Zinc in PDB 4kbp: Kidney Bean Purple Acid Phosphatase

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

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

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

Iron

(Fe)

4 atoms

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 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 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 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 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

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