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Fluorine in PDB 6jf7: K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii

Enzymatic activity of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii

All present enzymatic activity of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii:
3.5.1.88;

Protein crystallography data

The structure of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf7 was solved by K.H.Jung, T.H.Ho, I.H.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.513, 71.259, 110.974, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.8

Other elements in 6jf7:

The structure of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii (pdb code 6jf7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6jf7

Go back to Fluorine Binding Sites List in 6jf7
Fluorine binding site 1 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:29.6
occ:1.00
 F1 A:K3U202 0.0 29.6 1.0
C12 A:K3U202 1.3 33.8 1.0
ZN A:ZN201 1.9 20.1 1.0
F A:K3U202 2.1 33.2 1.0
F2 A:K3U202 2.1 64.3 1.0
C11 A:K3U202 2.4 35.6 1.0
NE2 A:GLN55 3.1 18.0 1.0
C3 A:K3U202 3.1 33.2 1.0
N A:LEU104 3.1 20.6 1.0
NE2 A:HIS145 3.2 16.0 1.0
SG A:CYS103 3.2 20.3 1.0
CA A:CYS103 3.2 20.3 1.0
NE2 A:HIS149 3.5 17.4 1.0
CB A:CYS103 3.6 21.1 1.0
C A:CYS103 3.7 21.0 1.0
OE1 A:GLN55 3.8 18.3 1.0
CD A:GLN55 3.8 17.5 1.0
CD2 A:HIS145 3.9 15.5 1.0
C4 A:K3U202 4.1 31.1 1.0
CE1 A:HIS145 4.1 19.2 1.0
CG A:LEU104 4.2 27.1 1.0
C2 A:K3U202 4.2 39.6 1.0
CA A:LEU104 4.2 22.1 1.0
CB A:LEU104 4.3 24.5 1.0
O A:GLY102 4.3 21.7 1.0
CD2 A:HIS149 4.4 16.0 1.0
OE2 A:GLU146 4.5 21.0 1.0
N A:CYS103 4.5 20.9 1.0
S A:K3U202 4.5 45.2 1.0
CE1 A:HIS149 4.5 17.1 1.0
N A:SER105 4.7 20.2 1.0
CD1 A:LEU104 4.7 28.5 1.0
C A:GLY102 4.8 20.7 1.0
O A:CYS103 4.9 18.3 1.0
O A:GLY50 4.9 17.8 1.0
O A:HOH311 5.0 20.9 1.0
OE1 A:GLU146 5.0 16.7 1.0

Fluorine binding site 2 out of 6 in 6jf7

Go back to Fluorine Binding Sites List in 6jf7
Fluorine binding site 2 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:33.2
occ:1.00
 F A:K3U202 0.0 33.2 1.0
C12 A:K3U202 1.3 33.8 1.0
F2 A:K3U202 2.0 64.3 1.0
F1 A:K3U202 2.1 29.6 1.0
C11 A:K3U202 2.3 35.6 1.0
OE2 A:GLU146 2.4 21.0 1.0
ZN A:ZN201 2.8 20.1 1.0
CD2 A:HIS145 3.0 15.5 1.0
C3 A:K3U202 3.1 33.2 1.0
NE2 A:HIS145 3.1 16.0 1.0
CD A:GLU146 3.1 19.1 1.0
C4 A:K3U202 3.2 31.1 1.0
OE1 A:GLU146 3.2 16.7 1.0
OE1 A:GLN55 3.6 18.3 1.0
NE2 A:HIS149 3.7 17.4 1.0
CD2 A:HIS149 3.9 16.0 1.0
O A:GLY50 3.9 17.8 1.0
NE2 A:GLN55 4.1 18.0 1.0
C A:GLY50 4.2 16.4 1.0
CG A:HIS145 4.2 16.0 1.0
CE1 A:HIS145 4.2 19.2 1.0
CD A:GLN55 4.3 17.5 1.0
CA A:ILE51 4.4 15.9 1.0
C5 A:K3U202 4.4 29.7 1.0
N A:ILE51 4.4 15.5 1.0
C2 A:K3U202 4.5 39.6 1.0
CG A:GLU146 4.6 17.2 1.0
C10 A:K3U202 4.7 29.2 1.0
ND1 A:HIS145 4.8 17.1 1.0
CA A:GLY50 4.8 17.8 1.0
SG A:CYS103 4.9 20.3 1.0

Fluorine binding site 3 out of 6 in 6jf7

Go back to Fluorine Binding Sites List in 6jf7
Fluorine binding site 3 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:64.3
occ:1.00
 F2 A:K3U202 0.0 64.3 1.0
C12 A:K3U202 1.3 33.8 1.0
F A:K3U202 2.0 33.2 1.0
F1 A:K3U202 2.1 29.6 1.0
C11 A:K3U202 2.3 35.6 1.0
OE1 A:GLN55 2.6 18.3 1.0
NE2 A:GLN55 3.1 18.0 1.0
O A:GLY50 3.2 17.8 1.0
CD A:GLN55 3.2 17.5 1.0
CD1 A:LEU104 3.5 28.5 1.0
ZN A:ZN201 3.6 20.1 1.0
CG A:LEU104 3.6 27.1 1.0
CA A:ILE51 3.7 15.9 1.0
C3 A:K3U202 3.7 33.2 1.0
OE2 A:GLU146 3.7 21.0 1.0
C A:GLY50 3.9 16.4 1.0
OE1 A:GLU146 4.1 16.7 1.0
N A:ILE51 4.1 15.5 1.0
CB A:LEU104 4.2 24.5 1.0
N A:LEU104 4.3 20.6 1.0
CB A:ILE51 4.3 16.3 1.0
CG1 A:ILE51 4.3 17.1 1.0
NE2 A:HIS149 4.3 17.4 1.0
CD A:GLU146 4.3 19.1 1.0
C4 A:K3U202 4.4 31.1 1.0
C2 A:K3U202 4.6 39.6 1.0
CD2 A:HIS149 4.6 16.0 1.0
C A:ILE51 4.7 14.9 1.0
N A:ALA52 4.7 14.2 1.0
NE2 A:HIS145 4.7 16.0 1.0
CG A:GLN55 4.7 16.6 1.0
CA A:LEU104 4.9 22.1 1.0
CD2 A:HIS145 4.9 15.5 1.0
CD2 A:LEU104 5.0 31.9 1.0

Fluorine binding site 4 out of 6 in 6jf7

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Fluorine binding site 4 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:62.8
occ:1.00
 F1 B:K3U202 0.0 62.8 1.0
C12 B:K3U202 1.3 36.2 1.0
C11 B:K3U202 2.1 36.5 1.0
F B:K3U202 2.2 28.4 1.0
F2 B:K3U202 2.2 28.6 1.0
NE2 B:GLN55 3.0 17.5 1.0
OE1 B:GLN55 3.1 19.4 1.0
CD1 B:LEU104 3.2 34.7 1.0
O B:GLY50 3.2 17.4 1.0
CG B:LEU104 3.2 32.6 1.0
CD B:GLN55 3.5 17.6 1.0
C3 B:K3U202 3.6 38.2 1.0
ZN B:ZN201 3.6 20.7 1.0
CB B:LEU104 3.7 29.6 1.0
N B:LEU104 4.0 25.8 1.0
OE2 B:GLU146 4.1 19.8 1.0
C B:GLY50 4.1 15.7 1.0
CA B:ILE51 4.2 14.6 1.0
C2 B:K3U202 4.3 42.3 1.0
C4 B:K3U202 4.4 35.9 1.0
CA B:LEU104 4.5 27.6 1.0
OE1 B:GLU146 4.5 20.3 1.0
N B:ILE51 4.6 14.4 1.0
CD2 B:LEU104 4.6 37.0 1.0
CB B:ILE51 4.7 13.8 1.0
CG1 B:ILE51 4.7 14.7 1.0
NE2 B:HIS149 4.7 15.5 1.0
CD B:GLU146 4.7 19.9 1.0
O1 B:K3U202 4.9 37.8 1.0
NE2 B:HIS145 4.9 21.1 1.0
CG B:GLN55 4.9 16.3 1.0
S B:K3U202 5.0 61.1 1.0
SG B:CYS103 5.0 25.6 1.0
CD2 B:HIS149 5.0 16.5 1.0

Fluorine binding site 5 out of 6 in 6jf7

Go back to Fluorine Binding Sites List in 6jf7
Fluorine binding site 5 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:28.4
occ:1.00
 F B:K3U202 0.0 28.4 1.0
C12 B:K3U202 1.3 36.2 1.0
F1 B:K3U202 2.2 62.8 1.0
F2 B:K3U202 2.2 28.6 1.0
C11 B:K3U202 2.2 36.5 1.0
OE2 B:GLU146 2.4 19.8 1.0
ZN B:ZN201 2.8 20.7 1.0
CD B:GLU146 3.1 19.9 1.0
OE1 B:GLU146 3.1 20.3 1.0
C3 B:K3U202 3.2 38.2 1.0
CD2 B:HIS145 3.2 19.5 1.0
NE2 B:HIS145 3.3 21.1 1.0
C4 B:K3U202 3.4 35.9 1.0
OE1 B:GLN55 3.5 19.4 1.0
O B:GLY50 3.7 17.4 1.0
CD2 B:HIS149 3.8 16.5 1.0
NE2 B:HIS149 3.8 15.5 1.0
NE2 B:GLN55 3.9 17.5 1.0
CD B:GLN55 4.1 17.6 1.0
C B:GLY50 4.1 15.7 1.0
CA B:ILE51 4.4 14.6 1.0
CG B:HIS145 4.4 18.6 1.0
N B:ILE51 4.4 14.4 1.0
CE1 B:HIS145 4.5 21.2 1.0
CG B:GLU146 4.5 17.4 1.0
C2 B:K3U202 4.5 42.3 1.0
C5 B:K3U202 4.6 33.5 1.0
CA B:GLY50 4.9 15.8 1.0
SG B:CYS103 4.9 25.6 1.0
C10 B:K3U202 5.0 33.8 1.0

Fluorine binding site 6 out of 6 in 6jf7

Go back to Fluorine Binding Sites List in 6jf7
Fluorine binding site 6 out of 6 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:28.6
occ:1.00
 F2 B:K3U202 0.0 28.6 1.0
C12 B:K3U202 1.3 36.2 1.0
ZN B:ZN201 1.9 20.7 1.0
F1 B:K3U202 2.2 62.8 1.0
F B:K3U202 2.2 28.4 1.0
C11 B:K3U202 2.4 36.5 1.0
C3 B:K3U202 3.1 38.2 1.0
SG B:CYS103 3.1 25.6 1.0
NE2 B:HIS145 3.1 21.1 1.0
N B:LEU104 3.2 25.8 1.0
NE2 B:GLN55 3.2 17.5 1.0
CA B:CYS103 3.2 27.2 1.0
CB B:CYS103 3.6 27.5 1.0
NE2 B:HIS149 3.6 15.5 1.0
C B:CYS103 3.7 28.7 1.0
CD2 B:HIS145 3.9 19.5 1.0
CD B:GLN55 4.0 17.6 1.0
CE1 B:HIS145 4.1 21.2 1.0
C4 B:K3U202 4.1 35.9 1.0
OE1 B:GLN55 4.1 19.4 1.0
C2 B:K3U202 4.1 42.3 1.0
CB B:LEU104 4.2 29.6 1.0
CA B:LEU104 4.2 27.6 1.0
CG B:LEU104 4.3 32.6 1.0
O B:GLY102 4.3 25.3 1.0
CD2 B:HIS149 4.4 16.5 1.0
N B:CYS103 4.4 28.6 1.0
S B:K3U202 4.4 61.1 1.0
N B:SER105 4.5 24.4 1.0
OE2 B:GLU146 4.6 19.8 1.0
CE1 B:HIS149 4.7 16.0 1.0
C B:GLY102 4.8 28.1 1.0
CD1 B:LEU104 4.8 34.7 1.0
C B:LEU104 4.9 27.1 1.0
O B:CYS103 4.9 27.9 1.0
O B:HOH315 4.9 24.0 1.0

Reference:

K.H.Jung, T.H.Ho, I.H.Lee, L.W.Kang. K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii To Be Published.
Page generated: Thu Aug 1 21:33:16 2024

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