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Zinc 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:

Iron (Fe) 4 atoms
Sodium (Na) 5 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6of5

Go back to Zinc Binding Sites List in 6of5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:28.2
occ:0.77
 OD1 A:ASN201 2.1 31.1 1.0
NE2 A:HIS286 2.1 22.1 1.0
OD2 A:ASP164 2.1 25.9 1.0
ND1 A:HIS323 2.2 34.9 1.0
OAB A:MFJ528 2.4 42.1 0.7
OAD A:MFJ528 2.7 37.2 0.7
PBH A:MFJ528 3.0 35.5 0.7
CE1 A:HIS286 3.0 24.2 1.0
CE1 A:HIS323 3.1 32.4 1.0
CG A:ASP164 3.1 26.4 1.0
CD2 A:HIS286 3.2 26.3 1.0
CG A:ASN201 3.2 34.1 1.0
OAC A:MFJ528 3.2 33.5 0.7
CG A:HIS323 3.3 33.7 1.0
FE A:FE502 3.3 30.9 0.7
OD1 A:ASP164 3.4 24.7 1.0
CA A:HIS323 3.5 29.1 1.0
CB A:HIS323 3.7 26.7 1.0
OD2 A:ASP135 3.7 28.0 1.0
ND2 A:ASN201 3.8 33.4 1.0
ND1 A:HIS286 4.2 26.5 1.0
NE2 A:HIS323 4.2 31.9 1.0
CG A:HIS286 4.3 25.8 1.0
CD2 A:HIS202 4.3 33.4 1.0
O A:HIS323 4.3 25.6 1.0
N A:HIS323 4.3 29.6 1.0
CD2 A:HIS323 4.3 24.0 1.0
N A:ASN201 4.4 30.9 1.0
CB A:ASN201 4.4 26.3 1.0
C A:HIS323 4.4 35.0 1.0
CB A:ASP164 4.5 26.2 1.0
CBG A:MFJ528 4.8 43.1 0.7
CG A:ASP135 4.8 26.7 1.0
OH A:TYR253 4.9 24.3 1.0
CA A:ASN201 4.9 31.4 1.0
CAH A:MFJ528 4.9 47.1 0.7
N A:HIS202 5.0 28.6 1.0

Zinc binding site 2 out of 4 in 6of5

Go back to Zinc Binding Sites List in 6of5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:39.5
occ:1.00
 OD1 B:ASN201 2.1 36.6 1.0
ND1 B:HIS323 2.2 33.8 1.0
NE2 B:HIS286 2.2 34.9 1.0
OD2 B:ASP164 2.3 33.4 1.0
CE1 B:HIS323 3.0 33.2 1.0
CD2 B:HIS286 3.2 29.9 1.0
CG B:ASN201 3.2 35.1 1.0
CE1 B:HIS286 3.2 27.2 1.0
CG B:ASP164 3.2 34.7 1.0
CG B:HIS323 3.3 30.9 1.0
FE B:FE502 3.4 38.5 0.8
CA B:HIS323 3.5 32.3 1.0
OD1 B:ASP164 3.5 33.9 1.0
CB B:HIS323 3.8 34.2 1.0
ND2 B:ASN201 3.9 37.1 1.0
OD1 B:ASP135 3.9 30.6 1.0
NE2 B:HIS323 4.2 35.9 1.0
CD2 B:HIS202 4.2 33.1 1.0
O B:HIS323 4.2 38.2 1.0
ND1 B:HIS286 4.3 26.9 1.0
N B:ASN201 4.3 24.7 1.0
CD2 B:HIS323 4.3 29.6 1.0
CG B:HIS286 4.3 31.6 1.0
N B:HIS323 4.3 35.4 1.0
CB B:ASN201 4.4 31.7 1.0
C B:HIS323 4.4 33.8 1.0
CB B:ASP164 4.5 25.9 1.0
NE2 B:HIS202 4.8 36.3 1.0
OH B:TYR253 4.9 30.6 1.0
CA B:ASN201 4.9 27.6 1.0
CG B:ASP135 5.0 33.8 1.0

Zinc binding site 3 out of 4 in 6of5

Go back to Zinc Binding Sites List in 6of5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:35.9
occ:0.91
 NE2 D:HIS286 2.1 28.4 1.0
ND1 D:HIS323 2.1 34.0 1.0
OD1 D:ASN201 2.2 36.8 1.0
OD2 D:ASP164 2.4 33.2 1.0
CE1 D:HIS323 3.0 34.1 1.0
CE1 D:HIS286 3.0 27.9 1.0
CD2 D:HIS286 3.1 29.5 1.0
CG D:HIS323 3.1 35.1 1.0
CG D:ASN201 3.2 38.7 1.0
CG D:ASP164 3.3 33.6 1.0
CA D:HIS323 3.3 29.5 1.0
FE D:FE502 3.3 46.5 0.7
CB D:HIS323 3.5 28.5 1.0
OD1 D:ASP164 3.7 31.3 1.0
OD2 D:ASP135 3.7 32.5 1.0
ND2 D:ASN201 3.8 33.0 1.0
O D:HIS323 4.0 34.1 1.0
NE2 D:HIS323 4.1 27.9 1.0
ND1 D:HIS286 4.1 28.2 1.0
C D:HIS323 4.2 32.1 1.0
CG D:HIS286 4.2 27.1 1.0
CD2 D:HIS323 4.2 26.5 1.0
N D:HIS323 4.3 30.5 1.0
CB D:ASN201 4.3 36.3 1.0
N D:ASN201 4.4 35.0 1.0
CD2 D:HIS202 4.4 29.3 1.0
CB D:ASP164 4.5 31.8 1.0
CG D:ASP135 4.8 35.1 1.0
OH D:TYR253 4.9 27.1 1.0
CA D:ASN201 4.9 32.4 1.0

Zinc binding site 4 out of 4 in 6of5

Go back to Zinc Binding Sites List in 6of5
Zinc 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 Zinc with other atoms in the Zn 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:Zn501

b:31.4
occ:0.86
 NE2 C:HIS286 2.0 30.9 1.0
OD1 C:ASN201 2.1 35.7 1.0
ND1 C:HIS323 2.1 29.2 1.0
OD2 C:ASP164 2.5 32.5 1.0
CE1 C:HIS286 3.0 26.0 1.0
CE1 C:HIS323 3.1 36.8 1.0
CD2 C:HIS286 3.1 24.8 1.0
CG C:HIS323 3.2 30.7 1.0
CG C:ASN201 3.2 35.9 1.0
CA C:HIS323 3.3 26.2 1.0
CG C:ASP164 3.3 35.0 1.0
FE C:FE502 3.4 40.4 0.7
CB C:HIS323 3.5 28.7 1.0
OD1 C:ASP164 3.6 32.1 1.0
OD2 C:ASP135 3.7 35.7 1.0
ND2 C:ASN201 3.8 30.6 1.0
O C:HIS323 4.0 26.4 1.0
ND1 C:HIS286 4.1 28.5 1.0
C C:HIS323 4.2 30.3 1.0
CG C:HIS286 4.2 30.4 1.0
NE2 C:HIS323 4.2 30.5 1.0
N C:HIS323 4.2 27.9 1.0
N C:ASN201 4.2 25.2 1.0
CD2 C:HIS323 4.3 29.1 1.0
CB C:ASN201 4.3 33.9 1.0
CD2 C:HIS202 4.5 31.4 1.0
CB C:ASP164 4.6 29.1 1.0
OH C:TYR253 4.7 33.3 1.0
CA C:ASN201 4.8 32.3 1.0
CG C:ASP135 4.9 31.5 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: Tue Oct 29 04:20:37 2024

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