Atomistry » Zinc » PDB 1k52-1kjp » 1kbp
Atomistry »
  Zinc »
    PDB 1k52-1kjp »
      1kbp »

Zinc in PDB 1kbp: 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: 1kbp 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 / 2.65
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 (%) 19.5 / 23.3

Other elements in 1kbp:

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

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Kidney Bean Purple Acid Phosphatase (pdb code 1kbp). 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: 1kbp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1kbp

Go back to Zinc Binding Sites List in 1kbp
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:40.6
occ:1.00
NE2 A:HIS286 2.1 16.2 1.0
ND1 A:HIS323 2.2 26.3 1.0
OD1 A:ASN201 2.3 31.6 1.0
OD2 A:ASP164 2.3 29.8 1.0
CE1 A:HIS323 3.0 23.8 1.0
CD2 A:HIS286 3.1 14.1 1.0
CE1 A:HIS286 3.1 20.1 1.0
CG A:ASP164 3.2 28.9 1.0
FE A:FE438 3.3 33.8 1.0
CG A:ASN201 3.3 25.3 1.0
CG A:HIS323 3.4 21.8 1.0
OD1 A:ASP164 3.4 32.2 1.0
CA A:HIS323 3.6 16.5 1.0
ND2 A:ASN201 3.8 29.2 1.0
CB A:HIS323 3.8 16.3 1.0
OD2 A:ASP135 3.9 31.2 1.0
ND1 A:HIS286 4.2 17.6 1.0
NE2 A:HIS323 4.2 28.8 1.0
CG A:HIS286 4.2 11.2 1.0
N A:ASN201 4.3 21.1 1.0
CD2 A:HIS202 4.3 14.8 1.0
CD2 A:HIS323 4.4 22.6 1.0
N A:HIS323 4.4 17.6 1.0
O A:HIS323 4.4 31.4 1.0
CB A:ASP164 4.5 22.1 1.0
C A:HIS323 4.6 19.8 1.0
CB A:ASN201 4.6 27.3 1.0
CA A:ASN201 5.0 25.8 1.0
CG A:ASP135 5.0 30.9 1.0

Zinc binding site 2 out of 4 in 1kbp

Go back to Zinc Binding Sites List in 1kbp
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:49.6
occ:1.00
NE2 B:HIS286 2.2 32.9 1.0
ND1 B:HIS323 2.2 37.1 1.0
OD1 B:ASN201 2.2 46.3 1.0
OD2 B:ASP164 2.3 42.4 1.0
CE1 B:HIS323 3.0 33.6 1.0
CD2 B:HIS286 3.1 34.8 1.0
CE1 B:HIS286 3.2 36.8 1.0
CG B:ASP164 3.2 43.2 1.0
CG B:ASN201 3.3 43.9 1.0
FE B:FE438 3.3 52.5 1.0
CG B:HIS323 3.3 34.9 1.0
OD1 B:ASP164 3.4 46.9 1.0
CA B:HIS323 3.6 36.2 1.0
ND2 B:ASN201 3.7 45.0 1.0
CB B:HIS323 3.8 35.5 1.0
OD2 B:ASP135 3.9 35.6 1.0
NE2 B:HIS323 4.2 35.9 1.0
CG B:HIS286 4.3 31.8 1.0
ND1 B:HIS286 4.3 30.9 1.0
CD2 B:HIS202 4.3 49.7 1.0
CD2 B:HIS323 4.4 37.0 1.0
O B:HIS323 4.4 40.2 1.0
N B:ASN201 4.4 34.5 1.0
N B:HIS323 4.5 31.8 1.0
C B:HIS323 4.5 38.8 1.0
CB B:ASP164 4.5 36.8 1.0
CB B:ASN201 4.6 41.9 1.0
CG B:ASP135 4.9 31.5 1.0
CA B:ASN201 5.0 37.6 1.0
NE2 B:HIS202 5.0 54.6 1.0

Zinc binding site 3 out of 4 in 1kbp

Go back to Zinc Binding Sites List in 1kbp
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:42.6
occ:1.00
NE2 C:HIS286 2.2 21.9 1.0
ND1 C:HIS323 2.3 27.6 1.0
OD1 C:ASN201 2.3 32.8 1.0
OD2 C:ASP164 2.3 29.1 1.0
CE1 C:HIS323 3.0 27.8 1.0
FE C:FE438 3.2 30.4 1.0
CE1 C:HIS286 3.2 26.3 1.0
CD2 C:HIS286 3.2 24.8 1.0
CG C:ASP164 3.2 27.6 1.0
CG C:ASN201 3.3 28.8 1.0
CG C:HIS323 3.4 20.7 1.0
OD1 C:ASP164 3.5 28.7 1.0
CA C:HIS323 3.6 20.7 1.0
ND2 C:ASN201 3.7 31.1 1.0
CB C:HIS323 3.9 18.9 1.0
OD2 C:ASP135 4.0 26.3 1.0
NE2 C:HIS323 4.2 24.9 1.0
CD2 C:HIS202 4.3 27.5 1.0
ND1 C:HIS286 4.3 23.6 1.0
O C:HIS323 4.4 34.1 1.0
CG C:HIS286 4.4 18.4 1.0
N C:ASN201 4.4 15.1 1.0
N C:HIS323 4.4 23.0 1.0
CD2 C:HIS323 4.4 24.7 1.0
C C:HIS323 4.5 24.5 1.0
CB C:ASP164 4.5 25.4 1.0
CB C:ASN201 4.6 24.6 1.0
NE2 C:HIS325 5.0 28.0 1.0
OH C:TYR167 5.0 32.9 1.0
NE2 C:HIS202 5.0 34.0 1.0
CG C:ASP135 5.0 29.4 1.0

Zinc binding site 4 out of 4 in 1kbp

Go back to Zinc Binding Sites List in 1kbp
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:44.3
occ:1.00
NE2 D:HIS286 2.1 18.5 1.0
OD2 D:ASP164 2.2 28.0 1.0
ND1 D:HIS323 2.3 29.5 1.0
OD1 D:ASN201 2.3 36.3 1.0
CE1 D:HIS286 3.1 17.8 1.0
CE1 D:HIS323 3.1 29.3 1.0
CG D:ASP164 3.1 27.5 1.0
CD2 D:HIS286 3.1 19.7 1.0
FE D:FE438 3.3 33.8 1.0
OD1 D:ASP164 3.3 27.7 1.0
CG D:ASN201 3.4 34.4 1.0
CG D:HIS323 3.4 27.5 1.0
CA D:HIS323 3.6 27.9 1.0
ND2 D:ASN201 3.8 32.9 1.0
CB D:HIS323 3.9 24.6 1.0
OD2 D:ASP135 3.9 26.7 1.0
ND1 D:HIS286 4.2 17.1 1.0
CG D:HIS286 4.3 16.1 1.0
NE2 D:HIS323 4.3 29.1 1.0
CD2 D:HIS202 4.3 26.8 1.0
N D:ASN201 4.3 20.2 1.0
N D:HIS323 4.4 18.8 1.0
CB D:ASP164 4.4 28.8 1.0
CD2 D:HIS323 4.5 29.4 1.0
O D:HIS323 4.5 35.4 1.0
C D:HIS323 4.6 30.6 1.0
CB D:ASN201 4.6 30.4 1.0
CG D:ASP135 4.9 28.4 1.0
CA D:ASN201 5.0 25.9 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 02:54:40 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy