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Zinc 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:

Iron (Fe) 4 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6g46

Go back to Zinc Binding Sites List in 6g46
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:34.9
occ:1.00
 OD1 A:ASN201 1.9 31.9 1.0
NE2 A:HIS286 2.0 26.5 1.0
OAB A:ELH515 2.2 36.6 0.8
OD2 A:ASP164 2.2 26.5 1.0
ND1 A:HIS323 2.3 30.1 1.0
CE1 A:HIS286 2.9 28.4 1.0
CAM A:ELH515 2.9 27.1 0.8
OAA A:ELH515 3.0 34.3 0.8
CG A:ASN201 3.0 32.6 1.0
CE1 A:HIS323 3.1 27.5 1.0
CD2 A:HIS286 3.1 25.9 1.0
CG A:ASP164 3.1 27.6 1.0
OD1 A:ASP164 3.4 25.9 1.0
CG A:HIS323 3.4 28.7 1.0
FE A:FE502 3.5 32.1 0.8
CA A:HIS323 3.5 29.6 1.0
ND2 A:ASN201 3.5 29.0 1.0
OD2 A:ASP135 3.7 30.6 1.0
CB A:HIS323 3.8 26.4 1.0
ND1 A:HIS286 4.0 27.7 1.0
CAN A:ELH515 4.2 40.1 0.8
CG A:HIS286 4.2 29.8 1.0
N A:ASN201 4.2 25.2 1.0
O A:HIS323 4.3 32.6 1.0
CD2 A:HIS202 4.3 27.6 1.0
NE2 A:HIS323 4.3 29.5 1.0
CB A:ASN201 4.3 25.4 1.0
N A:HIS323 4.4 25.4 1.0
CB A:ASP164 4.4 29.1 1.0
C A:HIS323 4.4 32.0 1.0
CD2 A:HIS323 4.4 28.1 1.0
OH A:TYR253 4.8 25.3 1.0
NAK A:ELH515 4.8 53.5 0.8
CA A:ASN201 4.8 27.6 1.0
CG A:ASP135 4.9 27.0 1.0
NE2 A:HIS202 4.9 35.9 1.0
N A:HIS202 5.0 26.8 1.0

Zinc binding site 2 out of 4 in 6g46

Go back to Zinc Binding Sites List in 6g46
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:36.3
occ:1.00
 OD1 B:ASN201 2.0 36.9 1.0
NE2 B:HIS286 2.1 30.1 1.0
OD2 B:ASP164 2.3 30.1 1.0
ND1 B:HIS323 2.3 30.4 1.0
OAB B:ELH512 2.3 38.3 0.9
CG B:ASN201 3.0 33.8 1.0
CD2 B:HIS286 3.1 29.2 1.0
CE1 B:HIS323 3.1 33.3 1.0
CE1 B:HIS286 3.1 28.9 1.0
CG B:ASP164 3.1 30.9 1.0
CAM B:ELH512 3.2 31.8 0.9
OAA B:ELH512 3.3 37.6 0.9
CG B:HIS323 3.4 33.3 1.0
OD1 B:ASP164 3.4 30.6 1.0
ND2 B:ASN201 3.5 28.5 1.0
CA B:HIS323 3.5 30.8 1.0
FE B:FE502 3.6 30.2 0.7
CB B:HIS323 3.7 30.4 1.0
OD2 B:ASP135 3.8 33.5 1.0
O B:HIS323 4.2 31.2 1.0
ND1 B:HIS286 4.2 29.4 1.0
CG B:HIS286 4.3 29.0 1.0
CD2 B:HIS202 4.3 30.6 1.0
N B:ASN201 4.3 31.3 1.0
NE2 B:HIS323 4.3 34.6 1.0
CB B:ASN201 4.4 26.1 1.0
C B:HIS323 4.4 31.7 1.0
CAN B:ELH512 4.4 45.9 0.9
CD2 B:HIS323 4.4 34.1 1.0
N B:HIS323 4.4 31.2 1.0
CB B:ASP164 4.5 27.9 1.0
OH B:TYR253 4.8 27.7 1.0
CA B:ASN201 4.9 27.8 1.0
NE2 B:HIS202 4.9 31.9 1.0
NAK B:ELH512 4.9 55.7 0.9
CG B:ASP135 4.9 29.8 1.0

Zinc binding site 3 out of 4 in 6g46

Go back to Zinc Binding Sites List in 6g46
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:32.9
occ:0.95
 OD1 D:ASN201 2.0 34.7 1.0
NE2 D:HIS286 2.1 28.7 1.0
ND1 D:HIS323 2.1 27.8 1.0
O2 D:SO4512 2.2 28.2 0.7
OD2 D:ASP164 2.3 30.2 1.0
CE1 D:HIS323 3.0 27.9 1.0
O4 D:SO4512 3.0 39.5 0.7
CE1 D:HIS286 3.0 25.1 1.0
S D:SO4512 3.1 40.4 0.7
CD2 D:HIS286 3.1 24.9 1.0
CG D:ASP164 3.2 32.2 1.0
CG D:ASN201 3.2 32.5 1.0
CG D:HIS323 3.2 32.1 1.0
OD1 D:ASP164 3.4 31.1 1.0
CA D:HIS323 3.5 29.4 1.0
FE D:FE502 3.6 32.7 0.7
CB D:HIS323 3.7 28.8 1.0
OD1 D:ASP135 3.7 32.8 1.0
ND2 D:ASN201 3.8 28.2 1.0
O3 D:SO4512 4.0 33.2 0.7
O D:HIS323 4.1 28.2 1.0
ND1 D:HIS286 4.1 30.6 1.0
NE2 D:HIS323 4.1 26.5 1.0
O1 D:SO4512 4.2 33.4 0.7
CG D:HIS286 4.2 28.0 1.0
CD2 D:HIS202 4.3 33.2 1.0
N D:ASN201 4.3 27.8 1.0
CD2 D:HIS323 4.3 30.4 1.0
C D:HIS323 4.3 28.1 1.0
CB D:ASN201 4.4 30.7 1.0
N D:HIS323 4.5 29.1 1.0
CB D:ASP164 4.5 26.3 1.0
OH D:TYR253 4.8 23.1 1.0
CA D:ASN201 4.9 27.5 1.0
CG D:ASP135 4.9 29.0 1.0
NE2 D:HIS202 4.9 32.8 1.0

Zinc binding site 4 out of 4 in 6g46

Go back to Zinc Binding Sites List in 6g46
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:35.9
occ:1.00
 OD1 C:ASN201 1.9 35.2 1.0
NE2 C:HIS286 2.2 26.3 1.0
ND1 C:HIS323 2.3 26.6 1.0
OD2 C:ASP164 2.3 33.4 1.0
O1 C:SO4510 2.4 28.8 0.6
CG C:ASN201 3.1 32.8 1.0
O3 C:SO4510 3.1 29.9 0.6
CG C:ASP164 3.1 29.8 1.0
CE1 C:HIS323 3.2 31.4 1.0
CD2 C:HIS286 3.2 25.2 1.0
CE1 C:HIS286 3.2 26.5 1.0
S C:SO4510 3.2 35.9 0.6
CG C:HIS323 3.4 29.3 1.0
FE C:FE502 3.4 33.2 0.9
OD1 C:ASP164 3.5 26.8 1.0
CA C:HIS323 3.5 28.9 1.0
OD2 C:ASP135 3.7 32.6 1.0
ND2 C:ASN201 3.7 23.6 1.0
CB C:HIS323 3.7 25.3 1.0
O2 C:SO4510 4.0 33.6 0.6
O C:HIS323 4.1 25.9 1.0
CB C:ASN201 4.3 25.1 1.0
N C:ASN201 4.3 26.2 1.0
ND1 C:HIS286 4.3 27.4 1.0
CG C:HIS286 4.3 30.4 1.0
NE2 C:HIS323 4.3 31.2 1.0
C C:HIS323 4.3 28.9 1.0
CD2 C:HIS202 4.4 31.8 1.0
CB C:ASP164 4.4 27.4 1.0
O4 C:SO4510 4.4 38.0 0.6
N C:HIS323 4.4 30.3 1.0
CD2 C:HIS323 4.4 27.4 1.0
CG C:ASP135 4.8 30.0 1.0
CA C:ASN201 4.8 29.8 1.0
OH C:TYR253 4.9 28.1 1.0
OH C:TYR167 5.0 31.5 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: Mon Oct 28 21:35:53 2024

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