Atomistry » Sodium » PDB 6nxx-6ont » 6ofd
Atomistry »
  Sodium »
    PDB 6nxx-6ont »
      6ofd »

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

Go back to Sodium Binding Sites List in 6ofd
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

Go back to Sodium Binding Sites List in 6ofd
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

Go back to Sodium Binding Sites List in 6ofd
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

Go back to Sodium Binding Sites List in 6ofd
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 Dec 15 12:41:21 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy