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

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

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

Resolution Low / High (Å) 20.05 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.174, 126.174, 298.044, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 19.9

Other elements in 6ofd:

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

Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase (pdb code 6ofd). 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 Octadecyloxy(Naphthalen-1-Yl)Methylphosphonic Acid in Complex with Red Kidney Bean Purple Acid Phosphatase, PDB code: 6ofd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ofd

Go back to Iron Binding Sites List in 6ofd
Iron binding site 1 out of 4 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:27.2
occ:0.75
 O A:HOH619 2.0 34.0 1.0
OH A:TYR167 2.0 26.9 1.0
OD2 A:ASP135 2.0 29.0 1.0
OD2 A:ASP164 2.4 23.3 1.0
NE2 A:HIS325 2.4 27.6 1.0
CG A:ASP135 3.0 24.2 1.0
CZ A:TYR167 3.1 24.4 1.0
CD2 A:HIS325 3.3 20.5 1.0
CG A:ASP164 3.3 24.5 1.0
CB A:ASP135 3.3 19.4 1.0
ZN A:ZN501 3.4 26.5 1.0
OBH A:MF1517 3.4 44.9 0.5
CE1 A:HIS325 3.5 29.5 1.0
CB A:ASP164 3.6 22.7 1.0
CE2 A:TYR167 3.6 24.1 1.0
OBF A:MF1517 3.9 45.3 0.5
O A:HIS323 4.0 25.6 1.0
OD1 A:ASP135 4.1 24.1 1.0
CE1 A:TYR167 4.2 23.8 1.0
OBG A:MF1517 4.2 38.0 0.5
CD2 A:HIS202 4.3 28.4 1.0
PBE A:MF1517 4.3 44.2 0.5
CA A:HIS323 4.3 19.1 1.0
CA A:ASP135 4.3 20.1 1.0
OD1 A:ASP164 4.5 24.4 1.0
CG A:HIS325 4.5 27.4 1.0
C A:HIS323 4.5 23.7 1.0
CE1 A:HIS286 4.5 19.7 1.0
ND1 A:HIS325 4.5 28.4 1.0
NE2 A:HIS286 4.6 22.8 1.0
NE2 A:HIS202 4.7 31.4 1.0
N A:HIS323 4.7 23.4 1.0
OBF A:MF1517 4.8 46.0 0.5
OD1 A:ASN201 4.9 27.9 1.0
CB A:ASN364 4.9 22.6 1.0
ND1 A:HIS323 5.0 25.3 1.0

Iron binding site 2 out of 4 in 6ofd

Go back to Iron Binding Sites List in 6ofd
Iron binding site 2 out of 4 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:28.5
occ:0.72
 OD2 B:ASP135 2.0 25.3 1.0
OH B:TYR167 2.1 27.1 1.0
OD2 B:ASP164 2.2 27.9 1.0
O B:HOH847 2.4 35.5 1.0
NE2 B:HIS325 2.5 25.1 1.0
CG B:ASP135 3.1 24.6 1.0
CZ B:TYR167 3.2 26.4 1.0
CG B:ASP164 3.2 26.4 1.0
ZN B:ZN501 3.3 27.6 1.0
CD2 B:HIS325 3.4 21.7 1.0
CE1 B:HIS325 3.5 26.1 1.0
CB B:ASP135 3.6 21.1 1.0
CB B:ASP164 3.6 21.9 1.0
CE2 B:TYR167 3.6 23.9 1.0
CD2 B:HIS202 4.0 24.3 1.0
O B:HIS323 4.0 26.2 1.0
OD1 B:ASP135 4.1 27.3 1.0
CA B:HIS323 4.3 25.3 1.0
OD1 B:ASP164 4.3 23.6 1.0
CE1 B:TYR167 4.4 23.2 1.0
NE2 B:HIS202 4.4 30.2 1.0
CA B:ASP135 4.5 22.2 1.0
C B:HIS323 4.5 24.8 1.0
CE1 B:HIS286 4.5 22.4 1.0
NE2 B:HIS286 4.6 24.9 1.0
CG B:HIS325 4.6 29.9 1.0
ND1 B:HIS325 4.6 30.2 1.0
N B:HIS323 4.8 22.0 1.0
OD1 B:ASN201 4.8 28.1 1.0
ND1 B:HIS323 4.9 22.3 1.0
CD2 B:TYR167 5.0 23.6 1.0

Iron binding site 3 out of 4 in 6ofd

Go back to Iron Binding Sites List in 6ofd
Iron binding site 3 out of 4 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:28.2
occ:0.60
 OH D:TYR167 1.9 23.7 1.0
OD2 D:ASP135 2.0 26.8 1.0
O D:HOH784 2.2 30.4 1.0
OD2 D:ASP164 2.3 25.1 1.0
NE2 D:HIS325 2.4 22.8 1.0
CG D:ASP135 3.1 26.6 1.0
CZ D:TYR167 3.1 23.5 1.0
CD2 D:HIS325 3.3 23.5 1.0
CG D:ASP164 3.3 24.8 1.0
ZN D:ZN501 3.4 22.5 0.9
CB D:ASP135 3.4 19.6 1.0
CE1 D:HIS325 3.5 24.6 1.0
CE2 D:TYR167 3.6 27.3 1.0
CB D:ASP164 3.7 20.6 1.0
O D:HIS323 3.9 22.1 1.0
CE1 D:TYR167 4.2 26.3 1.0
CD2 D:HIS202 4.2 28.2 1.0
OD1 D:ASP135 4.2 24.2 1.0
CA D:HIS323 4.3 19.8 1.0
CA D:ASP135 4.4 19.9 1.0
NE2 D:HIS202 4.4 27.8 1.0
OD1 D:ASP164 4.5 24.2 1.0
CG D:HIS325 4.5 26.3 1.0
C D:HIS323 4.5 24.6 1.0
CE1 D:HIS286 4.6 19.2 1.0
ND1 D:HIS325 4.6 25.6 1.0
NE2 D:HIS286 4.6 21.4 1.0
N D:HIS323 4.7 20.4 1.0
OD1 D:ASN201 4.9 27.6 1.0
ND1 D:HIS323 4.9 20.8 1.0
CB D:ASN364 5.0 22.9 1.0

Iron binding site 4 out of 4 in 6ofd

Go back to Iron Binding Sites List in 6ofd
Iron binding site 4 out of 4 in the The Crystal Structure of Octadecyloxy(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 Octadecyloxy(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:25.3
occ:0.63
 OH C:TYR167 1.9 25.9 1.0
O C:HOH623 1.9 32.9 1.0
OD2 C:ASP135 1.9 29.5 1.0
OD2 C:ASP164 2.2 23.7 1.0
NE2 C:HIS325 2.5 30.8 1.0
CG C:ASP135 3.0 25.5 1.0
CZ C:TYR167 3.0 24.4 1.0
CG C:ASP164 3.2 26.0 1.0
CB C:ASP135 3.4 21.5 1.0
CD2 C:HIS325 3.4 24.1 1.0
CB C:ASP164 3.5 18.0 1.0
ZN C:ZN501 3.5 26.5 1.0
CE1 C:HIS325 3.5 27.8 1.0
CE2 C:TYR167 3.6 26.3 1.0
O C:HIS323 4.0 23.7 1.0
OD1 C:ASP135 4.1 26.6 1.0
CE1 C:TYR167 4.1 23.2 1.0
CD2 C:HIS202 4.3 26.4 1.0
OD1 C:ASP164 4.3 21.5 1.0
CA C:ASP135 4.3 23.6 1.0
CA C:HIS323 4.4 21.4 1.0
CE1 C:HIS286 4.5 22.3 1.0
CG C:HIS325 4.6 31.6 1.0
C C:HIS323 4.6 24.7 1.0
ND1 C:HIS325 4.6 28.8 1.0
NE2 C:HIS286 4.7 21.9 1.0
NE2 C:HIS202 4.8 27.4 1.0
OD1 C:ASN201 4.8 28.4 1.0
N C:HIS323 4.8 23.9 1.0
CB C:ASN364 4.9 21.3 1.0
CD2 C:TYR167 5.0 23.8 1.0
ND1 C:HIS323 5.0 20.6 1.0
CA C:ASP164 5.0 21.4 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 04:21:06 2024

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