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Iron 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:

Zinc (Zn) 4 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 1kbp

Go back to Iron Binding Sites List in 1kbp
Iron binding site 1 out of 4 in the Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe438

b:33.8
occ:1.00
OH A:TYR167 2.1 27.1 1.0
OD2 A:ASP135 2.1 31.2 1.0
NE2 A:HIS325 2.3 25.4 1.0
OD2 A:ASP164 2.3 29.8 1.0
CZ A:TYR167 3.2 22.8 1.0
CG A:ASP135 3.2 30.9 1.0
CD2 A:HIS325 3.3 28.9 1.0
CE1 A:HIS325 3.3 28.1 1.0
CG A:ASP164 3.3 28.9 1.0
ZN A:ZN439 3.3 40.6 1.0
CE2 A:TYR167 3.7 24.5 1.0
CB A:ASP164 3.7 22.1 1.0
CB A:ASP135 3.9 22.1 1.0
OD1 A:ASP135 4.2 28.3 1.0
CD2 A:HIS202 4.2 14.8 1.0
CE1 A:TYR167 4.3 11.0 1.0
O A:HIS323 4.4 31.4 1.0
ND1 A:HIS325 4.4 30.3 1.0
CG A:HIS325 4.4 28.8 1.0
OD1 A:ASP164 4.4 32.2 1.0
CA A:HIS323 4.5 16.5 1.0
NE2 A:HIS286 4.5 16.2 1.0
CE1 A:HIS286 4.6 20.1 1.0
NE2 A:HIS202 4.6 15.2 1.0
CA A:ASP135 4.7 20.7 1.0
C A:HIS323 4.8 19.8 1.0
N A:HIS323 4.9 17.6 1.0
ND1 A:HIS323 4.9 26.3 1.0

Iron binding site 2 out of 4 in 1kbp

Go back to Iron Binding Sites List in 1kbp
Iron binding site 2 out of 4 in the Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe438

b:52.5
occ:1.00
OH B:TYR167 2.0 41.5 1.0
OD2 B:ASP135 2.0 35.6 1.0
OD2 B:ASP164 2.2 42.4 1.0
NE2 B:HIS325 2.3 51.9 1.0
CZ B:TYR167 3.1 35.7 1.0
CG B:ASP135 3.2 31.5 1.0
CG B:ASP164 3.2 43.2 1.0
CE1 B:HIS325 3.3 57.1 1.0
ZN B:ZN439 3.3 49.6 1.0
CD2 B:HIS325 3.3 56.6 1.0
CB B:ASP164 3.6 36.8 1.0
CE2 B:TYR167 3.7 33.2 1.0
CB B:ASP135 3.8 33.2 1.0
CD2 B:HIS202 4.1 49.7 1.0
OD1 B:ASP135 4.1 35.3 1.0
CE1 B:TYR167 4.3 23.7 1.0
OD1 B:ASP164 4.3 46.9 1.0
O B:HIS323 4.4 40.2 1.0
ND1 B:HIS325 4.4 56.4 1.0
NE2 B:HIS286 4.5 32.9 1.0
CG B:HIS325 4.5 56.2 1.0
NE2 B:HIS202 4.5 54.6 1.0
CE1 B:HIS286 4.5 36.8 1.0
CA B:HIS323 4.5 36.2 1.0
CA B:ASP135 4.7 30.4 1.0
C B:HIS323 4.8 38.8 1.0
N B:HIS323 4.9 31.8 1.0
ND1 B:HIS323 5.0 37.1 1.0

Iron binding site 3 out of 4 in 1kbp

Go back to Iron Binding Sites List in 1kbp
Iron binding site 3 out of 4 in the Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe438

b:30.4
occ:1.00
OD2 C:ASP135 2.0 26.3 1.0
OH C:TYR167 2.1 32.9 1.0
OD2 C:ASP164 2.2 29.1 1.0
NE2 C:HIS325 2.4 28.0 1.0
ZN C:ZN439 3.2 42.6 1.0
CZ C:TYR167 3.2 21.7 1.0
CG C:ASP135 3.2 29.4 1.0
CG C:ASP164 3.3 27.6 1.0
CD2 C:HIS325 3.3 26.9 1.0
CE1 C:HIS325 3.4 28.2 1.0
CB C:ASP164 3.7 25.4 1.0
CE2 C:TYR167 3.7 14.8 1.0
CB C:ASP135 3.9 23.6 1.0
OD1 C:ASP135 4.1 33.3 1.0
CD2 C:HIS202 4.2 27.5 1.0
CE1 C:TYR167 4.3 21.4 1.0
O C:HIS323 4.4 34.1 1.0
OD1 C:ASP164 4.4 28.7 1.0
NE2 C:HIS286 4.4 21.9 1.0
CA C:HIS323 4.4 20.7 1.0
CE1 C:HIS286 4.5 26.3 1.0
ND1 C:HIS325 4.5 23.7 1.0
CG C:HIS325 4.5 28.3 1.0
NE2 C:HIS202 4.6 34.0 1.0
CA C:ASP135 4.7 20.7 1.0
C C:HIS323 4.7 24.5 1.0
N C:HIS323 4.8 23.0 1.0
ND1 C:HIS323 4.9 27.6 1.0

Iron binding site 4 out of 4 in 1kbp

Go back to Iron Binding Sites List in 1kbp
Iron binding site 4 out of 4 in the Kidney Bean Purple Acid Phosphatase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Kidney Bean Purple Acid Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe438

b:33.8
occ:1.00
OD2 D:ASP135 2.0 26.7 1.0
OH D:TYR167 2.0 29.1 1.0
OD2 D:ASP164 2.2 28.0 1.0
NE2 D:HIS325 2.4 38.6 1.0
CG D:ASP135 3.1 28.4 1.0
CZ D:TYR167 3.1 25.7 1.0
CG D:ASP164 3.2 27.5 1.0
ZN D:ZN439 3.3 44.3 1.0
CD2 D:HIS325 3.3 44.3 1.0
CE1 D:HIS325 3.4 42.5 1.0
CB D:ASP164 3.6 28.8 1.0
CE2 D:TYR167 3.7 19.6 1.0
CB D:ASP135 3.8 28.9 1.0
OD1 D:ASP135 4.1 22.1 1.0
CD2 D:HIS202 4.1 26.8 1.0
CE1 D:TYR167 4.2 23.6 1.0
OD1 D:ASP164 4.3 27.7 1.0
NE2 D:HIS286 4.4 18.5 1.0
CE1 D:HIS286 4.4 17.8 1.0
O D:HIS323 4.5 35.4 1.0
CA D:HIS323 4.5 27.9 1.0
ND1 D:HIS325 4.5 43.7 1.0
CG D:HIS325 4.5 43.9 1.0
NE2 D:HIS202 4.6 22.4 1.0
CA D:ASP135 4.6 29.5 1.0
N D:HIS323 4.8 18.8 1.0
C D:HIS323 4.8 30.6 1.0
ND1 D:HIS323 5.0 29.5 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: Sat Aug 3 09:08:08 2024

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