Iron in PDB 7k5e: 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7

Enzymatic activity of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7

All present enzymatic activity of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7:
1.16.3.1;

Protein crystallography data

The structure of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7, PDB code: 7k5e was solved by S.Lovell, K.P.Battaile, A.Soldano, A.Punchi-Hewage, K.Meraz, J.K.Annor-Gyamfi, H.Yao, R.A.Bunce, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.36 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 129.852, 194.284, 203.140, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.3

Other elements in 7k5e:

The structure of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Potassium (K) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 (pdb code 7k5e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7, PDB code: 7k5e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 7k5e

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Iron binding site 1 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:25.6
occ:1.00
FE A:HEM202 0.0 25.6 1.0
NB A:HEM202 2.0 20.6 1.0
NC A:HEM202 2.0 27.9 1.0
ND A:HEM202 2.0 26.3 1.0
NA A:HEM202 2.1 25.1 1.0
SD A:MET52 2.4 23.6 1.0
C4D A:HEM202 3.0 27.7 1.0
C1D A:HEM202 3.1 22.0 1.0
C4B A:HEM202 3.1 25.1 1.0
C1B A:HEM202 3.1 21.9 1.0
C4C A:HEM202 3.1 25.1 1.0
C1A A:HEM202 3.1 24.2 1.0
C1C A:HEM202 3.1 26.4 1.0
C4A A:HEM202 3.1 22.1 1.0
CE A:MET52 3.4 19.6 1.0
CHA A:HEM202 3.4 28.2 1.0
CHD A:HEM202 3.4 22.2 1.0
CHC A:HEM202 3.4 24.0 1.0
CHB A:HEM202 3.5 23.9 1.0
CG A:MET52 3.5 23.6 1.0
CB A:MET52 4.2 22.4 1.0
C3D A:HEM202 4.2 24.9 1.0
C2D A:HEM202 4.3 22.5 1.0
C3B A:HEM202 4.3 25.6 1.0
C2B A:HEM202 4.3 25.5 1.0
C3C A:HEM202 4.3 27.4 1.0
C2C A:HEM202 4.3 26.3 1.0
C2A A:HEM202 4.3 24.9 1.0
C3A A:HEM202 4.3 23.9 1.0

Iron binding site 2 out of 7 in 7k5e

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Iron binding site 2 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:25.6
occ:1.00
FE B:HEM202 0.0 25.6 1.0
NA B:HEM202 2.0 21.7 1.0
NB B:HEM202 2.0 22.4 1.0
NC B:HEM202 2.1 25.4 1.0
ND B:HEM202 2.1 25.1 1.0
SD E:MET52 2.4 25.3 1.0
SD B:MET52 2.4 24.2 1.0
C1B B:HEM202 3.0 23.0 1.0
C4A B:HEM202 3.1 24.4 1.0
C1A B:HEM202 3.1 27.2 1.0
C4B B:HEM202 3.1 26.7 1.0
C1C B:HEM202 3.1 28.5 1.0
C4D B:HEM202 3.1 25.2 1.0
C4C B:HEM202 3.1 28.2 1.0
C1D B:HEM202 3.1 29.7 1.0
CE B:MET52 3.4 23.7 1.0
CHC B:HEM202 3.4 29.8 1.0
CHA B:HEM202 3.4 25.4 1.0
CHB B:HEM202 3.4 23.9 1.0
CE E:MET52 3.5 22.5 1.0
CG E:MET52 3.5 25.7 1.0
CHD B:HEM202 3.5 31.2 1.0
CG B:MET52 3.6 27.1 1.0
CB B:MET52 4.2 23.9 1.0
CB E:MET52 4.2 21.0 1.0
C3B B:HEM202 4.3 29.3 1.0
C3A B:HEM202 4.3 25.5 1.0
C2B B:HEM202 4.3 24.0 1.0
C2A B:HEM202 4.3 25.3 1.0
C3D B:HEM202 4.3 26.1 1.0
C3C B:HEM202 4.3 27.1 1.0
C2D B:HEM202 4.3 29.2 1.0
C2C B:HEM202 4.3 28.4 1.0

Iron binding site 3 out of 7 in 7k5e

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Iron binding site 3 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:25.4
occ:1.00
FE C:HEM201 0.0 25.4 1.0
NB C:HEM201 2.0 24.7 1.0
NC C:HEM201 2.0 27.4 1.0
NA C:HEM201 2.0 26.4 1.0
ND C:HEM201 2.1 22.6 1.0
SD C:MET52 2.4 20.9 1.0
SD I:MET52 2.4 21.5 1.0
C4B C:HEM201 3.0 29.6 1.0
C1B C:HEM201 3.0 24.9 1.0
C1A C:HEM201 3.0 25.7 1.0
C4A C:HEM201 3.0 20.0 1.0
C1C C:HEM201 3.0 25.9 1.0
C4C C:HEM201 3.0 27.3 1.0
C1D C:HEM201 3.1 25.2 1.0
C4D C:HEM201 3.1 25.9 1.0
CE C:MET52 3.3 23.1 1.0
CHB C:HEM201 3.4 23.1 1.0
CE I:MET52 3.4 18.6 1.0
CHC C:HEM201 3.4 28.6 1.0
CHD C:HEM201 3.4 27.3 1.0
CHA C:HEM201 3.4 26.7 1.0
CG I:MET52 3.5 20.8 1.0
CG C:MET52 3.5 20.8 1.0
CB I:MET52 4.2 18.1 1.0
CB C:MET52 4.2 18.2 1.0
C2A C:HEM201 4.2 22.7 1.0
C3B C:HEM201 4.2 29.6 1.0
C3C C:HEM201 4.3 28.9 1.0
C3A C:HEM201 4.3 23.0 1.0
C2B C:HEM201 4.3 30.4 1.0
C2C C:HEM201 4.3 26.2 1.0
C2D C:HEM201 4.3 22.2 1.0
C3D C:HEM201 4.3 23.4 1.0

Iron binding site 4 out of 7 in 7k5e

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Iron binding site 4 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:27.1
occ:0.50
FE D:HEM202 0.0 27.1 0.5
NC D:HEM202 2.0 23.3 0.5
NB D:HEM202 2.1 23.3 0.5
NA D:HEM202 2.1 23.8 0.5
ND D:HEM202 2.1 23.8 0.5
SD D:MET52 2.4 22.7 1.0
C1C D:HEM202 3.0 26.2 0.5
C4B D:HEM202 3.1 26.1 0.5
C1A D:HEM202 3.1 27.0 0.5
C4D D:HEM202 3.1 27.0 0.5
C4C D:HEM202 3.1 25.8 0.5
C4A D:HEM202 3.1 26.1 0.5
C1B D:HEM202 3.1 25.8 0.5
C1D D:HEM202 3.1 26.0 0.5
CE D:MET52 3.2 25.6 1.0
CHC D:HEM202 3.4 24.4 0.5
CHA D:HEM202 3.4 23.6 0.5
CHB D:HEM202 3.5 26.8 0.5
CHD D:HEM202 3.5 26.9 0.5
CG D:MET52 3.5 23.0 1.0
CB D:MET52 4.2 21.0 1.0
C2C D:HEM202 4.3 27.3 0.5
C3B D:HEM202 4.3 27.2 0.5
C2A D:HEM202 4.3 25.5 0.5
C2B D:HEM202 4.3 25.6 0.5
C3C D:HEM202 4.3 25.1 0.5
C3A D:HEM202 4.3 23.7 0.5
C3D D:HEM202 4.3 25.5 0.5
C2D D:HEM202 4.3 23.7 0.5

Iron binding site 5 out of 7 in 7k5e

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Iron binding site 5 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:24.3
occ:1.00
FE F:HEM201 0.0 24.3 1.0
ND F:HEM201 2.0 24.6 1.0
NC F:HEM201 2.0 22.1 1.0
NB F:HEM201 2.0 24.2 1.0
NA F:HEM201 2.1 26.5 1.0
SD K:MET52 2.3 21.6 1.0
SD F:MET52 2.3 22.3 1.0
C4D F:HEM201 3.0 25.9 1.0
C1C F:HEM201 3.0 24.6 1.0
C4B F:HEM201 3.0 22.3 1.0
C4C F:HEM201 3.0 22.9 1.0
C1D F:HEM201 3.0 26.1 1.0
C1A F:HEM201 3.1 25.4 1.0
C1B F:HEM201 3.1 27.9 1.0
C4A F:HEM201 3.1 21.8 1.0
CE F:MET52 3.3 24.8 1.0
CE K:MET52 3.3 23.4 1.0
CHC F:HEM201 3.4 21.6 1.0
CHA F:HEM201 3.4 27.8 1.0
CHD F:HEM201 3.4 25.2 1.0
CG K:MET52 3.5 21.8 1.0
CHB F:HEM201 3.5 26.1 1.0
CG F:MET52 3.5 23.5 1.0
C3D F:HEM201 4.2 23.0 1.0
C2C F:HEM201 4.2 23.2 1.0
CB K:MET52 4.2 23.5 1.0
CB F:MET52 4.2 22.2 1.0
C2D F:HEM201 4.2 22.9 1.0
C3C F:HEM201 4.2 24.3 1.0
C3B F:HEM201 4.3 24.8 1.0
C2A F:HEM201 4.3 24.5 1.0
C2B F:HEM201 4.3 24.3 1.0
C3A F:HEM201 4.3 23.9 1.0

Iron binding site 6 out of 7 in 7k5e

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Iron binding site 6 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:20.9
occ:1.00
FE H:HEM201 0.0 20.9 1.0
NC H:HEM201 2.0 18.5 1.0
NB H:HEM201 2.0 18.4 1.0
NA H:HEM201 2.0 19.2 1.0
ND H:HEM201 2.1 20.1 1.0
SD J:MET52 2.3 18.8 1.0
SD H:MET52 2.4 18.8 1.0
C4C H:HEM201 3.0 24.0 1.0
C1A H:HEM201 3.0 18.2 1.0
C1B H:HEM201 3.1 21.5 1.0
C1C H:HEM201 3.1 22.0 1.0
C1D H:HEM201 3.1 20.6 1.0
C4B H:HEM201 3.1 17.6 1.0
C4D H:HEM201 3.1 19.0 1.0
C4A H:HEM201 3.1 20.3 1.0
CE H:MET52 3.3 21.4 1.0
CE J:MET52 3.4 19.5 1.0
CHD H:HEM201 3.4 20.9 1.0
CHA H:HEM201 3.4 22.9 1.0
CHC H:HEM201 3.5 22.7 1.0
CHB H:HEM201 3.5 19.1 1.0
CG J:MET52 3.5 19.3 1.0
CG H:MET52 3.6 22.2 1.0
CB J:MET52 4.2 14.8 1.0
C3C H:HEM201 4.2 23.2 1.0
CB H:MET52 4.2 17.1 1.0
C2C H:HEM201 4.3 19.6 1.0
C3B H:HEM201 4.3 19.9 1.0
C2A H:HEM201 4.3 22.8 1.0
C2D H:HEM201 4.3 23.2 1.0
C3D H:HEM201 4.3 19.4 1.0
C2B H:HEM201 4.3 20.0 1.0
C3A H:HEM201 4.3 23.0 1.0

Iron binding site 7 out of 7 in 7k5e

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Iron binding site 7 out of 7 in the 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 1.75 A Resolution Structure of Wt Bfrb From Pseudomonas Aeruginosa in Complex with A Protein-Protein Interaction Inhibitor Jag-5-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe201

b:24.0
occ:0.50
FE L:HEM201 0.0 24.0 0.5
NA L:HEM201 2.0 29.1 0.5
NB L:HEM201 2.0 28.6 0.5
NC L:HEM201 2.1 26.1 0.5
ND L:HEM201 2.1 29.2 0.5
SD L:MET52 2.4 31.2 1.0
CE L:MET52 3.0 23.9 1.0
C1A L:HEM201 3.0 30.1 0.5
C4A L:HEM201 3.0 28.6 0.5
C4B L:HEM201 3.0 27.2 0.5
C1B L:HEM201 3.0 24.4 0.5
C1C L:HEM201 3.1 27.9 0.5
C4D L:HEM201 3.1 30.0 0.5
C4C L:HEM201 3.1 27.0 0.5
C1D L:HEM201 3.2 27.5 0.5
CHB L:HEM201 3.4 24.2 0.5
CHC L:HEM201 3.4 27.7 0.5
CHA L:HEM201 3.4 30.1 0.5
CHD L:HEM201 3.5 24.2 0.5
CG L:MET52 3.7 26.0 1.0
C2A L:HEM201 4.2 30.0 0.5
C3A L:HEM201 4.2 29.7 0.5
C3B L:HEM201 4.2 28.0 0.5
C2B L:HEM201 4.2 28.3 0.5
C2C L:HEM201 4.3 24.1 0.5
C3D L:HEM201 4.3 31.6 0.5
C3C L:HEM201 4.3 27.8 0.5
C2D L:HEM201 4.4 27.4 0.5
CB L:MET52 4.5 28.2 1.0
CD1 L:ILE49 5.0 34.3 1.0

Reference:

A.Soldano, H.Yao, A.N.D.Punchi Hewage, K.Meraz, J.K.Annor-Gyamfi, R.A.Bunce, K.P.Battaile, S.Lovell, M.Rivera. Small Molecule Inhibitors of the Bacterioferritin (Bfrb)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas Aeruginosa Cells. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 33269912
DOI: 10.1021/ACSINFECDIS.0C00669
Page generated: Thu Dec 17 11:41:54 2020

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