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Zinc in PDB 4kbp: 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: 4kbp 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 / 2.70
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 (%) 19.2 / 22.8

Other elements in 4kbp:

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 4kbp). 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: 4kbp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4kbp

Go back to Zinc Binding Sites List in 4kbp
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:25.4
occ:1.00
O3 A:PO4440 2.0 20.6 1.0
NE2 A:HIS286 2.1 8.2 1.0
OD1 A:ASN201 2.1 24.9 1.0
ND1 A:HIS323 2.1 21.1 1.0
OD2 A:ASP164 2.2 25.8 1.0
CE1 A:HIS323 2.9 24.0 1.0
CE1 A:HIS286 3.0 12.7 1.0
CD2 A:HIS286 3.1 14.6 1.0
P A:PO4440 3.1 28.9 1.0
CG A:ASN201 3.1 24.0 1.0
CG A:ASP164 3.1 30.9 1.0
OD1 A:ASP164 3.3 39.5 1.0
FE A:FE438 3.3 29.1 1.0
CG A:HIS323 3.3 21.1 1.0
O2 A:PO4440 3.4 22.3 1.0
ND2 A:ASN201 3.4 25.6 1.0
O1 A:PO4440 3.6 34.5 1.0
CA A:HIS323 3.8 16.5 1.0
CB A:HIS323 3.9 17.6 1.0
NE2 A:HIS323 4.1 23.5 1.0
ND1 A:HIS286 4.2 15.8 1.0
CG A:HIS286 4.2 10.2 1.0
CD2 A:HIS202 4.2 17.8 1.0
CD2 A:HIS323 4.3 17.8 1.0
N A:ASN201 4.4 17.4 1.0
O A:HIS323 4.5 23.7 1.0
CB A:ASN201 4.5 26.3 1.0
O4 A:PO4440 4.5 36.4 1.0
CB A:ASP164 4.5 23.7 1.0
OD1 A:ASP135 4.5 26.2 1.0
N A:HIS323 4.6 15.3 1.0
C A:HIS323 4.6 16.3 1.0
OD2 A:ASP135 4.8 21.8 1.0
NE2 A:HIS202 4.9 20.6 1.0
CA A:ASN201 5.0 22.8 1.0

Zinc binding site 2 out of 4 in 4kbp

Go back to Zinc Binding Sites List in 4kbp
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:43.9
occ:1.00
NE2 B:HIS286 2.0 29.8 1.0
O3 B:PO4440 2.0 38.8 1.0
ND1 B:HIS323 2.1 32.5 1.0
OD1 B:ASN201 2.2 43.3 1.0
OD2 B:ASP164 2.3 39.3 1.0
CE1 B:HIS323 2.8 33.8 1.0
CE1 B:HIS286 3.0 33.4 1.0
CD2 B:HIS286 3.0 30.7 1.0
CG B:ASN201 3.1 41.4 1.0
P B:PO4440 3.2 34.0 1.0
CG B:ASP164 3.2 39.5 1.0
CG B:HIS323 3.3 33.9 1.0
OD1 B:ASP164 3.3 46.3 1.0
FE B:FE438 3.4 50.0 1.0
O2 B:PO4440 3.5 36.4 1.0
ND2 B:ASN201 3.5 38.7 1.0
CA B:HIS323 3.7 32.2 1.0
O1 B:PO4440 3.7 44.8 1.0
CB B:HIS323 3.9 33.5 1.0
NE2 B:HIS323 4.1 34.1 1.0
ND1 B:HIS286 4.1 29.0 1.0
CG B:HIS286 4.1 30.0 1.0
CD2 B:HIS202 4.3 47.2 1.0
CD2 B:HIS323 4.3 36.5 1.0
O B:HIS323 4.4 41.4 1.0
N B:ASN201 4.4 32.3 1.0
O4 B:PO4440 4.5 48.0 1.0
OD1 B:ASP135 4.5 36.0 1.0
CB B:ASN201 4.5 37.8 1.0
CB B:ASP164 4.5 30.5 1.0
N B:HIS323 4.5 26.9 1.0
C B:HIS323 4.6 35.0 1.0
OD2 B:ASP135 4.8 30.9 1.0
NE2 B:HIS202 4.9 48.3 1.0
OH B:TYR253 5.0 27.5 1.0
CA B:ASN201 5.0 34.1 1.0

Zinc binding site 3 out of 4 in 4kbp

Go back to Zinc Binding Sites List in 4kbp
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:31.0
occ:1.00
O3 C:PO4440 2.0 29.3 1.0
NE2 C:HIS286 2.1 18.6 1.0
ND1 C:HIS323 2.1 21.9 1.0
OD1 C:ASN201 2.2 28.5 1.0
OD2 C:ASP164 2.3 26.0 1.0
CE1 C:HIS323 2.8 27.3 1.0
CE1 C:HIS286 3.0 19.5 1.0
CD2 C:HIS286 3.0 18.7 1.0
P C:PO4440 3.1 26.4 1.0
CG C:ASN201 3.2 26.7 1.0
CG C:ASP164 3.2 31.3 1.0
CG C:HIS323 3.3 18.2 1.0
FE C:FE438 3.4 27.8 1.0
O2 C:PO4440 3.4 26.0 1.0
OD1 C:ASP164 3.4 37.4 1.0
ND2 C:ASN201 3.5 31.1 1.0
O1 C:PO4440 3.7 36.4 1.0
CA C:HIS323 3.7 21.1 1.0
CB C:HIS323 3.9 16.9 1.0
NE2 C:HIS323 4.1 23.1 1.0
ND1 C:HIS286 4.1 23.7 1.0
CG C:HIS286 4.2 21.0 1.0
CD2 C:HIS202 4.3 27.8 1.0
CD2 C:HIS323 4.3 20.7 1.0
O4 C:PO4440 4.4 42.4 1.0
O C:HIS323 4.4 31.6 1.0
N C:ASN201 4.4 17.5 1.0
N C:HIS323 4.5 21.4 1.0
CB C:ASN201 4.5 23.9 1.0
OD1 C:ASP135 4.5 22.6 1.0
CB C:ASP164 4.6 25.9 1.0
C C:HIS323 4.6 23.2 1.0
OD2 C:ASP135 4.7 18.9 1.0
NE2 C:HIS202 4.9 33.6 1.0
OH C:TYR253 4.9 32.0 1.0
NE2 C:HIS296 5.0 33.1 1.0

Zinc binding site 4 out of 4 in 4kbp

Go back to Zinc Binding Sites List in 4kbp
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:33.0
occ:1.00
O3 D:PO4440 2.0 31.5 1.0
NE2 D:HIS286 2.1 19.1 1.0
OD1 D:ASN201 2.2 30.1 1.0
OD2 D:ASP164 2.2 22.0 1.0
ND1 D:HIS323 2.2 23.1 1.0
CE1 D:HIS323 2.9 29.6 1.0
CE1 D:HIS286 3.0 13.8 1.0
CD2 D:HIS286 3.1 20.5 1.0
CG D:ASP164 3.1 28.2 1.0
P D:PO4440 3.1 34.1 1.0
CG D:ASN201 3.1 32.9 1.0
OD1 D:ASP164 3.2 28.4 1.0
FE D:FE438 3.3 31.8 1.0
O2 D:PO4440 3.3 28.6 1.0
CG D:HIS323 3.4 19.9 1.0
ND2 D:ASN201 3.4 33.9 1.0
O1 D:PO4440 3.7 46.1 1.0
CA D:HIS323 3.8 26.7 1.0
CB D:HIS323 4.0 22.6 1.0
CD2 D:HIS202 4.1 30.3 1.0
NE2 D:HIS323 4.2 27.5 1.0
ND1 D:HIS286 4.2 21.7 1.0
CG D:HIS286 4.2 15.1 1.0
N D:ASN201 4.4 19.9 1.0
CD2 D:HIS323 4.4 22.9 1.0
O4 D:PO4440 4.4 49.4 1.0
CB D:ASP164 4.4 28.1 1.0
CB D:ASN201 4.5 32.7 1.0
OD1 D:ASP135 4.5 27.4 1.0
O D:HIS323 4.5 33.2 1.0
N D:HIS323 4.6 20.8 1.0
C D:HIS323 4.7 29.6 1.0
OD2 D:ASP135 4.8 16.1 1.0
NE2 D:HIS202 4.8 23.9 1.0
CA D:ASN201 4.9 25.4 1.0
N D:HIS202 4.9 28.0 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: Sun Oct 27 01:05:54 2024

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