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Zinc 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:

Iron (Fe) 4 atoms
Chlorine (Cl) 6 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8brn

Go back to Zinc Binding Sites List in 8brn
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn501

b:22.1
occ:0.92
 OD1 A:ASN201 2.1 20.6 1.0
NE2 A:HIS286 2.2 16.8 1.0
OD2 A:ASP164 2.2 13.5 1.0
ND1 A:HIS323 2.3 17.4 1.0
O A:HOH643 2.3 17.4 0.5
O A:HOH643 2.4 21.3 0.5
CD2 A:HIS286 3.1 15.8 1.0
CG A:ASP164 3.2 19.1 1.0
CG A:ASN201 3.2 27.2 1.0
CE1 A:HIS323 3.2 18.8 1.0
CE1 A:HIS286 3.2 15.1 1.0
O25 A:R9X532 3.3 32.3 0.6
CG A:HIS323 3.3 19.0 1.0
FE A:FE502 3.4 22.4 0.8
CA A:HIS323 3.4 14.8 1.0
OD1 A:ASP164 3.5 17.2 1.0
CB A:HIS323 3.6 13.4 1.0
OD2 A:ASP135 3.6 20.7 1.0
ND2 A:ASN201 3.8 17.9 1.0
O A:HIS323 4.1 19.3 1.0
P24 A:R9X532 4.1 44.6 0.6
O27 A:R9X532 4.1 29.9 0.6
O26 A:R9X532 4.2 33.5 0.6
C A:HIS323 4.2 21.1 1.0
CG A:HIS286 4.3 19.2 1.0
N A:HIS323 4.3 13.1 1.0
ND1 A:HIS286 4.3 16.7 1.0
N A:ASN201 4.3 17.6 1.0
NE2 A:HIS323 4.3 17.2 1.0
CD2 A:HIS202 4.4 21.6 1.0
CB A:ASN201 4.4 19.6 1.0
CD2 A:HIS323 4.4 17.5 1.0
CB A:ASP164 4.5 16.2 1.0
CG A:ASP135 4.8 17.0 1.0
CA A:ASN201 4.9 16.0 1.0
OH A:TYR253 4.9 16.0 1.0

Zinc binding site 2 out of 4 in 8brn

Go back to Zinc Binding Sites List in 8brn
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn501

b:24.3
occ:1.00
 O B:HOH601 2.0 23.6 0.4
OD1 B:ASN201 2.1 21.6 1.0
NE2 B:HIS286 2.2 19.7 1.0
ND1 B:HIS323 2.3 17.9 1.0
OD2 B:ASP164 2.3 19.0 1.0
O27 B:R9X531 2.7 34.0 0.6
O26 B:R9X531 3.0 25.9 0.6
CD2 B:HIS286 3.1 15.1 1.0
CE1 B:HIS323 3.1 17.6 1.0
CG B:ASP164 3.2 17.0 1.0
CG B:ASN201 3.3 25.0 1.0
CE1 B:HIS286 3.3 18.4 1.0
CG B:HIS323 3.3 16.1 1.0
P24 B:R9X531 3.4 42.7 0.6
CA B:HIS323 3.4 17.4 1.0
FE B:FE502 3.4 27.1 0.9
OD1 B:ASP164 3.5 19.6 1.0
CB B:HIS323 3.7 16.8 1.0
OD2 B:ASP135 3.7 16.0 1.0
ND2 B:ASN201 3.8 25.0 1.0
O25 B:R9X531 4.0 40.6 0.6
O B:HIS323 4.1 20.3 1.0
N B:ASN201 4.2 17.6 1.0
NE2 B:HIS323 4.3 16.2 1.0
C B:HIS323 4.3 23.6 1.0
CG B:HIS286 4.3 18.4 1.0
ND1 B:HIS286 4.4 19.1 1.0
CD2 B:HIS202 4.4 24.2 1.0
N B:HIS323 4.4 17.0 1.0
CD2 B:HIS323 4.4 17.5 1.0
CB B:ASN201 4.5 23.9 1.0
CB B:ASP164 4.5 17.6 1.0
OH B:TYR253 4.8 18.8 1.0
CG B:ASP135 4.9 18.1 1.0
CA B:ASN201 4.9 19.3 1.0

Zinc binding site 3 out of 4 in 8brn

Go back to Zinc Binding Sites List in 8brn
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
C:Zn606

b:23.7
occ:1.00
 OD1 C:ASN201 2.2 21.1 1.0
NE2 C:HIS286 2.2 16.7 1.0
OD2 C:ASP164 2.2 21.1 1.0
ND1 C:HIS323 2.2 15.9 1.0
O C:HOH706 2.3 27.1 1.0
CD2 C:HIS286 3.1 15.0 1.0
CE1 C:HIS323 3.1 17.0 1.0
CG C:ASP164 3.2 21.3 1.0
CE1 C:HIS286 3.3 19.3 1.0
CG C:ASN201 3.3 27.3 1.0
CG C:HIS323 3.3 14.9 1.0
CA C:HIS323 3.4 16.5 1.0
FE C:FE607 3.4 25.1 0.8
OD1 C:ASP164 3.5 17.2 1.0
O27 C:R9X633 3.5 38.6 0.6
CB C:HIS323 3.7 12.9 1.0
OD2 C:ASP135 3.7 24.9 1.0
O25 C:R9X633 3.9 36.5 0.6
ND2 C:ASN201 4.0 24.1 1.0
O C:HIS323 4.1 18.8 1.0
P24 C:R9X633 4.2 46.2 0.6
C C:HIS323 4.2 21.1 1.0
N C:HIS323 4.3 16.5 1.0
CG C:HIS286 4.3 15.2 1.0
N C:ASN201 4.3 20.6 1.0
NE2 C:HIS323 4.3 16.7 1.0
ND1 C:HIS286 4.3 16.2 1.0
O26 C:R9X633 4.4 40.0 0.6
CD2 C:HIS323 4.4 16.1 1.0
CB C:ASN201 4.4 20.9 1.0
CD2 C:HIS202 4.4 26.6 1.0
CB C:ASP164 4.4 18.8 1.0
OH C:TYR253 4.8 19.9 1.0
CG C:ASP135 4.8 22.3 1.0
CA C:ASN201 4.9 18.4 1.0

Zinc binding site 4 out of 4 in 8brn

Go back to Zinc Binding Sites List in 8brn
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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
D:Zn501

b:22.5
occ:0.98
 OD1 D:ASN201 2.1 20.8 1.0
O D:HOH632 2.2 22.8 1.0
OD2 D:ASP164 2.2 19.4 1.0
NE2 D:HIS286 2.2 19.7 1.0
ND1 D:HIS323 2.3 15.9 1.0
O27 D:R9X535 3.0 31.2 0.5
CD2 D:HIS286 3.1 14.4 1.0
CG D:ASP164 3.1 21.1 1.0
CE1 D:HIS323 3.1 20.3 1.0
CG D:ASN201 3.2 21.9 1.0
CE1 D:HIS286 3.3 18.4 1.0
CG D:HIS323 3.3 20.4 1.0
FE D:FE502 3.3 24.7 0.8
CA D:HIS323 3.4 16.6 1.0
OD1 D:ASP164 3.4 18.5 1.0
OD2 D:ASP135 3.7 20.2 1.0
CB D:HIS323 3.7 13.4 1.0
ND2 D:ASN201 3.7 22.7 1.0
P24 D:R9X535 3.8 44.4 0.5
O26 D:R9X535 3.9 34.4 0.5
O25 D:R9X535 4.0 35.1 0.5
O D:HIS323 4.1 16.6 1.0
C D:HIS323 4.2 21.7 1.0
CG D:HIS286 4.3 18.1 1.0
N D:ASN201 4.3 14.2 1.0
NE2 D:HIS323 4.3 20.0 1.0
N D:HIS323 4.3 18.9 1.0
ND1 D:HIS286 4.4 19.6 1.0
CD2 D:HIS202 4.4 21.6 1.0
CB D:ASN201 4.4 19.2 1.0
CD2 D:HIS323 4.4 19.2 1.0
CB D:ASP164 4.4 15.9 1.0
OH D:TYR253 4.8 16.2 1.0
CG D:ASP135 4.8 18.9 1.0
CA D:ASN201 4.9 14.2 1.0
N D:HIS202 5.0 17.5 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: Wed Oct 30 18:24:59 2024

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