Fluorine in PDB 6jff: K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

Enzymatic activity of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

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

Protein crystallography data

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

Resolution Low / High (Å) 46.81 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 44.682, 121.818, 146.314, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Other elements in 6jff:

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

Nickel (Ni) 4 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 3 in 6jff

Go back to Fluorine Binding Sites List in 6jff
Fluorine binding site 1 out of 3 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


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 Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:0.7
occ:1.00
 F1 B:K3U202 0.0 0.7 1.0
C12 B:K3U202 1.3 98.9 1.0
F2 B:K3U202 2.1 98.9 1.0
NI B:NI201 2.1 63.4 1.0
F B:K3U202 2.2 59.4 1.0
C11 B:K3U202 2.3 95.4 1.0
C3 B:K3U202 2.7 95.8 1.0
SG B:CYS103 2.9 45.2 1.0
CB B:CYS103 3.0 44.0 1.0
CA B:CYS103 3.1 39.3 1.0
NE2 B:HIS145 3.2 42.1 1.0
C4 B:K3U202 3.5 84.4 1.0
N B:LEU104 3.5 42.3 1.0
C B:CYS103 3.8 38.0 1.0
O B:GLY102 3.8 47.5 1.0
C2 B:K3U202 4.0 0.4 1.0
NE2 B:GLN55 4.0 34.0 1.0
CD2 B:HIS145 4.0 41.9 1.0
NE2 B:HIS149 4.0 34.4 1.0
CE1 B:HIS145 4.1 39.5 1.0
OE2 B:GLU146 4.2 57.6 1.0
N B:CYS103 4.2 41.9 1.0
C B:GLY102 4.5 47.0 1.0
C5 B:K3U202 4.5 83.2 1.0
CG B:LEU104 4.5 54.1 1.0
OE1 B:GLN55 4.5 37.8 1.0
CD B:GLN55 4.7 37.7 1.0
O1 B:K3U202 4.7 99.5 1.0
CE1 B:HIS149 4.8 33.2 1.0
CA B:LEU104 4.8 39.9 1.0
CB B:LEU104 4.8 47.2 1.0
S B:K3U202 4.9 0.8 1.0
O B:GLY50 5.0 44.1 1.0
CD1 B:LEU104 5.0 58.8 1.0

Fluorine binding site 2 out of 3 in 6jff

Go back to Fluorine Binding Sites List in 6jff
Fluorine binding site 2 out of 3 in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


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 Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:59.4
occ:1.00
 F B:K3U202 0.0 59.4 1.0
C12 B:K3U202 1.4 98.9 1.0
F1 B:K3U202 2.2 0.7 1.0
F2 B:K3U202 2.3 98.9 1.0
C11 B:K3U202 2.5 95.4 1.0
OE2 B:GLU146 2.5 57.6 1.0
NI B:NI201 2.5 63.4 1.0
OE1 B:GLN55 3.0 37.8 1.0
OE1 B:GLU146 3.2 55.8 1.0
CD B:GLU146 3.2 49.7 1.0
NE2 B:HIS149 3.3 34.4 1.0
C3 B:K3U202 3.7 95.8 1.0
NE2 B:GLN55 3.7 34.0 1.0
CD B:GLN55 3.7 37.7 1.0
NE2 B:HIS145 3.7 42.1 1.0
O B:GLY50 3.8 44.1 1.0
CD2 B:HIS149 3.8 31.9 1.0
CD2 B:HIS145 3.9 41.9 1.0
C4 B:K3U202 3.9 84.4 1.0
C B:GLY50 3.9 45.8 1.0
CA B:LEU51 4.2 38.2 1.0
N B:LEU51 4.2 38.1 1.0
SG B:CYS103 4.3 45.2 1.0
CE1 B:HIS149 4.4 33.2 1.0
CA B:GLY50 4.6 48.3 1.0
CG B:GLU146 4.7 46.3 1.0
N B:ALA52 4.9 29.7 1.0
C B:LEU51 4.9 32.9 1.0
C2 B:K3U202 4.9 0.4 1.0

Fluorine binding site 3 out of 3 in 6jff

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


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 Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:98.9
occ:1.00
 F2 B:K3U202 0.0 98.9 1.0
C12 B:K3U202 1.3 98.9 1.0
F1 B:K3U202 2.1 0.7 1.0
F B:K3U202 2.3 59.4 1.0
C11 B:K3U202 2.3 95.4 1.0
NE2 B:GLN55 3.0 34.0 1.0
CG B:LEU104 3.2 54.1 1.0
CD1 B:LEU104 3.2 58.8 1.0
C3 B:K3U202 3.5 95.8 1.0
N B:LEU104 3.5 42.3 1.0
NI B:NI201 3.5 63.4 1.0
OE1 B:GLN55 3.5 37.8 1.0
CB B:LEU104 3.6 47.2 1.0
O B:GLY50 3.6 44.1 1.0
CD B:GLN55 3.7 37.7 1.0
SG B:CYS103 3.9 45.2 1.0
CA B:LEU104 4.2 39.9 1.0
C2 B:K3U202 4.2 0.4 1.0
CA B:CYS103 4.3 39.3 1.0
C B:GLY50 4.4 45.8 1.0
C B:CYS103 4.4 38.0 1.0
CD1 B:LEU51 4.5 43.1 1.0
OE2 B:GLU146 4.5 57.6 1.0
O1 B:K3U202 4.5 99.5 1.0
C4 B:K3U202 4.5 84.4 1.0
CD2 B:LEU104 4.6 52.9 1.0
CB B:CYS103 4.6 44.0 1.0
NE2 B:HIS149 4.7 34.4 1.0
N B:SER105 4.8 32.8 1.0
CA B:LEU51 4.8 38.2 1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.
Page generated: Sun Dec 13 12:54:31 2020

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