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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

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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

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