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Fluorine in PDB 2ivd: Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen

Enzymatic activity of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen

All present enzymatic activity of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen:
1.3.3.4;

Protein crystallography data

The structure of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen, PDB code: 2ivd was solved by H.R.Corradi, A.V.Corrigall, E.Boix, C.G.Mohan, E.D.Sturrock, P.N.Meissner, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.3
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 148.918, 148.918, 131.924, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.3

Other elements in 2ivd:

The structure of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen (pdb code 2ivd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen, PDB code: 2ivd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2ivd

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Fluorine binding site 1 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1465

b:51.6
occ:1.00
 F1 A:ACJ1465 0.0 51.6 1.0
C1 A:ACJ1465 1.3 51.0 1.0
F3 A:ACJ1465 2.1 53.0 1.0
F2 A:ACJ1465 2.2 51.9 1.0
C2 A:ACJ1465 2.3 50.5 1.0
C3 A:ACJ1465 2.7 49.9 1.0
O A:ILE168 3.2 24.6 1.0
C A:ILE168 3.4 24.4 1.0
N A:ALA170 3.5 23.1 1.0
C5 A:ACJ1465 3.6 50.0 1.0
N A:TYR169 3.7 24.0 1.0
C A:TYR169 3.7 23.3 1.0
CB A:ALA170 3.8 22.9 1.0
O A:THR166 3.8 24.7 1.0
CA A:TYR169 3.9 23.3 1.0
C4 A:ACJ1465 4.1 50.1 1.0
O A:GLY167 4.1 25.2 1.0
CA A:ILE168 4.2 24.5 1.0
CG1 A:ILE412 4.2 30.4 1.0
CA A:ALA170 4.2 23.0 1.0
O A:TYR169 4.2 23.5 1.0
N A:ILE168 4.2 24.7 1.0
C A:GLY167 4.2 24.8 1.0
CD1 A:ILE311 4.3 30.2 1.0
CD1 A:ILE412 4.6 30.3 1.0
C6 A:ACJ1465 4.7 49.8 1.0
C A:THR166 4.9 24.5 1.0
C7 A:ACJ1465 4.9 50.4 1.0
CB A:ILE412 5.0 30.8 1.0
CG2 A:ILE412 5.0 31.2 1.0

Fluorine binding site 2 out of 6 in 2ivd

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Fluorine binding site 2 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1465

b:51.9
occ:1.00
 F2 A:ACJ1465 0.0 51.9 1.0
C1 A:ACJ1465 1.3 51.0 1.0
F3 A:ACJ1465 2.2 53.0 1.0
F1 A:ACJ1465 2.2 51.6 1.0
C2 A:ACJ1465 2.3 50.5 1.0
C5 A:ACJ1465 2.7 50.0 1.0
O A:ILE168 3.3 24.6 1.0
C5X A:FAD1466 3.4 25.8 1.0
C3 A:ACJ1465 3.5 49.9 1.0
N5 A:FAD1466 3.6 25.7 1.0
C6 A:FAD1466 3.6 25.8 1.0
C9A A:FAD1466 3.8 25.9 1.0
O A:GLY167 3.9 25.2 1.0
C A:ILE168 3.9 24.4 1.0
C6 A:ACJ1465 4.1 49.8 1.0
C4X A:FAD1466 4.1 25.6 1.0
C7 A:FAD1466 4.2 25.4 1.0
N10 A:FAD1466 4.3 26.2 1.0
CA A:ILE168 4.3 24.5 1.0
C9 A:FAD1466 4.3 25.9 1.0
CD1 A:ILE412 4.5 30.3 1.0
C10 A:FAD1466 4.5 25.9 1.0
C8 A:FAD1466 4.5 25.7 1.0
C A:GLY167 4.6 24.8 1.0
C4 A:ACJ1465 4.7 50.1 1.0
CG1 A:ILE412 4.8 30.4 1.0
N A:TYR169 4.8 24.0 1.0
N A:ILE168 4.8 24.7 1.0
C7 A:ACJ1465 4.9 50.4 1.0
C4 A:FAD1466 4.9 25.6 1.0

Fluorine binding site 3 out of 6 in 2ivd

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Fluorine binding site 3 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1465

b:53.0
occ:1.00
 F3 A:ACJ1465 0.0 53.0 1.0
C1 A:ACJ1465 1.3 51.0 1.0
F1 A:ACJ1465 2.1 51.6 1.0
F2 A:ACJ1465 2.2 51.9 1.0
C2 A:ACJ1465 2.3 50.5 1.0
C5 A:ACJ1465 3.2 50.0 1.0
CD1 A:ILE311 3.2 30.2 1.0
C3 A:ACJ1465 3.2 49.9 1.0
C7 A:FAD1466 3.2 25.4 1.0
C6 A:FAD1466 3.3 25.8 1.0
CD1 A:ILE412 3.6 30.3 1.0
C8 A:FAD1466 3.7 25.7 1.0
CG1 A:ILE412 3.7 30.4 1.0
C5X A:FAD1466 3.8 25.8 1.0
C7M A:FAD1466 4.0 23.7 1.0
C9 A:FAD1466 4.2 25.9 1.0
C9A A:FAD1466 4.2 25.9 1.0
C6 A:ACJ1465 4.4 49.8 1.0
C4 A:ACJ1465 4.4 50.1 1.0
CG1 A:ILE311 4.5 30.1 1.0
N5 A:FAD1466 4.6 25.7 1.0
CG2 A:ILE311 4.7 29.0 1.0
O A:ILE168 4.8 24.6 1.0
CB A:ALA170 4.8 22.9 1.0
C8M A:FAD1466 4.9 27.0 1.0
C7 A:ACJ1465 4.9 50.4 1.0

Fluorine binding site 4 out of 6 in 2ivd

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Fluorine binding site 4 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1468

b:55.3
occ:1.00
 F1 B:ACJ1468 0.0 55.3 1.0
C1 B:ACJ1468 1.3 54.5 1.0
C2 B:ACJ1468 2.2 54.0 1.0
F2 B:ACJ1468 2.2 54.9 1.0
F3 B:ACJ1468 2.3 56.0 1.0
C5 B:ACJ1468 2.5 54.0 1.0
O B:HOH2055 3.2 39.2 1.0
C5X B:FAD1469 3.3 26.7 1.0
N5 B:FAD1469 3.4 26.7 1.0
C3 B:ACJ1468 3.5 53.1 1.0
O B:ILE168 3.6 25.7 1.0
C6 B:FAD1469 3.6 26.7 1.0
C9A B:FAD1469 3.8 27.1 1.0
C6 B:ACJ1468 3.8 53.9 1.0
C4X B:FAD1469 3.9 26.6 1.0
O B:GLY167 4.0 24.8 1.0
C B:ILE168 4.2 25.6 1.0
N10 B:FAD1469 4.2 27.4 1.0
C10 B:FAD1469 4.3 27.0 1.0
C7 B:FAD1469 4.3 26.8 1.0
CD1 B:ILE412 4.4 28.6 1.0
C9 B:FAD1469 4.4 27.0 1.0
CG1 B:ILE412 4.5 29.1 1.0
C4 B:ACJ1468 4.5 53.2 1.0
CA B:ILE168 4.6 25.6 1.0
C4 B:FAD1469 4.6 27.5 1.0
C8 B:FAD1469 4.6 27.1 1.0
C B:GLY167 4.7 24.9 1.0
C7 B:ACJ1468 4.7 53.8 1.0
O B:HOH2133 4.8 27.6 1.0
C1' B:FAD1469 5.0 28.6 1.0
N B:ILE168 5.0 25.6 1.0

Fluorine binding site 5 out of 6 in 2ivd

Go back to Fluorine Binding Sites List in 2ivd
Fluorine binding site 5 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1468

b:54.9
occ:1.00
 F2 B:ACJ1468 0.0 54.9 1.0
C1 B:ACJ1468 1.3 54.5 1.0
C2 B:ACJ1468 2.1 54.0 1.0
F3 B:ACJ1468 2.2 56.0 1.0
F1 B:ACJ1468 2.2 55.3 1.0
C3 B:ACJ1468 2.6 53.1 1.0
O B:ILE168 3.0 25.7 1.0
C B:ILE168 3.1 25.6 1.0
C5 B:ACJ1468 3.4 54.0 1.0
N B:ALA170 3.5 24.0 1.0
N B:TYR169 3.5 25.1 1.0
O B:THR166 3.7 23.3 1.0
C B:TYR169 3.7 24.6 1.0
O B:GLY167 3.8 24.8 1.0
C B:GLY167 3.8 24.9 1.0
CA B:ILE168 3.8 25.6 1.0
CA B:TYR169 3.8 24.6 1.0
N B:ILE168 3.9 25.6 1.0
C4 B:ACJ1468 3.9 53.2 1.0
CB B:ALA170 3.9 24.1 1.0
CD1 B:ILE412 4.2 28.6 1.0
CA B:ALA170 4.3 23.8 1.0
O B:TYR169 4.3 24.9 1.0
O B:HOH2055 4.4 39.2 1.0
CG1 B:ILE412 4.5 29.1 1.0
C6 B:ACJ1468 4.5 53.9 1.0
CA B:GLY167 4.6 24.2 1.0
C B:THR166 4.7 23.6 1.0
C7 B:ACJ1468 4.7 53.8 1.0
CD1 B:ILE311 4.9 31.2 1.0

Fluorine binding site 6 out of 6 in 2ivd

Go back to Fluorine Binding Sites List in 2ivd
Fluorine binding site 6 out of 6 in the Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus with Acifluorfen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1468

b:56.0
occ:1.00
 F3 B:ACJ1468 0.0 56.0 1.0
C1 B:ACJ1468 1.3 54.5 1.0
C2 B:ACJ1468 2.1 54.0 1.0
F2 B:ACJ1468 2.2 54.9 1.0
F1 B:ACJ1468 2.3 55.3 1.0
C3 B:ACJ1468 2.8 53.1 1.0
CD1 B:ILE412 3.1 28.6 1.0
C5 B:ACJ1468 3.1 54.0 1.0
CD1 B:ILE311 3.2 31.2 1.0
C6 B:FAD1469 3.7 26.7 1.0
C7 B:FAD1469 3.7 26.8 1.0
CG1 B:ILE412 3.9 29.1 1.0
C4 B:ACJ1468 4.0 53.2 1.0
C5X B:FAD1469 4.1 26.7 1.0
C8 B:FAD1469 4.2 27.1 1.0
C6 B:ACJ1468 4.3 53.9 1.0
C7M B:FAD1469 4.4 25.3 1.0
CB B:ALA170 4.4 24.1 1.0
CG1 B:ILE311 4.4 30.0 1.0
C9A B:FAD1469 4.6 27.1 1.0
C9 B:FAD1469 4.7 27.0 1.0
C7 B:ACJ1468 4.7 53.8 1.0
N5 B:FAD1469 4.7 26.7 1.0
O B:ILE168 4.8 25.7 1.0
CG2 B:ILE311 4.9 29.4 1.0
CB B:ILE311 4.9 29.5 1.0
CB B:ILE412 5.0 28.5 1.0

Reference:

H.R.Corradi, A.V.Corrigall, E.Boix, C.G.Mohan, E.D.Sturrock, P.N.Meissner, K.R.Acharya. Crystal Structure of Protoporphyrinogen Oxidase From Myxococcus Xanthus and Its Complex with the Inhibitor Acifluorfen. J.Biol.Chem. V. 281 38625 2006.
ISSN: ISSN 0021-9258
PubMed: 17046834
DOI: 10.1074/JBC.M606640200
Page generated: Sun Dec 13 11:37:28 2020

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