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Iron in PDB 6of5: The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

Enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase

All present enzymatic activity of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase:
3.1.3.2;

Protein crystallography data

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5 was solved by D.Feder, G.Schenk, L.W.Guddat, W.M.Hussein, R.P.Mcgeary, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.808, 126.808, 298.211, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 23.1

Other elements in 6of5:

The structure of The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6of5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6of5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 1 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

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

b:30.9
occ:0.66
 OAC A:MFJ528 1.8 33.5 0.7
OH A:TYR167 2.0 30.9 1.0
OD2 A:ASP135 2.0 28.0 1.0
OD2 A:ASP164 2.4 25.9 1.0
NE2 A:HIS325 2.5 31.5 1.0
OAD A:MFJ528 2.9 37.2 0.7
PBH A:MFJ528 2.9 35.5 0.7
CG A:ASP135 3.0 26.7 1.0
CZ A:TYR167 3.2 30.6 1.0
CG A:ASP164 3.3 26.4 1.0
ZN A:ZN501 3.3 28.2 0.8
CB A:ASP135 3.4 21.8 1.0
CD2 A:HIS325 3.4 28.8 1.0
CE1 A:HIS325 3.5 31.9 1.0
CB A:ASP164 3.6 26.2 1.0
OAB A:MFJ528 3.7 42.1 0.7
CE2 A:TYR167 3.8 27.5 1.0
OD1 A:ASP135 4.1 25.0 1.0
O A:HIS323 4.2 25.6 1.0
CD2 A:HIS202 4.2 33.4 1.0
CE1 A:TYR167 4.2 25.7 1.0
CBG A:MFJ528 4.3 43.1 0.7
OBC A:MFJ528 4.4 44.2 0.7
CA A:HIS323 4.4 29.1 1.0
OD1 A:ASP164 4.4 24.7 1.0
CA A:ASP135 4.4 25.0 1.0
CE1 A:HIS286 4.5 24.2 1.0
NE2 A:HIS286 4.6 22.1 1.0
CG A:HIS325 4.6 31.6 1.0
ND1 A:HIS325 4.6 34.1 1.0
NE2 A:HIS202 4.6 31.2 1.0
C A:HIS323 4.7 35.0 1.0
N A:HIS323 4.7 29.6 1.0
ND1 A:HIS323 4.9 34.9 1.0
OD1 A:ASN201 5.0 31.1 1.0

Iron binding site 2 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 2 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

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

b:38.5
occ:0.79
 OH B:TYR167 2.0 33.1 1.0
OD1 B:ASP135 2.0 30.6 1.0
OD2 B:ASP164 2.4 33.4 1.0
NE2 B:HIS325 2.5 34.1 1.0
CG B:ASP135 3.1 33.8 1.0
CZ B:TYR167 3.1 29.2 1.0
CD2 B:HIS325 3.4 32.3 1.0
ZN B:ZN501 3.4 39.5 1.0
CG B:ASP164 3.4 34.7 1.0
CE1 B:HIS325 3.5 27.2 1.0
CE2 B:TYR167 3.7 27.9 1.0
CB B:ASP135 3.7 31.2 1.0
CB B:ASP164 3.7 25.9 1.0
O B:HIS323 4.0 38.2 1.0
CD2 B:HIS202 4.1 33.1 1.0
OD2 B:ASP135 4.2 29.9 1.0
CE1 B:TYR167 4.2 30.7 1.0
NE2 B:HIS202 4.3 36.3 1.0
CA B:HIS323 4.4 32.3 1.0
OD1 B:ASP164 4.5 33.9 1.0
C B:HIS323 4.6 33.8 1.0
CG B:HIS325 4.6 34.9 1.0
ND1 B:HIS325 4.6 35.7 1.0
CA B:ASP135 4.6 31.6 1.0
NE2 B:HIS286 4.6 34.9 1.0
CE1 B:HIS286 4.7 27.2 1.0
N B:HIS323 4.8 35.4 1.0
OD1 B:ASN201 4.9 36.6 1.0
ND1 B:HIS323 4.9 33.8 1.0

Iron binding site 3 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 3 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

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

b:46.5
occ:0.72
 OD2 D:ASP135 1.9 32.5 1.0
OH D:TYR167 2.0 29.2 1.0
OD2 D:ASP164 2.6 33.2 1.0
NE2 D:HIS325 2.6 33.1 1.0
CG D:ASP135 3.1 35.1 1.0
CZ D:TYR167 3.1 32.8 1.0
ZN D:ZN501 3.3 35.9 0.9
CD2 D:HIS325 3.4 34.3 1.0
CG D:ASP164 3.6 33.6 1.0
CE2 D:TYR167 3.6 33.9 1.0
CE1 D:HIS325 3.7 32.2 1.0
CB D:ASP135 3.7 26.9 1.0
CB D:ASP164 3.9 31.8 1.0
O D:HIS323 3.9 34.1 1.0
OD1 D:ASP135 4.1 32.4 1.0
CD2 D:HIS202 4.2 29.3 1.0
CE1 D:TYR167 4.3 27.5 1.0
CA D:HIS323 4.3 29.5 1.0
C D:HIS323 4.5 32.1 1.0
NE2 D:HIS286 4.6 28.4 1.0
NE2 D:HIS202 4.6 32.4 1.0
CE1 D:HIS286 4.6 27.9 1.0
CA D:ASP135 4.6 25.7 1.0
CG D:HIS325 4.6 36.5 1.0
OD1 D:ASN201 4.7 36.8 1.0
OD1 D:ASP164 4.7 31.3 1.0
ND1 D:HIS325 4.7 34.5 1.0
ND1 D:HIS323 4.8 34.0 1.0
N D:HIS323 4.8 30.5 1.0

Iron binding site 4 out of 4 in 6of5

Go back to Iron Binding Sites List in 6of5
Iron binding site 4 out of 4 in the The Crystal Structure of Dodecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

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

b:40.4
occ:0.74
 OH C:TYR167 2.0 30.6 1.0
OD2 C:ASP135 2.0 35.7 1.0
OD2 C:ASP164 2.2 32.5 1.0
NE2 C:HIS325 2.6 35.9 1.0
CG C:ASP135 3.1 31.5 1.0
CZ C:TYR167 3.2 32.3 1.0
CG C:ASP164 3.2 35.0 1.0
ZN C:ZN501 3.4 31.4 0.9
CD2 C:HIS325 3.5 34.4 1.0
CB C:ASP135 3.5 27.4 1.0
CB C:ASP164 3.7 29.1 1.0
CE1 C:HIS325 3.7 36.3 1.0
CE2 C:TYR167 3.7 33.1 1.0
O C:HIS323 3.8 26.4 1.0
OD1 C:ASP135 4.1 34.1 1.0
CA C:HIS323 4.2 26.2 1.0
CE1 C:TYR167 4.3 30.2 1.0
OD1 C:ASP164 4.3 32.1 1.0
CD2 C:HIS202 4.4 31.4 1.0
C C:HIS323 4.4 30.3 1.0
CE1 C:HIS286 4.5 26.0 1.0
NE2 C:HIS286 4.5 30.9 1.0
CA C:ASP135 4.6 29.0 1.0
CG C:HIS325 4.7 35.3 1.0
N C:HIS323 4.7 27.9 1.0
NE2 C:HIS202 4.7 33.5 1.0
ND1 C:HIS325 4.7 37.8 1.0
OD1 C:ASN201 4.8 35.7 1.0
ND1 C:HIS323 4.9 29.2 1.0

Reference:

D.Feder, M.W.Kan, W.M.Hussein, L.W.Guddat, G.Schenk, R.P.Mcgeary. Synthesis, Evaluation and Structural Investigations of Potent Purple Acid Phosphatase Inhibitors As Drug Leads For Osteoporosis. Eur.J.Med.Chem. V. 182 11611 2019.
ISSN: ISSN 0223-5234
PubMed: 31445230
DOI: 10.1016/J.EJMECH.2019.111611
Page generated: Wed Aug 7 04:20:57 2024

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