Atomistry » Zinc » PDB 3jyg-3ked » 3kbp
Atomistry »
  Zinc »
    PDB 3jyg-3ked »
      3kbp »

Zinc in PDB 3kbp: Kidney Bean Purple Acid Phosphatase

Enzymatic activity of Kidney Bean Purple Acid Phosphatase

All present enzymatic activity of Kidney Bean Purple Acid Phosphatase:
3.1.3.2;

Protein crystallography data

The structure of Kidney Bean Purple Acid Phosphatase, PDB code: 3kbp was solved by T.Klabunde, N.Strater, B.Krebs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 132.700, 347.300, 128.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22

Other elements in 3kbp:

The structure of Kidney Bean Purple Acid Phosphatase also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Kidney Bean Purple Acid Phosphatase (pdb code 3kbp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Kidney Bean Purple Acid Phosphatase, PDB code: 3kbp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3kbp

Go back to Zinc Binding Sites List in 3kbp
Zinc binding site 1 out of 4 in the 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 Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn439

b:13.8
occ:1.00
O3 A:WO4440 2.1 22.0 1.0
OD1 A:ASN201 2.1 20.4 1.0
NE2 A:HIS286 2.1 11.4 1.0
ND1 A:HIS323 2.1 13.9 1.0
OD2 A:ASP164 2.3 15.2 1.0
CE1 A:HIS323 2.9 15.7 1.0
CD2 A:HIS286 3.1 10.2 1.0
CE1 A:HIS286 3.1 17.3 1.0
CG A:ASN201 3.1 20.0 1.0
W A:WO4440 3.2 45.0 1.0
FE A:FE438 3.2 13.8 1.0
CG A:ASP164 3.2 21.1 1.0
CG A:HIS323 3.3 15.7 1.0
O2 A:WO4440 3.4 21.2 1.0
OD1 A:ASP164 3.4 27.3 1.0
ND2 A:ASN201 3.5 19.3 1.0
CA A:HIS323 3.6 15.2 1.0
CB A:HIS323 3.8 15.9 1.0
O1 A:WO4440 3.9 34.4 1.0
NE2 A:HIS323 4.1 16.1 1.0
ND1 A:HIS286 4.2 15.6 1.0
CG A:HIS286 4.2 11.4 1.0
CD2 A:HIS323 4.3 15.8 1.0
OD2 A:ASP135 4.3 19.8 1.0
O A:HIS323 4.3 20.2 1.0
N A:HIS323 4.4 9.7 1.0
CD2 A:HIS202 4.5 17.8 1.0
C A:HIS323 4.5 16.4 1.0
CB A:ASN201 4.5 22.2 1.0
CB A:ASP164 4.6 18.4 1.0
N A:ASN201 4.6 18.4 1.0
O4 A:WO4440 4.7 33.8 1.0
NE2 A:HIS296 4.8 21.5 1.0
OD1 A:ASP135 4.9 18.7 1.0

Zinc binding site 2 out of 4 in 3kbp

Go back to Zinc Binding Sites List in 3kbp
Zinc binding site 2 out of 4 in the 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 Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn439

b:31.2
occ:1.00
NE2 B:HIS286 2.1 26.7 1.0
ND1 B:HIS323 2.1 26.4 1.0
O3 B:WO4440 2.2 39.6 1.0
OD1 B:ASN201 2.2 34.4 1.0
OD2 B:ASP164 2.3 34.0 1.0
CE1 B:HIS323 2.9 24.8 1.0
CD2 B:HIS286 3.0 27.3 1.0
CE1 B:HIS286 3.1 26.3 1.0
CG B:HIS323 3.2 25.6 1.0
FE B:FE438 3.2 32.9 1.0
CG B:ASN201 3.3 34.5 1.0
CG B:ASP164 3.3 36.6 1.0
W B:WO4440 3.3 56.8 1.0
OD1 B:ASP164 3.5 42.2 1.0
CA B:HIS323 3.5 23.9 1.0
O2 B:WO4440 3.6 34.2 1.0
ND2 B:ASN201 3.6 36.2 1.0
CB B:HIS323 3.7 23.4 1.0
O1 B:WO4440 4.0 47.9 1.0
NE2 B:HIS323 4.1 29.8 1.0
ND1 B:HIS286 4.2 23.9 1.0
CG B:HIS286 4.2 28.9 1.0
O B:HIS323 4.3 34.1 1.0
CD2 B:HIS323 4.3 28.0 1.0
OD2 B:ASP135 4.3 33.2 1.0
N B:HIS323 4.3 18.1 1.0
C B:HIS323 4.4 31.0 1.0
CD2 B:HIS202 4.6 35.6 1.0
CB B:ASP164 4.6 35.8 1.0
CB B:ASN201 4.6 32.2 1.0
N B:ASN201 4.6 31.2 1.0
OD1 B:ASP135 4.8 33.3 1.0
NE2 B:HIS296 4.8 56.8 1.0
O4 B:WO4440 4.8 42.2 1.0
CG B:ASP135 4.9 30.7 1.0

Zinc binding site 3 out of 4 in 3kbp

Go back to Zinc Binding Sites List in 3kbp
Zinc binding site 3 out of 4 in the 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 Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn439

b:21.1
occ:1.00
NE2 C:HIS286 2.1 22.8 1.0
O3 C:WO4440 2.1 27.0 1.0
ND1 C:HIS323 2.2 18.2 1.0
OD1 C:ASN201 2.2 20.7 1.0
OD2 C:ASP164 2.3 21.9 1.0
CE1 C:HIS323 2.9 17.1 1.0
CD2 C:HIS286 3.0 21.9 1.0
CE1 C:HIS286 3.1 25.4 1.0
FE C:FE438 3.2 17.5 1.0
CG C:ASN201 3.2 20.2 1.0
W C:WO4440 3.2 45.5 1.0
CG C:ASP164 3.2 26.1 1.0
CG C:HIS323 3.3 15.6 1.0
OD1 C:ASP164 3.4 31.2 1.0
O2 C:WO4440 3.4 25.3 1.0
ND2 C:ASN201 3.6 24.3 1.0
CA C:HIS323 3.6 20.0 1.0
CB C:HIS323 3.8 16.2 1.0
O1 C:WO4440 4.0 30.0 1.0
NE2 C:HIS323 4.1 17.1 1.0
ND1 C:HIS286 4.2 22.8 1.0
CG C:HIS286 4.2 23.9 1.0
OD2 C:ASP135 4.3 22.6 1.0
CD2 C:HIS323 4.4 16.8 1.0
N C:HIS323 4.4 19.9 1.0
O C:HIS323 4.4 25.1 1.0
C C:HIS323 4.5 20.9 1.0
CD2 C:HIS202 4.5 29.2 1.0
N C:ASN201 4.6 15.3 1.0
CB C:ASN201 4.6 18.1 1.0
CB C:ASP164 4.6 21.4 1.0
O4 C:WO4440 4.7 27.5 1.0
OD1 C:ASP135 4.8 27.4 1.0
NE2 C:HIS296 4.9 18.4 1.0
CG C:ASP135 4.9 23.5 1.0

Zinc binding site 4 out of 4 in 3kbp

Go back to Zinc Binding Sites List in 3kbp
Zinc binding site 4 out of 4 in the 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 Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn439

b:27.2
occ:1.00
NE2 D:HIS286 2.1 29.5 1.0
O3 D:WO4440 2.2 35.0 1.0
OD2 D:ASP164 2.2 27.5 1.0
OD1 D:ASN201 2.2 33.7 1.0
ND1 D:HIS323 2.2 27.7 1.0
CE1 D:HIS323 3.0 28.4 1.0
CD2 D:HIS286 3.0 27.0 1.0
CE1 D:HIS286 3.1 27.4 1.0
CG D:ASP164 3.1 28.9 1.0
FE D:FE438 3.2 26.7 1.0
W D:WO4440 3.2 52.5 1.0
CG D:ASN201 3.2 34.7 1.0
OD1 D:ASP164 3.3 25.5 1.0
CG D:HIS323 3.4 26.5 1.0
O2 D:WO4440 3.4 30.3 1.0
ND2 D:ASN201 3.6 36.7 1.0
CA D:HIS323 3.7 30.5 1.0
CB D:HIS323 3.9 27.8 1.0
O1 D:WO4440 4.0 45.8 1.0
ND1 D:HIS286 4.2 26.2 1.0
CG D:HIS286 4.2 25.0 1.0
NE2 D:HIS323 4.2 27.6 1.0
OD2 D:ASP135 4.3 27.5 1.0
CD2 D:HIS202 4.4 31.4 1.0
O D:HIS323 4.4 34.7 1.0
CD2 D:HIS323 4.4 26.8 1.0
N D:HIS323 4.4 25.7 1.0
CB D:ASP164 4.5 28.5 1.0
N D:ASN201 4.5 25.4 1.0
C D:HIS323 4.5 33.2 1.0
CB D:ASN201 4.6 31.8 1.0
OD1 D:ASP135 4.7 26.0 1.0
O4 D:WO4440 4.8 36.3 1.0
CG D:ASP135 4.9 28.9 1.0
NE2 D:HIS296 4.9 28.3 1.0

Reference:

T.Klabunde, N.Strater, R.Frohlich, H.Witzel, B.Krebs. Mechanism of Fe(III)-Zn(II) Purple Acid Phosphatase Based on Crystal Structures. J.Mol.Biol. V. 259 737 1996.
ISSN: ISSN 0022-2836
PubMed: 8683579
DOI: 10.1006/JMBI.1996.0354
Page generated: Wed Dec 16 04:29:49 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy