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Sodium in PDB 8brn: Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor

Enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor, PDB code: 8brn was solved by D.Feder, W.M.Hussein, L.W.Guddat, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.859, 125.859, 298.339, 90, 90, 120
R / Rfree (%) 15.7 / 20.6

Other elements in 8brn:

The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Iron (Fe) 4 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor (pdb code 8brn). 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 Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor, PDB code: 8brn:

Sodium binding site 1 out of 1 in 8brn

Go back to Sodium Binding Sites List in 8brn
Sodium binding site 1 out of 1 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor


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 Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na530

b:21.5
occ:1.00
 O B:HOH798 3.1 24.8 1.0
O B:HOH646 3.2 19.4 0.8
O B:HOH820 3.3 23.1 0.9
N B:ARG108 3.3 35.1 1.0
N B:SER54 3.4 21.4 1.0
C B:GLY106 3.5 29.6 1.0
CB B:ARG108 3.5 36.7 1.0
CA B:GLY106 3.6 21.1 1.0
N B:LEU107 3.7 24.1 1.0
CA B:ARG108 3.9 37.3 1.0
CA B:GLY53 3.9 20.0 1.0
O B:GLY106 4.0 31.5 1.0
N B:ASN109 4.1 32.5 1.0
CG B:ARG108 4.1 44.1 1.0
O B:HOH817 4.2 20.4 1.0
C B:GLY53 4.2 24.1 1.0
CB B:SER54 4.2 26.5 1.0
CA B:SER54 4.3 23.5 1.0
O B:SER54 4.3 24.2 1.0
C B:LEU107 4.4 37.5 1.0
C B:ARG108 4.4 32.7 1.0
N B:GLY106 4.5 21.7 1.0
CA B:LEU107 4.6 25.9 1.0
ND2 B:ASN25 4.7 16.8 1.0
C B:SER54 4.8 22.8 1.0
OD1 B:ASN109 4.8 34.0 1.0

Reference:

D.Feder, S.H.Mohd-Pahmi, H.Adibi, L.W.Guddat, G.Schenk, R.P.Mcgeary, W.M.Hussein. Optimization of An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor of Purple Acid Phosphatase Using Rational Structure-Based Design Approaches. Eur.J.Med.Chem. V. 254 15383 2023.
ISSN: ISSN 0223-5234
PubMed: 37087894
DOI: 10.1016/J.EJMECH.2023.115383
Page generated: Wed Oct 9 10:48:28 2024

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