Atomistry » Zinc » PDB 6o3r-6ofd » 6of5
Atomistry »
  Zinc »
    PDB 6o3r-6ofd »
      6of5 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy