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Iron 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
Zinc (Zn) 4 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 3kbp

Go back to Iron Binding Sites List in 3kbp
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:13.8
occ:1.00
O2 A:WO4440 2.0 21.2 1.0
OD2 A:ASP135 2.0 19.8 1.0
OH A:TYR167 2.2 11.8 1.0
OD2 A:ASP164 2.2 15.2 1.0
NE2 A:HIS325 2.4 15.9 1.0
W A:WO4440 3.1 45.0 1.0
ZN A:ZN439 3.2 13.8 1.0
CG A:ASP135 3.2 19.2 1.0
CG A:ASP164 3.3 21.1 1.0
CD2 A:HIS325 3.3 20.1 1.0
CZ A:TYR167 3.3 4.1 1.0
O1 A:WO4440 3.4 34.4 1.0
CE1 A:HIS325 3.4 26.3 1.0
O3 A:WO4440 3.6 22.0 1.0
CB A:ASP164 3.7 18.4 1.0
CE2 A:TYR167 3.9 3.0 1.0
OD1 A:ASP135 3.9 18.7 1.0
CB A:ASP135 4.2 13.9 1.0
CD2 A:HIS202 4.2 17.8 1.0
NE2 A:HIS286 4.3 11.4 1.0
CE1 A:HIS286 4.4 17.3 1.0
OD1 A:ASP164 4.4 27.3 1.0
CA A:HIS323 4.5 15.2 1.0
CE1 A:TYR167 4.5 5.9 1.0
CG A:HIS325 4.5 21.1 1.0
ND1 A:HIS325 4.5 24.1 1.0
O A:HIS323 4.6 20.2 1.0
O4 A:WO4440 4.6 33.8 1.0
NE2 A:HIS202 4.7 18.3 1.0
C A:HIS323 4.8 16.4 1.0
N A:HIS323 4.8 9.7 1.0
ND1 A:HIS323 4.8 13.9 1.0
CA A:ASP135 4.8 12.2 1.0
OD1 A:ASN201 4.9 20.4 1.0

Iron binding site 2 out of 4 in 3kbp

Go back to Iron Binding Sites List in 3kbp
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:32.9
occ:1.00
O2 B:WO4440 1.9 34.2 1.0
OD2 B:ASP135 2.1 33.2 1.0
OH B:TYR167 2.2 31.7 1.0
OD2 B:ASP164 2.3 34.0 1.0
NE2 B:HIS325 2.4 42.9 1.0
W B:WO4440 3.0 56.8 1.0
ZN B:ZN439 3.2 31.2 1.0
CG B:ASP135 3.3 30.7 1.0
CZ B:TYR167 3.3 30.8 1.0
CG B:ASP164 3.3 36.6 1.0
O1 B:WO4440 3.3 47.9 1.0
CD2 B:HIS325 3.4 44.3 1.0
CE1 B:HIS325 3.4 49.5 1.0
O3 B:WO4440 3.6 39.6 1.0
CB B:ASP164 3.8 35.8 1.0
CE2 B:TYR167 3.8 30.7 1.0
OD1 B:ASP135 4.0 33.3 1.0
CD2 B:HIS202 4.1 35.6 1.0
CB B:ASP135 4.2 30.3 1.0
NE2 B:HIS286 4.4 26.7 1.0
OD1 B:ASP164 4.4 42.2 1.0
CE1 B:TYR167 4.4 25.2 1.0
CE1 B:HIS286 4.5 26.3 1.0
ND1 B:HIS325 4.5 48.1 1.0
NE2 B:HIS202 4.5 39.1 1.0
CG B:HIS325 4.5 46.9 1.0
CA B:HIS323 4.6 23.9 1.0
O4 B:WO4440 4.7 42.2 1.0
O B:HIS323 4.7 34.1 1.0
ND1 B:HIS323 4.9 26.4 1.0
C B:HIS323 4.9 31.0 1.0
CA B:ASP135 4.9 30.9 1.0
N B:HIS323 5.0 18.1 1.0

Iron binding site 3 out of 4 in 3kbp

Go back to Iron Binding Sites List in 3kbp
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:17.5
occ:1.00
OD2 C:ASP135 2.0 22.6 1.0
O2 C:WO4440 2.0 25.3 1.0
OD2 C:ASP164 2.2 21.9 1.0
OH C:TYR167 2.2 18.3 1.0
NE2 C:HIS325 2.4 20.8 1.0
W C:WO4440 3.0 45.5 1.0
CG C:ASP135 3.1 23.5 1.0
ZN C:ZN439 3.2 21.1 1.0
CG C:ASP164 3.3 26.1 1.0
CD2 C:HIS325 3.3 20.2 1.0
O1 C:WO4440 3.3 30.0 1.0
CZ C:TYR167 3.4 12.8 1.0
CE1 C:HIS325 3.4 24.5 1.0
O3 C:WO4440 3.6 27.0 1.0
CB C:ASP164 3.8 21.4 1.0
OD1 C:ASP135 3.8 27.4 1.0
CE2 C:TYR167 3.9 12.6 1.0
CB C:ASP135 4.1 20.5 1.0
CD2 C:HIS202 4.2 29.2 1.0
NE2 C:HIS286 4.3 22.8 1.0
CE1 C:HIS286 4.4 25.4 1.0
OD1 C:ASP164 4.4 31.2 1.0
CA C:HIS323 4.4 20.0 1.0
CE1 C:TYR167 4.5 10.3 1.0
CG C:HIS325 4.5 23.3 1.0
ND1 C:HIS325 4.5 23.2 1.0
O C:HIS323 4.7 25.1 1.0
O4 C:WO4440 4.7 27.5 1.0
NE2 C:HIS202 4.7 32.8 1.0
C C:HIS323 4.8 20.9 1.0
N C:HIS323 4.8 19.9 1.0
CA C:ASP135 4.8 18.7 1.0
ND1 C:HIS323 4.8 18.2 1.0

Iron binding site 4 out of 4 in 3kbp

Go back to Iron Binding Sites List in 3kbp
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:26.7
occ:1.00
O2 D:WO4440 2.0 30.3 1.0
OD2 D:ASP135 2.0 27.5 1.0
OH D:TYR167 2.2 28.3 1.0
OD2 D:ASP164 2.3 27.5 1.0
NE2 D:HIS325 2.4 34.4 1.0
W D:WO4440 3.1 52.5 1.0
CG D:ASP135 3.2 28.9 1.0
ZN D:ZN439 3.2 27.2 1.0
CD2 D:HIS325 3.3 38.4 1.0
O1 D:WO4440 3.3 45.8 1.0
CG D:ASP164 3.4 28.9 1.0
CZ D:TYR167 3.4 25.4 1.0
CE1 D:HIS325 3.4 40.7 1.0
O3 D:WO4440 3.7 35.0 1.0
CB D:ASP164 3.8 28.5 1.0
OD1 D:ASP135 3.8 26.0 1.0
CE2 D:TYR167 3.9 18.5 1.0
CB D:ASP135 4.2 31.3 1.0
CD2 D:HIS202 4.2 31.4 1.0
NE2 D:HIS286 4.3 29.5 1.0
CE1 D:HIS286 4.4 27.4 1.0
OD1 D:ASP164 4.4 25.5 1.0
CG D:HIS325 4.5 41.0 1.0
CA D:HIS323 4.5 30.5 1.0
ND1 D:HIS325 4.5 42.3 1.0
CE1 D:TYR167 4.5 26.8 1.0
O D:HIS323 4.7 34.7 1.0
NE2 D:HIS202 4.7 29.2 1.0
O4 D:WO4440 4.8 36.3 1.0
C D:HIS323 4.8 33.2 1.0
CA D:ASP135 4.8 30.8 1.0
ND1 D:HIS323 4.8 27.7 1.0
N D:HIS323 4.8 25.7 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 Dec 13 15:10:13 2020

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