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Fluorine in PDB 3i6d: Crystal Structure of Ppo From Bacillus Subtilis with Af

Enzymatic activity of Crystal Structure of Ppo From Bacillus Subtilis with Af

All present enzymatic activity of Crystal Structure of Ppo From Bacillus Subtilis with Af:
1.3.3.4;

Protein crystallography data

The structure of Crystal Structure of Ppo From Bacillus Subtilis with Af, PDB code: 3i6d was solved by Y.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.175, 96.175, 299.823, 90.00, 90.00, 90.00
R / Rfree (%) 27.2 / 29.3

Other elements in 3i6d:

The structure of Crystal Structure of Ppo From Bacillus Subtilis with Af also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ppo From Bacillus Subtilis with Af (pdb code 3i6d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Ppo From Bacillus Subtilis with Af, PDB code: 3i6d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3i6d

Go back to Fluorine Binding Sites List in 3i6d
Fluorine binding site 1 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F471

b:0.7
occ:1.00
 F1 A:ACJ471 0.0 0.7 1.0
C1 A:ACJ471 1.4 0.1 1.0
F2 A:ACJ471 2.3 0.6 1.0
F3 A:ACJ471 2.3 0.8 1.0
C2 A:ACJ471 2.4 0.8 1.0
C5 A:ACJ471 3.2 0.5 1.0
C3 A:ACJ471 3.4 0.1 1.0
C6 A:ACJ471 4.5 0.2 1.0
C4 A:ACJ471 4.6 0.6 1.0
CZ A:PHE227 4.7 88.3 1.0
CD1 A:LEU68 4.8 80.0 1.0

Fluorine binding site 2 out of 6 in 3i6d

Go back to Fluorine Binding Sites List in 3i6d
Fluorine binding site 2 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F471

b:0.6
occ:1.00
 F2 A:ACJ471 0.0 0.6 1.0
C1 A:ACJ471 1.4 0.1 1.0
F3 A:ACJ471 2.3 0.8 1.0
F1 A:ACJ471 2.3 0.7 1.0
C2 A:ACJ471 2.4 0.8 1.0
C5 A:ACJ471 2.8 0.5 1.0
C3 A:ACJ471 3.7 0.1 1.0
CD1 A:ILE176 3.9 81.4 1.0
C6 A:ACJ471 4.2 0.2 1.0
C4 A:ACJ471 4.9 0.6 1.0

Fluorine binding site 3 out of 6 in 3i6d

Go back to Fluorine Binding Sites List in 3i6d
Fluorine binding site 3 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F471

b:0.8
occ:1.00
 F3 A:ACJ471 0.0 0.8 1.0
C1 A:ACJ471 1.4 0.1 1.0
F2 A:ACJ471 2.3 0.6 1.0
F1 A:ACJ471 2.3 0.7 1.0
C2 A:ACJ471 2.4 0.8 1.0
C3 A:ACJ471 2.9 0.1 1.0
C5 A:ACJ471 3.7 0.5 1.0
C4 A:ACJ471 4.3 0.6 1.0
C6 A:ACJ471 4.8 0.2 1.0
CD2 A:LEU68 4.9 80.8 1.0

Fluorine binding site 4 out of 6 in 3i6d

Go back to Fluorine Binding Sites List in 3i6d
Fluorine binding site 4 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F471

b:0.9
occ:1.00
 F1 B:ACJ471 0.0 0.9 1.0
C1 B:ACJ471 1.4 0.8 1.0
F2 B:ACJ471 2.3 0.2 1.0
F3 B:ACJ471 2.3 0.3 1.0
C2 B:ACJ471 2.4 0.5 1.0
C5 B:ACJ471 2.8 0.6 1.0
C3 B:ACJ471 3.7 0.8 1.0
CD1 B:ILE176 3.9 81.7 1.0
C6 B:ACJ471 4.2 1.0 1.0
CE1 B:PHE190 4.3 75.6 1.0
CZ B:PHE190 4.4 74.9 1.0
C4 B:ACJ471 4.9 0.4 1.0

Fluorine binding site 5 out of 6 in 3i6d

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Fluorine binding site 5 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F471

b:0.2
occ:1.00
 F2 B:ACJ471 0.0 0.2 1.0
C1 B:ACJ471 1.4 0.8 1.0
F1 B:ACJ471 2.3 0.9 1.0
F3 B:ACJ471 2.3 0.3 1.0
C2 B:ACJ471 2.4 0.5 1.0
C3 B:ACJ471 2.9 0.8 1.0
C5 B:ACJ471 3.7 0.6 1.0
C4 B:ACJ471 4.3 0.4 1.0
CE1 B:PHE190 4.4 75.6 1.0
CD2 B:LEU68 4.8 78.4 1.0
C6 B:ACJ471 4.8 1.0 1.0
O B:HOH474 4.9 58.4 1.0

Fluorine binding site 6 out of 6 in 3i6d

Go back to Fluorine Binding Sites List in 3i6d
Fluorine binding site 6 out of 6 in the Crystal Structure of Ppo From Bacillus Subtilis with Af


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 Ppo From Bacillus Subtilis with Af within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F471

b:0.3
occ:1.00
 F3 B:ACJ471 0.0 0.3 1.0
C1 B:ACJ471 1.4 0.8 1.0
F1 B:ACJ471 2.3 0.9 1.0
F2 B:ACJ471 2.3 0.2 1.0
C2 B:ACJ471 2.4 0.5 1.0
C5 B:ACJ471 3.1 0.6 1.0
C3 B:ACJ471 3.4 0.8 1.0
C6 B:ACJ471 4.4 1.0 1.0
C4 B:ACJ471 4.7 0.4 1.0
CZ B:PHE227 4.9 86.1 1.0
CD1 B:LEU68 4.9 79.0 1.0

Reference:

X.Qin, L.Sun, X.Wen, X.Yang, Y.Tan, H.Jin, Q.Cao, W.Zhou, Z.Xi, Y.Shen. Structural Insight Into Unique Properties of Protoporphyrinogen Oxidase From Bacillus Subtilis J.Struct.Biol. V. 170 76 2010.
ISSN: ISSN 1047-8477
PubMed: 19944166
DOI: 10.1016/J.JSB.2009.11.012
Page generated: Mon Jul 14 16:58:20 2025

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