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Iron in PDB 3rde: Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase

Enzymatic activity of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase:
1.13.11.31;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase, PDB code: 3rde was solved by M.O.Funk, S.Xu, L.J.Marnett, T.C.Mueser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.450, 181.540, 91.610, 90.00, 92.86, 90.00
R / Rfree (%) 17.2 / 21.4

Other elements in 3rde:

The structure of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase also contains other interesting chemical elements:

Potassium (K) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase (pdb code 3rde). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase, PDB code: 3rde:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3rde

Go back to Iron Binding Sites List in 3rde
Iron binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1

b:8.9
occ:1.00
NE2 A:HIS541 2.1 8.2 1.0
NE2 A:HIS366 2.2 9.0 1.0
O A:HOH5 2.2 9.5 1.0
ND1 A:HIS545 2.3 9.7 1.0
NE2 A:HIS361 2.3 5.2 1.0
OXT A:ILE663 2.3 8.6 1.0
CE1 A:HIS361 3.0 8.7 1.0
CE1 A:HIS545 3.1 11.3 1.0
CE1 A:HIS541 3.1 8.1 1.0
CE1 A:HIS366 3.1 10.4 1.0
CD2 A:HIS541 3.1 8.1 1.0
C A:ILE663 3.2 9.2 1.0
CD2 A:HIS366 3.2 9.5 1.0
CG A:HIS545 3.4 7.9 1.0
CD2 A:HIS361 3.4 10.2 1.0
O A:ILE663 3.5 11.4 1.0
CB A:HIS545 3.8 6.6 1.0
ND1 A:HIS541 4.2 8.5 1.0
NE2 A:HIS545 4.2 13.1 1.0
ND1 A:HIS361 4.2 6.7 1.0
ND1 A:HIS366 4.3 8.6 1.0
CG A:HIS541 4.3 8.7 1.0
CG A:HIS366 4.3 10.7 1.0
C13 A:OYP664 4.4 9.8 1.0
CD2 A:HIS545 4.4 11.5 1.0
CG A:HIS361 4.4 8.0 1.0
CA A:ILE663 4.6 7.6 1.0
C14 A:OYP664 4.6 8.7 1.0
C12 A:OYP664 4.6 12.4 1.0
CG1 A:VAL661 4.8 4.5 1.0
N A:ILE663 4.9 9.6 1.0
CA A:HIS545 4.9 9.5 1.0
CG2 A:ILE663 4.9 10.1 1.0

Iron binding site 2 out of 4 in 3rde

Go back to Iron Binding Sites List in 3rde
Iron binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2

b:9.3
occ:1.00
NE2 B:HIS361 2.2 6.8 1.0
NE2 B:HIS541 2.2 7.1 1.0
NE2 B:HIS366 2.2 10.8 1.0
O B:HOH6 2.2 12.7 1.0
ND1 B:HIS545 2.3 9.5 1.0
OXT B:ILE663 2.3 9.4 1.0
CE1 B:HIS361 3.0 8.7 1.0
CE1 B:HIS545 3.1 10.9 1.0
CE1 B:HIS541 3.2 9.5 1.0
CD2 B:HIS541 3.2 8.8 1.0
CD2 B:HIS366 3.2 9.7 1.0
CE1 B:HIS366 3.2 10.4 1.0
C B:ILE663 3.2 10.7 1.0
CD2 B:HIS361 3.3 6.1 1.0
CG B:HIS545 3.4 9.6 1.0
O B:ILE663 3.5 9.2 1.0
CB B:HIS545 3.9 9.4 1.0
ND1 B:HIS361 4.2 7.1 1.0
NE2 B:HIS545 4.3 12.1 1.0
ND1 B:HIS541 4.3 9.5 1.0
ND1 B:HIS366 4.3 8.6 1.0
CG B:HIS541 4.3 10.9 1.0
CG B:HIS366 4.3 9.8 1.0
CG B:HIS361 4.3 5.9 1.0
C13 B:OYP664 4.4 12.3 1.0
CD2 B:HIS545 4.4 14.0 1.0
C14 B:OYP664 4.6 13.1 1.0
C12 B:OYP664 4.6 15.1 1.0
CA B:ILE663 4.7 11.6 1.0
CG1 B:VAL661 4.9 12.2 1.0
CA B:HIS545 4.9 9.2 1.0
N B:ILE663 5.0 11.2 1.0

Iron binding site 3 out of 4 in 3rde

Go back to Iron Binding Sites List in 3rde
Iron binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3

b:17.3
occ:1.00
NE2 C:HIS361 2.1 7.5 1.0
NE2 C:HIS541 2.2 15.8 1.0
OXT C:ILE663 2.3 17.7 1.0
NE2 C:HIS366 2.3 15.7 1.0
O C:HOH7 2.3 18.2 1.0
ND1 C:HIS545 2.3 19.8 1.0
CE1 C:HIS361 3.0 17.6 1.0
CE1 C:HIS545 3.1 22.7 1.0
CD2 C:HIS541 3.1 18.9 1.0
CD2 C:HIS361 3.1 20.1 1.0
CE1 C:HIS366 3.2 17.7 1.0
C C:ILE663 3.2 18.3 1.0
CE1 C:HIS541 3.3 18.2 1.0
CD2 C:HIS366 3.3 14.5 1.0
O C:ILE663 3.4 18.8 1.0
CG C:HIS545 3.4 17.7 1.0
CB C:HIS545 3.9 19.6 1.0
ND1 C:HIS361 4.1 13.6 1.0
CG C:HIS361 4.2 16.0 1.0
NE2 C:HIS545 4.3 22.0 1.0
CG C:HIS541 4.3 17.2 1.0
ND1 C:HIS366 4.3 18.4 1.0
ND1 C:HIS541 4.4 16.1 1.0
CG C:HIS366 4.4 16.5 1.0
C13 C:OYP664 4.4 16.0 1.0
CD2 C:HIS545 4.5 19.0 1.0
CA C:ILE663 4.6 17.7 1.0
C14 C:OYP664 4.6 15.8 1.0
C12 C:OYP664 4.7 16.6 1.0
CG2 C:ILE663 4.7 19.2 1.0
CG1 C:VAL661 4.8 18.1 1.0
CA C:HIS545 4.9 18.8 1.0
N C:ILE663 4.9 16.8 1.0

Iron binding site 4 out of 4 in 3rde

Go back to Iron Binding Sites List in 3rde
Iron binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Catalytic Domain of Porcine Leukocyte 12- Lipoxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe4

b:12.0
occ:1.00
NE2 D:HIS541 2.1 9.3 1.0
NE2 D:HIS361 2.2 10.7 1.0
O D:HOH8 2.2 13.7 1.0
NE2 D:HIS366 2.2 11.9 1.0
OXT D:ILE663 2.3 13.2 1.0
ND1 D:HIS545 2.3 13.7 1.0
CE1 D:HIS361 3.0 14.6 1.0
CE1 D:HIS541 3.1 13.9 1.0
CD2 D:HIS541 3.1 10.5 1.0
CE1 D:HIS545 3.1 13.9 1.0
CE1 D:HIS366 3.2 12.7 1.0
CD2 D:HIS366 3.2 16.0 1.0
C D:ILE663 3.3 14.8 1.0
CD2 D:HIS361 3.3 13.5 1.0
CG D:HIS545 3.4 12.0 1.0
O D:ILE663 3.5 12.3 1.0
CB D:HIS545 3.8 11.6 1.0
ND1 D:HIS361 4.2 14.0 1.0
ND1 D:HIS541 4.2 10.4 1.0
CG D:HIS541 4.2 9.1 1.0
NE2 D:HIS545 4.3 18.0 1.0
ND1 D:HIS366 4.3 13.7 1.0
CG D:HIS361 4.4 10.7 1.0
CG D:HIS366 4.4 13.8 1.0
C13 D:OYP664 4.4 15.1 1.0
CD2 D:HIS545 4.4 17.1 1.0
C12 D:OYP664 4.6 17.3 1.0
C14 D:OYP664 4.6 15.6 1.0
CA D:ILE663 4.7 13.5 1.0
CG1 D:VAL661 4.7 10.2 1.0
CA D:HIS545 4.9 10.4 1.0
N D:ILE663 5.0 14.4 1.0

Reference:

S.Xu, T.C.Mueser, L.J.Marnett, M.O.Funk. Crystal Structure of 12-Lipoxygenase Catalytic-Domain-Inhibitor Complex Identifies A Substrate-Binding Channel For Catalysis. Structure V. 20 1490 2012.
ISSN: ISSN 0969-2126
PubMed: 22795085
DOI: 10.1016/J.STR.2012.06.003
Page generated: Sun Dec 13 15:19:58 2020

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