Fluorine in PDB 6jfr: K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

Enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

All present enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus:
3.5.1.88;

Protein crystallography data

The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr 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) 49.99 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 95.792, 120.709, 47.281, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.4

Other elements in 6jfr:

The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus (pdb code 6jfr). 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 II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6jfr

Go back to Fluorine Binding Sites List in 6jfr
Fluorine binding site 1 out of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus


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 II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:77.7
occ:1.00
 F1 A:K3U203 0.0 77.7 1.0
C12 A:K3U203 1.3 88.2 1.0
F2 A:K3U203 2.2 93.6 1.0
F A:K3U203 2.3 70.8 1.0
C11 A:K3U203 2.3 86.5 1.0
N A:LEU112 2.6 35.4 1.0
C3 A:K3U203 2.9 89.5 1.0
NI A:NI201 3.0 58.2 1.0
CA A:CYS111 3.1 33.1 1.0
C A:CYS111 3.3 36.0 1.0
CB A:LEU112 3.4 29.3 1.0
C4 A:K3U203 3.5 94.3 1.0
CA A:LEU112 3.5 32.2 1.0
NE2 A:GLN65 3.6 26.7 1.0
CD2 A:LEU112 3.7 33.1 1.0
SG A:CYS111 3.8 26.5 1.0
CB A:CYS111 3.9 32.5 1.0
CG A:LEU112 4.0 31.5 1.0
N A:CYS111 4.2 32.9 1.0
C2 A:K3U203 4.2 89.8 1.0
OE2 A:GLU155 4.2 51.8 1.0
O A:GLY60 4.3 28.6 1.0
O A:GLY110 4.3 35.2 1.0
NE2 A:HIS154 4.4 29.6 1.0
OE1 A:GLN65 4.4 30.2 1.0
CD A:GLN65 4.4 29.4 1.0
N A:SER113 4.5 33.7 1.0
CD1 A:LEU112 4.5 30.2 1.0
O A:CYS111 4.5 31.7 1.0
C A:LEU112 4.6 31.7 1.0
C A:GLY110 4.7 32.3 1.0
O1 A:K3U203 4.8 88.2 1.0
C5 A:K3U203 5.0 91.5 1.0

Fluorine binding site 2 out of 3 in 6jfr

Go back to Fluorine Binding Sites List in 6jfr
Fluorine binding site 2 out of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus


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 II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:70.8
occ:1.00
 F A:K3U203 0.0 70.8 1.0
C12 A:K3U203 1.4 88.2 1.0
OE2 A:GLU155 2.0 51.8 1.0
F2 A:K3U203 2.1 93.6 1.0
F1 A:K3U203 2.3 77.7 1.0
NI A:NI201 2.3 58.2 1.0
C11 A:K3U203 2.5 86.5 1.0
CD A:GLU155 3.2 51.4 1.0
C4 A:K3U203 3.3 94.3 1.0
NE2 A:HIS154 3.3 29.6 1.0
C3 A:K3U203 3.4 89.5 1.0
CD2 A:HIS154 3.4 27.8 1.0
O A:GLY60 3.5 28.6 1.0
OE1 A:GLN65 3.5 30.2 1.0
OE1 A:GLU155 3.6 55.9 1.0
NE2 A:GLN65 3.8 26.7 1.0
NE2 A:HIS158 3.9 40.7 1.0
O A:HOH315 3.9 53.5 1.0
CD A:GLN65 4.0 29.4 1.0
CD2 A:HIS158 4.1 38.0 1.0
C A:GLY60 4.2 32.6 1.0
SG A:CYS111 4.4 26.5 1.0
CG A:GLU155 4.5 44.7 1.0
CE1 A:HIS154 4.6 26.6 1.0
CA A:CYS111 4.7 33.1 1.0
CG A:HIS154 4.7 27.4 1.0
C5 A:K3U203 4.7 91.5 1.0
C2 A:K3U203 4.7 89.8 1.0
N A:LEU112 4.8 35.4 1.0
CA A:LEU61 4.8 30.4 1.0
N A:LEU61 4.9 30.7 1.0
O1 A:K3U203 4.9 88.2 1.0
CD2 A:LEU112 5.0 33.1 1.0
CB A:CYS111 5.0 32.5 1.0
CA A:GLY60 5.0 34.0 1.0

Fluorine binding site 3 out of 3 in 6jfr

Go back to Fluorine Binding Sites List in 6jfr
Fluorine binding site 3 out of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus


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 II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:93.6
occ:1.00
 F2 A:K3U203 0.0 93.6 1.0
C12 A:K3U203 1.3 88.2 1.0
F A:K3U203 2.1 70.8 1.0
F1 A:K3U203 2.2 77.7 1.0
C11 A:K3U203 2.3 86.5 1.0
O A:GLY60 2.4 28.6 1.0
CD2 A:LEU112 3.0 33.1 1.0
OE1 A:GLN65 3.4 30.2 1.0
OE2 A:GLU155 3.4 51.8 1.0
C A:GLY60 3.5 32.6 1.0
NE2 A:GLN65 3.6 26.7 1.0
C3 A:K3U203 3.7 89.5 1.0
CB A:LEU112 3.8 29.3 1.0
CD A:GLN65 3.9 29.4 1.0
CD1 A:LEU61 4.0 34.3 1.0
CG A:LEU112 4.0 31.5 1.0
CA A:LEU61 4.0 30.4 1.0
NI A:NI201 4.0 58.2 1.0
N A:LEU61 4.2 30.7 1.0
CD A:GLU155 4.3 51.4 1.0
N A:LEU112 4.3 35.4 1.0
C4 A:K3U203 4.4 94.3 1.0
OE1 A:GLU155 4.5 55.9 1.0
CB A:LEU61 4.5 32.3 1.0
CA A:GLY60 4.6 34.0 1.0
C2 A:K3U203 4.6 89.8 1.0
O1 A:K3U203 4.7 88.2 1.0
CA A:LEU112 4.7 32.2 1.0
N A:GLY60 4.8 33.9 1.0
CG A:LEU61 4.8 34.5 1.0
O A:HOH315 4.8 53.5 1.0
CD1 A:LEU112 4.9 30.2 1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus To Be Published.
Page generated: Sun Dec 13 12:54:31 2020

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