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Chlorine 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
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with An Alpha-Aminonaphthylmethylphosphonic Acid Inhibitor, PDB code: 8brn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8brn

Go back to Chlorine Binding Sites List in 8brn
Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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
A:Cl528

b:24.2
occ:1.00
 O A:HOH853 3.1 25.1 0.9
O A:HOH661 3.2 22.2 1.0
O A:HOH692 3.3 23.1 1.0
N A:ARG108 3.3 27.2 1.0
N A:SER54 3.4 19.7 1.0
CB A:ARG108 3.5 30.6 0.5
CA A:GLY106 3.5 24.3 1.0
C A:GLY106 3.5 21.5 1.0
CB A:ARG108 3.5 30.6 0.5
N A:LEU107 3.7 21.1 1.0
CA A:ARG108 3.9 27.2 0.5
CA A:ARG108 3.9 27.2 0.5
CA A:GLY53 3.9 18.8 1.0
O A:GLY106 4.0 28.1 1.0
N A:ASN109 4.0 24.7 1.0
CB A:SER54 4.1 27.0 1.0
O A:HOH759 4.1 19.6 1.0
C A:GLY53 4.2 27.4 1.0
CG A:ARG108 4.2 33.3 0.5
CA A:SER54 4.2 25.6 1.0
O A:SER54 4.3 23.6 1.0
CG A:ARG108 4.3 33.3 0.5
C A:LEU107 4.4 30.8 1.0
C A:ARG108 4.4 34.4 1.0
N A:GLY106 4.5 17.0 1.0
CA A:LEU107 4.6 28.1 1.0
CD A:ARG108 4.7 36.2 0.5
ND2 A:ASN25 4.7 18.2 1.0
C A:SER54 4.8 21.7 1.0
CD A:ARG108 4.9 38.5 0.5
OD1 A:ASN109 5.0 28.1 1.0

Chlorine binding site 2 out of 6 in 8brn

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Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl binding site number 2 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
A:Cl529

b:19.8
occ:0.93
 O C:HOH897 3.0 15.5 1.0
O C:HOH875 3.0 20.4 1.0
N A:ARG258 3.2 16.4 1.0
NZ A:LYS306 3.4 18.9 1.0
CE A:LYS306 3.5 20.1 1.0
O C:GLU299 3.5 16.5 1.0
CA A:GLY257 3.7 16.3 1.0
CB A:ARG258 3.9 21.1 1.0
C A:GLY257 3.9 18.6 1.0
CE1 C:TYR253 4.0 16.6 1.0
O C:HOH895 4.0 17.2 1.0
CA A:ARG258 4.1 20.3 1.0
CB C:GLU299 4.3 17.5 1.0
C C:GLU299 4.4 16.0 1.0
CD1 C:TYR253 4.6 16.5 1.0
OG C:SER287 4.7 20.9 1.0
O A:ARG258 4.7 18.1 1.0
CA C:GLU299 4.8 20.7 1.0
OE1 C:GLU299 4.8 16.4 1.0
O C:SER252 4.8 14.9 1.0
CD A:LYS306 4.8 24.2 1.0
O A:HOH820 4.9 28.1 1.0
CZ C:TYR253 4.9 17.1 1.0
OH C:TYR253 4.9 19.9 1.0
C A:ARG258 5.0 21.6 1.0

Chlorine binding site 3 out of 6 in 8brn

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Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl529

b:19.8
occ:1.00
 NZ B:LYS306 3.0 18.5 1.0
O D:HOH744 3.1 12.3 1.0
O D:HOH673 3.1 15.2 1.0
N B:ARG258 3.1 20.1 1.0
CE B:LYS306 3.5 19.6 1.0
O D:GLU299 3.5 14.7 1.0
CA B:GLY257 3.6 18.4 1.0
C B:GLY257 3.9 20.2 1.0
CB B:ARG258 3.9 20.0 0.6
CB B:ARG258 3.9 20.1 0.4
CE1 D:TYR253 4.0 14.3 1.0
O D:HOH889 4.1 17.0 1.0
CA B:ARG258 4.1 18.5 0.6
CA B:ARG258 4.1 18.5 0.4
C D:GLU299 4.3 18.7 1.0
CB D:GLU299 4.4 14.9 1.0
O2 B:SO4510 4.4 18.4 0.6
CD1 D:TYR253 4.5 16.3 1.0
O B:ARG258 4.7 19.6 1.0
OG D:SER287 4.8 17.3 1.0
CA D:GLU299 4.8 20.9 1.0
OE1 D:GLU299 4.8 20.1 1.0
CD B:LYS306 4.9 23.2 1.0
O D:SER252 4.9 18.1 1.0
C B:ARG258 4.9 20.6 1.0
CZ D:TYR253 4.9 21.2 1.0

Chlorine binding site 4 out of 6 in 8brn

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Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl binding site number 4 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
C:Cl626

b:19.6
occ:1.00
 O A:HOH700 3.0 16.6 1.0
NZ C:LYS306 3.1 19.9 1.0
O A:HOH706 3.2 15.8 1.0
N C:ARG258 3.2 18.2 1.0
CE C:LYS306 3.5 21.6 1.0
O A:GLU299 3.5 17.2 1.0
CA C:GLY257 3.7 15.2 1.0
C C:GLY257 3.9 20.1 1.0
CB C:ARG258 4.0 22.2 1.0
CE1 A:TYR253 4.0 17.9 1.0
O A:HOH817 4.0 17.8 1.0
O4 C:SO4608 4.2 26.9 0.6
CA C:ARG258 4.2 19.1 1.0
C A:GLU299 4.4 20.0 1.0
CB A:GLU299 4.5 18.5 1.0
CD1 A:TYR253 4.6 14.6 1.0
O C:ARG258 4.7 20.6 1.0
OG A:SER287 4.7 20.2 1.0
O A:SER252 4.8 20.4 1.0
CA A:GLU299 4.8 17.6 1.0
CD C:LYS306 4.9 21.6 1.0
CZ A:TYR253 4.9 17.6 1.0
OE1 A:GLU299 4.9 19.9 1.0
C C:ARG258 4.9 18.2 1.0
OH A:TYR253 5.0 16.0 1.0

Chlorine binding site 5 out of 6 in 8brn

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Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl binding site number 5 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
D:Cl530

b:19.7
occ:1.00
 NZ D:LYS306 3.0 20.5 1.0
O B:HOH727 3.1 19.6 1.0
O B:HOH651 3.1 19.4 0.9
N D:ARG258 3.2 18.8 1.0
CE D:LYS306 3.4 21.8 1.0
O B:GLU299 3.6 18.2 1.0
CA D:GLY257 3.8 15.8 1.0
CB D:ARG258 3.9 20.6 0.6
CB D:ARG258 4.0 20.6 0.4
C D:GLY257 4.0 19.9 1.0
CE1 B:TYR253 4.1 18.1 1.0
O B:HOH828 4.1 16.4 1.0
CA D:ARG258 4.2 19.3 0.6
CA D:ARG258 4.2 19.4 0.4
CB B:GLU299 4.3 21.0 1.0
C B:GLU299 4.4 17.5 1.0
CD1 B:TYR253 4.7 14.8 1.0
OE1 B:GLU299 4.7 20.0 1.0
C1 D:GOL527 4.7 17.7 0.6
O D:ARG258 4.7 21.7 1.0
CA B:GLU299 4.7 19.3 1.0
OG B:SER287 4.8 20.1 1.0
CD D:LYS306 4.9 24.6 1.0
O1 D:GOL527 4.9 26.1 0.6
O B:SER252 4.9 18.1 1.0
CG B:GLU299 4.9 22.3 1.0
C D:ARG258 5.0 21.0 1.0

Chlorine binding site 6 out of 6 in 8brn

Go back to Chlorine Binding Sites List in 8brn
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl binding site number 6 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
D:Cl531

b:30.4
occ:1.00
 O D:HOH621 3.0 28.4 0.8
O D:HOH806 3.1 22.7 1.0
N D:ARG108 3.2 34.1 1.0
N D:SER54 3.2 23.2 1.0
O D:HOH779 3.3 25.3 1.0
CB D:ARG108 3.4 45.3 1.0
C D:GLY106 3.6 27.2 1.0
CA D:GLY106 3.6 23.8 1.0
N D:LEU107 3.7 19.2 1.0
CA D:GLY53 3.8 22.4 1.0
CA D:ARG108 3.8 37.8 1.0
C D:GLY53 4.0 35.8 1.0
N D:ASN109 4.0 35.8 1.0
CB D:SER54 4.1 31.5 1.0
CG D:ARG108 4.1 40.1 1.0
O D:GLY106 4.1 30.7 1.0
O D:SER54 4.2 24.5 1.0
CA D:SER54 4.2 27.0 1.0
C D:LEU107 4.3 36.4 1.0
O D:HOH668 4.3 23.6 1.0
CD D:ARG108 4.5 46.5 1.0
C D:ARG108 4.5 37.5 1.0
CA D:LEU107 4.6 25.6 1.0
N D:GLY106 4.6 21.9 1.0
ND2 D:ASN25 4.6 17.3 1.0
NH1 D:ARG108 4.6 46.0 1.0
C D:SER54 4.7 25.4 1.0
OD1 D:ASN109 4.7 37.5 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: Sun Jul 13 09:42:19 2025

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