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Fluorine in PDB 1sez: Crystal Structure of Protoporphyrinogen IX Oxidase

Enzymatic activity of Crystal Structure of Protoporphyrinogen IX Oxidase

All present enzymatic activity of Crystal Structure of Protoporphyrinogen IX Oxidase:
1.3.3.4;

Protein crystallography data

The structure of Crystal Structure of Protoporphyrinogen IX Oxidase, PDB code: 1sez was solved by M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, A.Messerschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.090, 147.250, 127.040, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 29.3

Other elements in 1sez:

The structure of Crystal Structure of Protoporphyrinogen IX Oxidase also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Protoporphyrinogen IX Oxidase (pdb code 1sez). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Protoporphyrinogen IX Oxidase, PDB code: 1sez:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 1sez

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Fluorine binding site 1 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:60.0
occ:1.00
 F1 A:OMN601 0.0 60.0 1.0
C5 A:OMN601 1.4 58.1 1.0
F3 A:OMN601 2.2 56.9 1.0
F2 A:OMN601 2.2 59.7 1.0
C4 A:OMN601 2.4 57.7 1.0
O A:ALA174 3.0 46.6 1.0
N1 A:OMN601 3.1 58.4 1.0
N A:GLY178 3.2 50.8 1.0
C1 A:OMN601 3.2 60.0 1.0
C3 A:OMN601 3.5 56.9 1.0
C A:CYS177 3.6 51.5 1.0
CA A:GLY178 3.6 49.4 1.0
N A:CYS177 3.8 53.4 1.0
CA A:CYS177 3.9 51.2 1.0
CE1 A:PHE439 4.0 40.2 1.0
C A:GLY175 4.1 51.1 1.0
C A:ALA174 4.1 46.7 1.0
C A:THR176 4.1 54.5 1.0
CD1 A:LEU334 4.2 49.5 1.0
N2 A:OMN601 4.2 58.4 1.0
O A:GLY175 4.2 50.8 1.0
O A:CYS177 4.2 52.9 1.0
CZ A:PHE439 4.3 40.5 1.0
N A:THR176 4.3 52.0 1.0
BR1 A:OMN601 4.3 52.9 1.0
CA A:GLY175 4.4 49.9 1.0
C2 A:OMN601 4.4 57.1 1.0
O A:THR176 4.5 54.4 1.0
CA A:THR176 4.7 54.1 1.0
N A:GLY175 4.7 47.4 1.0
CD1 A:PHE439 4.9 43.6 1.0

Fluorine binding site 2 out of 8 in 1sez

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Fluorine binding site 2 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:59.7
occ:1.00
 F2 A:OMN601 0.0 59.7 1.0
C5 A:OMN601 1.3 58.1 1.0
F1 A:OMN601 2.2 60.0 1.0
F3 A:OMN601 2.2 56.9 1.0
C4 A:OMN601 2.3 57.7 1.0
N1 A:OMN601 2.9 58.4 1.0
C1 A:OMN601 3.0 60.0 1.0
CD2 A:PHE392 3.2 43.1 1.0
CD1 A:LEU334 3.3 49.5 1.0
CG A:PHE392 3.4 43.6 1.0
C3 A:OMN601 3.6 56.9 1.0
CB A:PHE392 3.7 42.1 1.0
CE2 A:PHE392 3.8 42.4 1.0
CD1 A:PHE392 4.0 44.6 1.0
N2 A:OMN601 4.1 58.4 1.0
CE1 A:PHE439 4.3 40.2 1.0
CG A:LEU334 4.3 51.0 1.0
CZ A:PHE392 4.4 43.3 1.0
C2 A:OMN601 4.4 57.1 1.0
CE1 A:PHE392 4.5 42.9 1.0
BR1 A:OMN601 4.5 52.9 1.0
CZ A:PHE439 4.7 40.5 1.0
O A:ALA174 4.8 46.6 1.0
C6 A:FAD600 4.8 32.6 1.0
CD1 A:LEU369 4.8 40.1 1.0
C7M A:FAD600 4.9 27.7 1.0
CD2 A:LEU334 4.9 52.0 1.0

Fluorine binding site 3 out of 8 in 1sez

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Fluorine binding site 3 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:56.9
occ:1.00
 F3 A:OMN601 0.0 56.9 1.0
C5 A:OMN601 1.4 58.1 1.0
F1 A:OMN601 2.2 60.0 1.0
F2 A:OMN601 2.2 59.7 1.0
C4 A:OMN601 2.4 57.7 1.0
C3 A:OMN601 2.9 56.9 1.0
BR1 A:OMN601 3.0 52.9 1.0
O A:ALA174 3.3 46.6 1.0
CD1 A:LEU369 3.3 40.1 1.0
CB A:PHE392 3.6 42.1 1.0
N1 A:OMN601 3.7 58.4 1.0
CB A:LEU369 3.7 39.3 1.0
CG A:PHE392 3.9 43.6 1.0
CD1 A:LEU334 4.0 49.5 1.0
CA A:GLY178 4.0 49.4 1.0
CG A:LEU369 4.1 41.2 1.0
C2 A:OMN601 4.2 57.1 1.0
N A:GLY178 4.3 50.8 1.0
CD1 A:PHE392 4.3 44.6 1.0
C A:ALA174 4.4 46.7 1.0
C1 A:OMN601 4.5 60.0 1.0
CD2 A:PHE392 4.5 43.1 1.0
N2 A:OMN601 4.6 58.4 1.0
CA A:GLY175 5.0 49.9 1.0
CA A:PHE392 5.0 45.9 1.0

Fluorine binding site 4 out of 8 in 1sez

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Fluorine binding site 4 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:59.3
occ:1.00
 F4 A:OMN601 0.0 59.3 1.0
C12 A:OMN601 1.3 59.0 1.0
C11 A:OMN601 2.3 59.9 1.0
C6 A:OMN601 2.4 58.1 1.0
C2 A:OMN601 3.0 57.1 1.0
C A:GLY370 3.1 45.4 1.0
N A:THR371 3.2 43.8 1.0
BR1 A:OMN601 3.2 52.9 1.0
C3 A:OMN601 3.3 56.9 1.0
O A:GLY370 3.3 46.0 1.0
CD1 A:PHE392 3.6 44.6 1.0
CA A:GLY370 3.6 44.6 1.0
CA A:THR371 3.6 43.9 1.0
C10 A:OMN601 3.6 61.6 1.0
C7 A:OMN601 3.7 57.3 1.0
C A:THR371 3.7 44.0 1.0
CE1 A:PHE392 3.8 42.9 1.0
N A:LEU372 4.0 44.6 1.0
O A:VAL355 4.0 50.8 1.0
O A:THR371 4.1 44.2 1.0
C8 A:OMN601 4.2 59.2 1.0
N2 A:OMN601 4.2 58.4 1.0
CG A:LEU372 4.2 47.0 1.0
CD2 A:LEU356 4.3 47.8 1.0
N A:GLY370 4.4 43.3 1.0
CD2 A:LEU372 4.5 44.6 1.0
C4 A:OMN601 4.5 57.7 1.0
CA A:LEU372 4.8 46.4 1.0
CG A:PHE392 4.8 43.6 1.0
N1 A:OMN601 4.9 58.4 1.0
C A:VAL355 4.9 49.0 1.0
O A:THR390 5.0 46.1 1.0

Fluorine binding site 5 out of 8 in 1sez

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Fluorine binding site 5 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:63.4
occ:1.00
 F1 B:OMN604 0.0 63.4 1.0
C5 B:OMN604 1.4 63.4 1.0
F3 B:OMN604 2.2 64.9 1.0
F2 B:OMN604 2.2 63.3 1.0
C4 B:OMN604 2.4 62.4 1.0
O B:ALA174 2.9 54.3 1.0
N B:GLY178 3.0 55.0 1.0
N1 B:OMN604 3.1 62.1 1.0
C1 B:OMN604 3.3 63.7 1.0
CA B:GLY178 3.4 55.5 1.0
C3 B:OMN604 3.5 61.2 1.0
C B:CYS177 3.5 55.1 1.0
N B:CYS177 3.8 56.7 1.0
CA B:CYS177 4.0 55.3 1.0
CD1 B:LEU334 4.0 50.8 1.0
C B:ALA174 4.1 53.6 1.0
CE1 B:PHE439 4.1 45.3 1.0
C B:GLY175 4.2 55.0 1.0
N2 B:OMN604 4.2 63.2 1.0
O B:CYS177 4.2 54.0 1.0
BR1 B:OMN604 4.3 62.4 1.0
C B:THR176 4.3 57.4 1.0
O B:GLY175 4.3 54.7 1.0
C2 B:OMN604 4.4 62.6 1.0
CZ B:PHE439 4.4 45.2 1.0
N B:THR176 4.4 55.1 1.0
CA B:GLY175 4.5 54.2 1.0
N B:GLY175 4.8 53.6 1.0
CD1 B:LEU369 4.8 45.8 1.0
O B:THR176 4.8 59.6 1.0
C B:GLY178 4.9 57.0 1.0
CA B:THR176 4.9 56.6 1.0
CD1 B:PHE439 5.0 49.2 1.0

Fluorine binding site 6 out of 8 in 1sez

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Fluorine binding site 6 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:63.3
occ:1.00
 F2 B:OMN604 0.0 63.3 1.0
C5 B:OMN604 1.3 63.4 1.0
F3 B:OMN604 2.2 64.9 1.0
F1 B:OMN604 2.2 63.4 1.0
C4 B:OMN604 2.4 62.4 1.0
N1 B:OMN604 2.9 62.1 1.0
CD1 B:LEU334 3.0 50.8 1.0
C1 B:OMN604 3.0 63.7 1.0
CD2 B:PHE392 3.2 47.3 1.0
CG B:PHE392 3.5 46.5 1.0
C3 B:OMN604 3.6 61.2 1.0
CB B:PHE392 3.6 45.0 1.0
CE2 B:PHE392 4.0 46.0 1.0
CG B:LEU334 4.0 49.3 1.0
N2 B:OMN604 4.2 63.2 1.0
CE1 B:PHE439 4.2 45.3 1.0
CD1 B:PHE392 4.3 47.4 1.0
C2 B:OMN604 4.5 62.6 1.0
CD2 B:LEU334 4.6 49.8 1.0
BR1 B:OMN604 4.6 62.4 1.0
CD1 B:LEU369 4.7 45.8 1.0
CZ B:PHE439 4.7 45.2 1.0
CZ B:PHE392 4.7 46.6 1.0
O B:ALA174 4.8 54.3 1.0
C7M B:FAD610 4.8 49.3 1.0
N B:GLY178 4.9 55.0 1.0
CE1 B:PHE392 4.9 45.4 1.0
CA B:GLY178 5.0 55.5 1.0
C6 B:FAD610 5.0 50.8 1.0

Fluorine binding site 7 out of 8 in 1sez

Go back to Fluorine Binding Sites List in 1sez
Fluorine binding site 7 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:64.9
occ:1.00
 F3 B:OMN604 0.0 64.9 1.0
C5 B:OMN604 1.4 63.4 1.0
F1 B:OMN604 2.2 63.4 1.0
F2 B:OMN604 2.2 63.3 1.0
C4 B:OMN604 2.4 62.4 1.0
C3 B:OMN604 3.0 61.2 1.0
BR1 B:OMN604 3.1 62.4 1.0
CD1 B:LEU369 3.1 45.8 1.0
O B:ALA174 3.4 54.3 1.0
CB B:PHE392 3.5 45.0 1.0
CB B:LEU369 3.6 43.1 1.0
N1 B:OMN604 3.7 62.1 1.0
CD1 B:LEU334 3.8 50.8 1.0
CA B:GLY178 3.9 55.5 1.0
CG B:PHE392 4.0 46.5 1.0
CG B:LEU369 4.0 45.5 1.0
N B:GLY178 4.3 55.0 1.0
C2 B:OMN604 4.3 62.6 1.0
CD2 B:PHE392 4.5 47.3 1.0
C1 B:OMN604 4.5 63.7 1.0
C B:ALA174 4.5 53.6 1.0
CD1 B:PHE392 4.6 47.4 1.0
N2 B:OMN604 4.6 63.2 1.0
CG B:LEU334 4.9 49.3 1.0
CA B:PHE392 4.9 46.5 1.0
CD2 B:LEU369 4.9 45.9 1.0

Fluorine binding site 8 out of 8 in 1sez

Go back to Fluorine Binding Sites List in 1sez
Fluorine binding site 8 out of 8 in the Crystal Structure of Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Protoporphyrinogen IX Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:64.2
occ:1.00
 F4 B:OMN604 0.0 64.2 1.0
C12 B:OMN604 1.3 64.1 1.0
C11 B:OMN604 2.3 66.3 1.0
C6 B:OMN604 2.4 63.7 1.0
C B:GLY370 3.0 46.4 1.0
C2 B:OMN604 3.0 62.6 1.0
BR1 B:OMN604 3.1 62.4 1.0
N B:THR371 3.1 45.7 1.0
C3 B:OMN604 3.2 61.2 1.0
CA B:GLY370 3.3 45.2 1.0
O B:GLY370 3.4 46.8 1.0
CD1 B:PHE392 3.6 47.4 1.0
C10 B:OMN604 3.6 66.9 1.0
CA B:THR371 3.7 45.3 1.0
C7 B:OMN604 3.7 64.8 1.0
O B:VAL355 3.7 52.3 1.0
C B:THR371 3.8 46.8 1.0
CE1 B:PHE392 3.9 45.4 1.0
N2 B:OMN604 4.2 63.2 1.0
C8 B:OMN604 4.2 66.2 1.0
O B:THR371 4.2 47.7 1.0
CD2 B:LEU356 4.2 51.0 1.0
N B:GLY370 4.2 45.5 1.0
N B:LEU372 4.2 46.6 1.0
C4 B:OMN604 4.5 62.4 1.0
CG B:LEU372 4.5 46.2 1.0
CD2 B:LEU372 4.6 45.9 1.0
CG B:PHE392 4.7 46.5 1.0
C B:VAL355 4.8 52.2 1.0
O B:LEU369 4.9 46.8 1.0
N1 B:OMN604 4.9 62.1 1.0
C B:LEU369 4.9 45.5 1.0
CL1 B:OMN604 5.0 73.4 1.0

Reference:

M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, A.Messerschmidt. Crystal Structure of Protoporphyrinogen IX Oxidase: A Key Enzyme in Haem and Chlorophyll Biosynthesis. Embo J. V. 23 1720 2004.
ISSN: ISSN 0261-4189
PubMed: 15057273
DOI: 10.1038/SJ.EMBOJ.7600189
Page generated: Wed Jul 31 12:50:13 2024

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