Fluorine in PDB 5upg: Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090

Enzymatic activity of Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090

All present enzymatic activity of Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090, PDB code: 5upg was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.91 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 35.840, 47.400, 48.150, 111.27, 109.12, 98.12
R / Rfree (%) 14.7 / 18.6

Other elements in 5upg:

The structure of Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 (pdb code 5upg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090, PDB code: 5upg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5upg

Go back to Fluorine Binding Sites List in 5upg
Fluorine binding site 1 out of 3 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090


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 Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:5.4
occ:0.20
F08 A:8GJ401 0.0 5.4 0.2
C05 A:8GJ401 1.3 6.2 0.8
C07 A:8GJ401 1.4 6.4 0.2
C04 A:8GJ401 2.2 5.8 0.8
C09 A:8GJ401 2.3 6.5 0.2
C06 A:8GJ401 2.4 6.8 0.2
O A:HOH672 2.4 10.7 1.0
C06 A:8GJ401 2.4 6.0 0.8
C28 A:8GJ401 2.9 6.3 0.8
C10 A:8GJ401 2.9 6.9 0.2
C10 A:8GJ401 2.9 7.9 0.8
C28 A:8GJ401 2.9 6.7 0.2
N A:PHE193 3.1 7.5 1.0
CD1 A:LEU200 3.2 9.9 1.0
CA A:GLY192 3.3 5.1 1.0
C A:GLY192 3.5 5.5 1.0
C03 A:8GJ401 3.5 8.6 0.8
C03 A:8GJ401 3.6 8.1 0.2
C07 A:8GJ401 3.6 8.0 0.8
O A:PHE193 3.6 8.6 1.0
C05 A:8GJ401 3.6 7.1 0.2
O A:HOH700 3.9 18.7 1.0
C09 A:8GJ401 4.0 6.4 0.8
C04 A:8GJ401 4.1 7.3 0.2
C26 A:8GJ401 4.1 6.2 0.8
C11 A:8GJ401 4.1 6.6 0.2
C A:PHE193 4.1 8.7 1.0
C26 A:8GJ401 4.2 6.7 0.2
C11 A:8GJ401 4.2 5.9 0.8
CA A:PHE193 4.2 8.1 1.0
N A:GLY192 4.5 4.9 1.0
O A:GLY192 4.6 7.0 1.0
O02 A:8GJ401 4.6 9.9 0.8
CB A:ASP196 4.7 10.5 1.0
CG A:LEU200 4.7 8.6 1.0
O27 A:8GJ401 4.7 8.7 0.8
O02 A:8GJ401 4.7 10.2 0.2
F08 A:8GJ401 4.8 4.9 0.8
O27 A:8GJ401 4.8 8.2 0.2
OD2 A:ASP196 4.9 17.1 1.0
O A:HOH675 4.9 12.8 1.0
CB A:PHE193 5.0 6.4 1.0

Fluorine binding site 2 out of 3 in 5upg

Go back to Fluorine Binding Sites List in 5upg
Fluorine binding site 2 out of 3 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090


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 Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:4.9
occ:0.80
F08 A:8GJ401 0.0 4.9 0.8
C05 A:8GJ401 1.4 7.1 0.2
C07 A:8GJ401 1.4 8.0 0.8
C04 A:8GJ401 2.3 7.3 0.2
C09 A:8GJ401 2.3 6.4 0.8
C06 A:8GJ401 2.4 6.0 0.8
C06 A:8GJ401 2.4 6.8 0.2
C11 A:8GJ401 2.8 6.6 0.2
C10 A:8GJ401 2.9 6.9 0.2
C11 A:8GJ401 2.9 5.9 0.8
C10 A:8GJ401 2.9 7.9 0.8
CA A:GLY209 3.3 9.2 1.0
CB A:ALA214 3.5 8.7 1.0
C03 A:8GJ401 3.6 8.1 0.2
C03 A:8GJ401 3.6 8.6 0.8
C05 A:8GJ401 3.6 6.2 0.8
C07 A:8GJ401 3.6 6.4 0.2
CD1 A:LEU18 3.7 6.6 1.0
C A:GLY209 3.7 7.5 1.0
N A:SER210 3.8 7.1 1.0
C12 A:8GJ401 4.0 7.5 0.2
C04 A:8GJ401 4.1 5.8 0.8
C09 A:8GJ401 4.1 6.5 0.2
C28 A:8GJ401 4.1 6.7 0.2
C12 A:8GJ401 4.1 7.4 0.8
C28 A:8GJ401 4.1 6.3 0.8
O A:GLY209 4.4 10.9 1.0
OD1 A:ASN213 4.5 10.6 1.0
N A:GLY209 4.5 9.1 1.0
CB A:ALA206 4.5 9.0 1.0
O A:SER210 4.6 9.2 1.0
O02 A:8GJ401 4.6 10.2 0.2
O02 A:8GJ401 4.7 9.9 0.8
F08 A:8GJ401 4.8 5.4 0.2
CG2 A:VAL216 4.8 6.1 1.0
C01 A:8GJ401 4.8 7.9 0.2
CA A:SER210 4.8 11.8 1.0
N13 A:8GJ401 5.0 6.1 0.2
CA A:ALA214 5.0 6.2 1.0

Fluorine binding site 3 out of 3 in 5upg

Go back to Fluorine Binding Sites List in 5upg
Fluorine binding site 3 out of 3 in the Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090


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 Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:32.8
occ:1.00
F08 A:8GJ402 0.0 32.8 1.0
C07 A:8GJ402 1.4 26.3 1.0
C09 A:8GJ402 2.3 25.2 1.0
C06 A:8GJ402 2.4 26.6 1.0
C28 A:8GJ402 2.8 17.9 1.0
C10 A:8GJ402 2.9 20.6 1.0
CA A:GLY85 3.3 6.8 1.0
O A:ALA84 3.4 6.9 1.0
C03 A:8GJ402 3.6 24.6 1.0
C05 A:8GJ402 3.6 28.6 1.0
C A:ALA84 3.7 7.4 1.0
N A:GLY85 3.7 6.0 1.0
CE2 A:PHE152 4.0 14.7 1.0
C04 A:8GJ402 4.1 21.6 1.0
C26 A:8GJ402 4.1 23.6 1.0
CG2 A:ILE243 4.1 4.7 1.0
C11 A:8GJ402 4.2 21.2 1.0
CD2 A:PHE152 4.2 10.2 1.0
O A:HOH512 4.2 29.6 1.0
C A:GLY85 4.3 8.1 1.0
O A:GLY85 4.4 8.7 1.0
CB A:ALA84 4.5 5.5 1.0
O02 A:8GJ402 4.7 22.1 1.0
CA A:ALA84 4.7 8.1 1.0
O27 A:8GJ402 4.7 23.4 1.0
CD2 A:PHE181 4.7 4.8 1.0
CD1 A:ILE243 4.9 9.2 1.0
C01 A:8GJ402 4.9 27.4 1.0
CG A:PHE181 5.0 7.1 1.0
CZ A:PHE152 5.0 13.6 1.0

Reference:

J.N.Phan, S.L.Delker, D.D.Lorimer, T.E.Edwards. Crystal Structure of Lpxc From Pseudomonas Aeruginosa in Complex with Pf-5081090 To Be Published.
Page generated: Sun Dec 13 12:39:35 2020

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