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Fluorine in PDB 4ivm: Structure of Human Protoporphyrinogen IX Oxidase(R59G)

Enzymatic activity of Structure of Human Protoporphyrinogen IX Oxidase(R59G)

All present enzymatic activity of Structure of Human Protoporphyrinogen IX Oxidase(R59G):
1.3.3.4;

Protein crystallography data

The structure of Structure of Human Protoporphyrinogen IX Oxidase(R59G), PDB code: 4ivm was solved by Q.Xiaohong, W.Baifan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.59 / 2.77
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 136.098, 136.098, 158.361, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 24

Other elements in 4ivm:

The structure of Structure of Human Protoporphyrinogen IX Oxidase(R59G) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Protoporphyrinogen IX Oxidase(R59G) (pdb code 4ivm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Human Protoporphyrinogen IX Oxidase(R59G), PDB code: 4ivm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4ivm

Go back to Fluorine Binding Sites List in 4ivm
Fluorine binding site 1 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase(R59G)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Protoporphyrinogen IX Oxidase(R59G) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:22.2
occ:1.00
F1 B:ACJ501 0.0 22.2 1.0
C1 B:ACJ501 1.3 25.5 1.0
F3 B:ACJ501 2.2 20.7 1.0
F2 B:ACJ501 2.2 20.0 1.0
C2 B:ACJ501 2.3 20.5 1.0
C3 B:ACJ501 2.8 14.6 1.0
N B:ALA172 3.3 12.0 1.0
O B:GLY169 3.3 18.2 1.0
O B:ARG168 3.4 15.9 1.0
C5 B:ACJ501 3.4 19.7 1.0
O B:VAL170 3.5 18.1 1.0
C B:VAL170 3.6 18.3 1.0
CB B:ALA172 3.7 13.3 1.0
C B:GLY169 3.8 16.6 1.0
CD1 B:ILE419 3.8 10.0 1.0
CA B:ALA172 3.8 13.2 1.0
C B:PHE171 3.9 14.7 1.0
N B:PHE171 4.0 17.3 1.0
C4 B:ACJ501 4.1 18.0 1.0
N B:VAL170 4.2 18.3 1.0
CA B:VAL170 4.3 18.0 1.0
CA B:PHE171 4.3 14.9 1.0
C B:ARG168 4.5 15.9 1.0
CA B:GLY169 4.5 16.5 1.0
C6 B:ACJ501 4.6 17.2 1.0
O B:PHE171 4.8 16.3 1.0
C7 B:ACJ501 4.8 18.5 1.0
N B:GLY169 5.0 15.8 1.0

Fluorine binding site 2 out of 3 in 4ivm

Go back to Fluorine Binding Sites List in 4ivm
Fluorine binding site 2 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase(R59G)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Protoporphyrinogen IX Oxidase(R59G) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:20.0
occ:1.00
F2 B:ACJ501 0.0 20.0 1.0
C1 B:ACJ501 1.3 25.5 1.0
F3 B:ACJ501 2.2 20.7 1.0
F1 B:ACJ501 2.2 22.2 1.0
C2 B:ACJ501 2.3 20.5 1.0
C5 B:ACJ501 2.6 19.7 1.0
C6 B:FAD502 3.2 17.6 1.0
C5X B:FAD502 3.2 19.9 1.0
C7 B:FAD502 3.5 19.9 1.0
CD1 B:ILE419 3.6 10.0 1.0
C9A B:FAD502 3.6 20.0 1.0
C3 B:ACJ501 3.6 14.6 1.0
N5 B:FAD502 3.7 24.3 1.0
C8 B:FAD502 3.9 22.1 1.0
C9 B:FAD502 3.9 20.3 1.0
C6 B:ACJ501 4.0 17.2 1.0
O B:GLY169 4.2 18.2 1.0
O B:VAL170 4.3 18.1 1.0
N10 B:FAD502 4.4 16.8 1.0
C4X B:FAD502 4.4 23.7 1.0
C7M B:FAD502 4.6 19.9 1.0
C4 B:ACJ501 4.7 18.0 1.0
C10 B:FAD502 4.7 21.5 1.0
O B:HOH647 4.8 20.2 1.0
C7 B:ACJ501 4.8 18.5 1.0
C B:VAL170 4.9 18.3 1.0
CG1 B:ILE419 5.0 8.0 1.0

Fluorine binding site 3 out of 3 in 4ivm

Go back to Fluorine Binding Sites List in 4ivm
Fluorine binding site 3 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase(R59G)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Protoporphyrinogen IX Oxidase(R59G) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:20.7
occ:1.00
F3 B:ACJ501 0.0 20.7 1.0
C1 B:ACJ501 1.3 25.5 1.0
F1 B:ACJ501 2.2 22.2 1.0
F2 B:ACJ501 2.2 20.0 1.0
C2 B:ACJ501 2.3 20.5 1.0
C3 B:ACJ501 2.9 14.6 1.0
C5 B:ACJ501 3.2 19.7 1.0
CD1 B:ILE419 3.6 10.0 1.0
CB B:ALA172 3.8 13.3 1.0
C7 B:FAD502 4.0 19.9 1.0
CG2 B:VAL314 4.0 8.9 1.0
C4 B:ACJ501 4.2 18.0 1.0
C6 B:FAD502 4.2 17.6 1.0
CG1 B:VAL314 4.3 9.7 1.0
C6 B:ACJ501 4.4 17.2 1.0
C7M B:FAD502 4.4 19.9 1.0
C8 B:FAD502 4.5 22.1 1.0
CA B:ALA172 4.6 13.2 1.0
CD1 B:LEU344 4.6 9.3 1.0
N B:ALA172 4.7 12.0 1.0
CB B:VAL314 4.7 10.0 1.0
C7 B:ACJ501 4.8 18.5 1.0
O B:ARG168 4.8 15.9 1.0
C5X B:FAD502 4.8 19.9 1.0
CG1 B:ILE419 4.9 8.0 1.0
SD B:MET368 4.9 23.4 1.0

Reference:

B.Wang, X.Wen, X.Qin, Z.Wang, Y.Tan, Y.Shen, Z.Xi. Quantitative Structural Insight Into Human Variegate Porphyria Disease. J.Biol.Chem. V. 288 11731 2013.
ISSN: ISSN 0021-9258
PubMed: 23467411
DOI: 10.1074/JBC.M113.459768
Page generated: Sun Dec 13 12:04:51 2020

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