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Iron in PDB 6g46: Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid

Enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid

All present enzymatic activity of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid:
3.1.3.2;

Protein crystallography data

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 6g46 was solved by D.F.Feder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.26 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.208, 126.208, 297.119, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22.3

Other elements in 6g46:

The structure of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid (pdb code 6g46). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid, PDB code: 6g46:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6g46

Go back to Iron Binding Sites List in 6g46
Iron binding site 1 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:32.1
occ:0.80
 OAA A:ELH515 1.8 34.3 0.8
OH A:TYR167 2.0 31.5 1.0
OD2 A:ASP135 2.1 30.6 1.0
NE2 A:HIS325 2.3 29.0 1.0
OD2 A:ASP164 2.4 26.5 1.0
CG A:ASP135 3.0 27.0 1.0
CAM A:ELH515 3.0 27.1 0.8
CB A:ASP135 3.2 25.3 1.0
CZ A:TYR167 3.2 28.2 1.0
CD2 A:HIS325 3.2 28.7 1.0
CE1 A:HIS325 3.3 28.0 1.0
CG A:ASP164 3.3 27.6 1.0
ZN A:ZN501 3.5 34.9 1.0
CB A:ASP164 3.6 29.1 1.0
OAB A:ELH515 3.6 36.6 0.8
CE2 A:TYR167 3.8 26.5 1.0
CAN A:ELH515 3.9 40.1 0.8
O A:HIS323 4.0 32.6 1.0
CAJ A:ELH515 4.1 51.0 0.8
OD1 A:ASP135 4.1 30.8 1.0
CA A:ASP135 4.2 22.9 1.0
CE1 A:TYR167 4.3 27.7 1.0
CA A:HIS323 4.4 29.6 1.0
ND1 A:HIS325 4.4 29.8 1.0
CG A:HIS325 4.4 27.8 1.0
CD2 A:HIS202 4.4 27.6 1.0
CE1 A:HIS286 4.5 28.4 1.0
OD1 A:ASP164 4.5 25.9 1.0
C A:HIS323 4.6 32.0 1.0
NE2 A:HIS286 4.6 26.5 1.0
N A:HIS323 4.7 25.4 1.0
NE2 A:HIS202 4.7 35.9 1.0
CB A:ASN364 4.9 27.2 1.0

Iron binding site 2 out of 4 in 6g46

Go back to Iron Binding Sites List in 6g46
Iron binding site 2 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:30.2
occ:0.70
 OAA B:ELH512 1.7 37.6 0.9
OD2 B:ASP135 1.9 33.5 1.0
OH B:TYR167 2.0 31.4 1.0
NE2 B:HIS325 2.4 24.5 1.0
OD2 B:ASP164 2.4 30.1 1.0
CAM B:ELH512 2.9 31.8 0.9
CG B:ASP135 3.0 29.8 1.0
CZ B:TYR167 3.1 29.3 1.0
CD2 B:HIS325 3.3 29.2 1.0
CG B:ASP164 3.4 30.9 1.0
CE1 B:HIS325 3.4 27.0 1.0
CB B:ASP135 3.4 22.2 1.0
OAB B:ELH512 3.5 38.3 0.9
CB B:ASP164 3.6 27.9 1.0
CE1 B:TYR167 3.6 33.2 1.0
ZN B:ZN501 3.6 36.3 1.0
CAN B:ELH512 4.0 45.9 0.9
OD1 B:ASP135 4.1 29.2 1.0
O B:HIS323 4.1 31.2 1.0
CD2 B:HIS202 4.2 30.6 1.0
CE2 B:TYR167 4.3 25.6 1.0
CAJ B:ELH512 4.3 53.9 0.9
CA B:ASP135 4.3 30.4 1.0
NE2 B:HIS202 4.5 31.9 1.0
CA B:HIS323 4.5 30.8 1.0
CG B:HIS325 4.5 32.3 1.0
ND1 B:HIS325 4.5 27.8 1.0
OD1 B:ASP164 4.5 30.6 1.0
CE1 B:HIS286 4.7 28.9 1.0
C B:HIS323 4.7 31.7 1.0
NE2 B:HIS286 4.7 30.1 1.0
CB B:ASN364 4.8 31.8 1.0
N B:HIS323 4.9 31.2 1.0
CD1 B:TYR167 5.0 34.9 1.0

Iron binding site 3 out of 4 in 6g46

Go back to Iron Binding Sites List in 6g46
Iron binding site 3 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:32.7
occ:0.73
 OH D:TYR167 1.9 27.6 1.0
OD1 D:ASP135 2.1 32.8 1.0
NE2 D:HIS325 2.2 28.2 1.0
O2 D:SO4512 2.2 28.2 0.7
OD2 D:ASP164 2.4 30.2 1.0
O3 D:SO4512 2.5 33.2 0.7
S D:SO4512 2.9 40.4 0.7
CG D:ASP135 3.1 29.0 1.0
CZ D:TYR167 3.1 31.0 1.0
CD2 D:HIS325 3.2 27.7 1.0
CE1 D:HIS325 3.2 29.8 1.0
CG D:ASP164 3.4 32.2 1.0
CB D:ASP135 3.5 25.8 1.0
ZN D:ZN501 3.6 32.9 0.9
CE2 D:TYR167 3.6 31.4 1.0
CB D:ASP164 3.8 26.3 1.0
O1 D:SO4512 3.9 33.4 0.7
O D:HIS323 3.9 28.2 1.0
O4 D:SO4512 4.0 39.5 0.7
CE1 D:TYR167 4.2 30.7 1.0
OD2 D:ASP135 4.2 29.6 1.0
ND1 D:HIS325 4.3 29.8 1.0
CD2 D:HIS202 4.3 33.2 1.0
CG D:HIS325 4.3 32.5 1.0
CA D:ASP135 4.4 27.7 1.0
CA D:HIS323 4.5 29.4 1.0
NE2 D:HIS202 4.5 32.8 1.0
OD1 D:ASP164 4.6 31.1 1.0
C D:HIS323 4.6 28.1 1.0
CE1 D:HIS286 4.7 25.1 1.0
CB D:ASN364 4.8 25.0 1.0
NE2 D:HIS286 4.8 28.7 1.0
N D:HIS323 4.9 29.1 1.0
CD2 D:TYR167 5.0 28.6 1.0

Iron binding site 4 out of 4 in 6g46

Go back to Iron Binding Sites List in 6g46
Iron binding site 4 out of 4 in the Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Red Kidney Bean Purple Acid Phosphatase in Complex with 2-(Naphthalen- 1-Yl)Thiazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:33.2
occ:0.89
 OH C:TYR167 1.9 31.5 1.0
OD2 C:ASP135 2.1 32.6 1.0
O1 C:SO4510 2.2 28.8 0.6
OD2 C:ASP164 2.3 33.4 1.0
NE2 C:HIS325 2.4 33.5 1.0
O2 C:SO4510 2.6 33.6 0.6
S C:SO4510 2.9 35.9 0.6
CG C:ASP135 3.1 30.0 1.0
CZ C:TYR167 3.1 27.9 1.0
CD2 C:HIS325 3.3 31.8 1.0
CG C:ASP164 3.3 29.8 1.0
CE1 C:HIS325 3.4 32.5 1.0
ZN C:ZN501 3.4 35.9 1.0
CB C:ASP135 3.4 28.2 1.0
CB C:ASP164 3.6 27.4 1.0
CE2 C:TYR167 3.6 31.6 1.0
O4 C:SO4510 4.0 38.0 0.6
O3 C:SO4510 4.0 29.9 0.6
O C:HIS323 4.1 25.9 1.0
OD1 C:ASP135 4.2 35.0 1.0
CE1 C:TYR167 4.3 28.3 1.0
CD2 C:HIS202 4.3 31.8 1.0
CA C:HIS323 4.4 28.9 1.0
CG C:HIS325 4.4 33.2 1.0
CA C:ASP135 4.5 29.2 1.0
ND1 C:HIS325 4.5 33.8 1.0
OD1 C:ASP164 4.5 26.8 1.0
C C:HIS323 4.6 28.9 1.0
NE2 C:HIS286 4.6 26.3 1.0
CE1 C:HIS286 4.6 26.5 1.0
NE2 C:HIS202 4.7 28.2 1.0
N C:HIS323 4.8 30.3 1.0
CB C:ASN364 4.9 28.0 1.0
OD1 C:ASN201 4.9 35.2 1.0

Reference:

W.M.Hussein, D.Feder, G.Schenk, L.W.Guddat, R.P.Mcgeary. Purple Acid Phosphatase Inhibitors As Leads For Osteoporosis Chemotherapeutics. Eur J Med Chem V. 157 462 2018.
ISSN: ISSN 1768-3254
PubMed: 30107365
DOI: 10.1016/J.EJMECH.2018.08.004
Page generated: Tue Aug 6 18:53:13 2024

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