP60 3.7 28.5 1.0
NH1 A:ARG68 3.7 38.9 1.0
N A:GLY65 3.8 35.8 1.0
S A:SO4522 3.8 43.4 1.0
CA A:SER61 3.9 25.3 1.0
CB A:SER61 3.9 30.4 1.0
C A:GLY65 4.0 31.7 1.0
O3 A:SO4522 4.0 37.5 1.0
O A:SER61 4.0 30.8 1.0
CB A:ASN64 4.0 36.5 1.0
C A:ASN64 4.2 31.5 1.0
CA A:GLY65 4.2 28.3 1.0
C A:SER61 4.4 35.5 1.0
CA A:ASN64 4.6 33.9 1.0
N A:LYS67 4.6 26.8 1.0
O2 A:SO4522 4.6 41.7 1.0
O1 A:SO4522 4.8 39.1 1.0
O A:ASN64 4.8 31.9 1.0
N A:TRP60 4.8 24.5 1.0
CZ A:ARG68 4.9 44.6 1.0
N A:ASN64 4.9 30.9 1.0
O A:TRP60 4.9 23.9 1.0
O A:TYR59 4.9 27.4 1.0
CG A:TRP60 4.9 23.7 1.0
CG A:ARG66 4.9 43.6 1.0
CE2 A:TYR101 5.0 23.6 1.0

Sodium binding site 3 out of 5 in 6ofd

Go back to Sodium Binding Sites List in 6ofd
Sodium binding site 3 out of 5 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:Na511

b:55.2
occ:1.00
 O2 D:SO4512 2.2 37.6 0.6
O D:HOH979 3.0 36.7 1.0
O D:THR305 3.0 27.4 1.0
O D:HOH650 3.1 39.1 1.0
O A:HOH780 3.2 27.8 1.0
S D:SO4512 3.4 33.6 0.6
O D:HOH627 3.6 28.0 1.0
O3 D:SO4512 3.7 39.5 0.6
O D:HOH942 3.7 44.1 1.0
O1 D:SO4512 3.9 33.2 0.6
C D:THR305 4.1 24.2 1.0
CA D:LYS306 4.4 27.0 1.0
O D:LYS306 4.5 28.6 1.0
O4 D:SO4512 4.6 27.5 0.6
O D:HOH959 4.6 36.1 1.0
O D:HOH800 4.6 28.4 1.0
N D:LYS306 4.8 21.4 1.0
CD D:LYS306 4.8 25.4 1.0
C D:LYS306 4.8 26.8 1.0
O D:HOH786 5.0 26.3 1.0

Sodium binding site 4 out of 5 in 6ofd

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Sodium binding site 4 out of 5 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:Na508

b:28.4
occ:1.00
 O2 B:SO4516 2.2 28.7 0.5
OE1 C:GLU299 2.7 28.7 1.0
OH C:TYR253 2.9 22.3 1.0
OG C:SER287 3.0 26.3 1.0
S B:SO4516 3.0 8.4 0.5
O4 B:SO4516 3.1 30.5 0.5
CE1 C:TYR253 3.4 23.6 1.0
O3 B:SO4516 3.4 29.4 0.5
NE2 C:HIS323 3.5 21.9 1.0
CB C:SER287 3.5 18.4 1.0
CZ C:TYR253 3.6 23.6 1.0
CB C:GLU299 3.6 25.5 1.0
CD C:GLU299 3.7 30.9 1.0
CD2 C:HIS323 3.8 21.6 1.0
CG C:GLU299 4.2 28.1 1.0
O C:HOH832 4.2 31.4 1.0
O C:HOH775 4.3 29.8 1.0
O1 B:SO4516 4.4 27.1 0.5
CE1 C:HIS323 4.4 24.1 1.0
O B:HOH717 4.5 31.3 1.0
CB B:ARG258 4.5 27.8 1.0
O C:GLU299 4.6 24.1 1.0
CD1 C:TYR253 4.6 17.9 1.0
C C:GLU299 4.7 24.4 1.0
CA C:GLU299 4.8 25.1 1.0
CG C:HIS323 4.8 21.7 1.0
CA C:SER287 4.8 16.1 1.0
OE2 C:GLU299 4.8 33.4 1.0
CE2 C:TYR253 4.9 22.4 1.0
O B:ARG258 5.0 19.8 1.0

Sodium binding site 5 out of 5 in 6ofd

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Sodium binding site 5 out of 5 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:Na509

b:15.6
occ:1.00
 O B:HOH747 2.9 25.2 1.0
NZ C:LYS306 3.0 23.7 1.0
O B:HOH659 3.0 18.9 1.0
N C:ARG258 3.2 20.2 1.0
CE C:LYS306 3.6 21.3 1.0
O B:GLU299 3.6 24.1 1.0
CA C:GLY257 3.7 18.0 1.0
CB C:ARG258 4.0 24.8 1.0
C C:GLY257 4.0 21.0 1.0
CE1 B:TYR253 4.0 20.6 1.0
O B:HOH762 4.0 27.5 1.0
CA C:ARG258 4.2 25.8 1.0
C B:GLU299 4.4 27.2 1.0
CB B:GLU299 4.4 26.5 1.0
CD1 B:TYR253 4.6 21.3 1.0
O C:ARG258 4.6 17.8 1.0
OE1 B:GLU299 4.7 27.0 1.0
OG B:SER287 4.8 27.3 1.0
CA B:GLU299 4.8 23.1 1.0
O B:SER252 4.9 21.6 1.0
CZ B:TYR253 4.9 24.1 1.0
C C:ARG258 4.9 23.7 0.9
CG B:GLU299 5.0 26.4 1.0
O1 C:EDO520 5.0 27.7 1.0
OH B:TYR253 5.0 23.6 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 12:30:56 2024

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