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Iron in PDB 6nlg: 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)

Enzymatic activity of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)

All present enzymatic activity of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1):
1.16.3.1;

Protein crystallography data

The structure of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1), PDB code: 6nlg was solved by S.Lovell, A.Punchi-Hewage, K.P.Battaile, H.Yao, B.Nammalwar, K.K.Gnanasekaran, R.A.Bunce, A.B.Reitz, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 1.50
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 153.814, 153.814, 153.406, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 15.8

Other elements in 6nlg:

The structure of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) also contains other interesting chemical elements:

Potassium (K) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) (pdb code 6nlg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1), PDB code: 6nlg:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nlg

Go back to Iron Binding Sites List in 6nlg
Iron binding site 1 out of 4 in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:14.1
occ:0.50
 FE A:HEM202 0.0 14.1 0.5
FE A:HEM202 0.1 18.7 0.5
ND A:HEM202 1.9 14.3 0.5
NA A:HEM202 1.9 14.4 0.5
ND A:HEM202 2.0 13.7 0.5
NA A:HEM202 2.0 13.5 0.5
NB A:HEM202 2.0 15.3 0.5
NC A:HEM202 2.1 16.1 0.5
NB A:HEM202 2.1 17.0 0.5
NC A:HEM202 2.2 17.0 0.5
SD B:MET52 2.3 14.5 1.0
SD A:MET52 2.4 14.7 1.0
C4D A:HEM202 2.9 16.3 0.5
C1D A:HEM202 2.9 16.3 0.5
C4D A:HEM202 2.9 16.2 0.5
C1A A:HEM202 2.9 16.1 0.5
C4A A:HEM202 3.0 16.1 0.5
C1A A:HEM202 3.0 16.1 0.5
C1B A:HEM202 3.0 16.5 0.5
C1D A:HEM202 3.0 17.5 0.5
C4C A:HEM202 3.0 16.6 0.5
C4B A:HEM202 3.0 16.7 0.5
C4A A:HEM202 3.1 17.4 0.5
C1B A:HEM202 3.1 16.2 0.5
C4B A:HEM202 3.1 16.0 0.5
C1C A:HEM202 3.1 16.9 0.5
C4C A:HEM202 3.1 16.4 0.5
C1C A:HEM202 3.2 16.1 0.5
CE B:MET52 3.3 18.6 1.0
CHA A:HEM202 3.3 15.4 0.5
CHA A:HEM202 3.3 15.4 0.5
CE A:MET52 3.4 16.5 1.0
CHB A:HEM202 3.4 17.2 0.5
CHD A:HEM202 3.4 17.5 0.5
CG B:MET52 3.5 13.4 1.0
CHB A:HEM202 3.5 17.8 0.5
CHD A:HEM202 3.5 18.0 0.5
CHC A:HEM202 3.5 16.6 0.5
CHC A:HEM202 3.5 16.7 0.5
CG A:MET52 3.6 13.4 1.0
C2A A:HEM202 4.1 16.0 0.5
C3D A:HEM202 4.1 16.1 0.5
C3A A:HEM202 4.1 16.3 0.5
C2D A:HEM202 4.1 16.3 0.5
CB B:MET52 4.2 13.6 1.0
C2A A:HEM202 4.2 18.4 0.5
C3D A:HEM202 4.2 18.4 0.5
C3A A:HEM202 4.2 18.2 0.5
C2B A:HEM202 4.2 18.4 0.5
C2D A:HEM202 4.2 18.2 0.5
C3C A:HEM202 4.3 18.5 0.5
C3B A:HEM202 4.3 18.1 0.5
CB A:MET52 4.3 13.4 1.0
C2C A:HEM202 4.3 18.1 0.5
C2B A:HEM202 4.3 17.1 0.5
C3B A:HEM202 4.4 17.3 0.5
C3C A:HEM202 4.4 17.2 0.5
C2C A:HEM202 4.4 17.2 0.5

Iron binding site 2 out of 4 in 6nlg

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Iron binding site 2 out of 4 in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:18.7
occ:0.50
 FE A:HEM202 0.0 18.7 0.5
FE A:HEM202 0.1 14.1 0.5
ND A:HEM202 1.9 13.7 0.5
NA A:HEM202 1.9 13.5 0.5
ND A:HEM202 1.9 14.3 0.5
NA A:HEM202 2.0 14.4 0.5
NB A:HEM202 2.0 17.0 0.5
NC A:HEM202 2.1 17.0 0.5
NB A:HEM202 2.1 15.3 0.5
NC A:HEM202 2.2 16.1 0.5
SD A:MET52 2.3 14.7 1.0
SD B:MET52 2.4 14.5 1.0
C4D A:HEM202 2.9 16.2 0.5
C1D A:HEM202 2.9 17.5 0.5
C4D A:HEM202 2.9 16.3 0.5
C1A A:HEM202 2.9 16.1 0.5
C4A A:HEM202 2.9 17.4 0.5
C1A A:HEM202 3.0 16.1 0.5
C1D A:HEM202 3.0 16.3 0.5
C1B A:HEM202 3.0 16.2 0.5
C4C A:HEM202 3.0 16.4 0.5
C4A A:HEM202 3.1 16.1 0.5
C4B A:HEM202 3.1 16.0 0.5
C1B A:HEM202 3.1 16.5 0.5
C4B A:HEM202 3.1 16.7 0.5
C1C A:HEM202 3.1 16.1 0.5
C4C A:HEM202 3.1 16.6 0.5
C1C A:HEM202 3.2 16.9 0.5
CE B:MET52 3.3 18.6 1.0
CHA A:HEM202 3.3 15.4 0.5
CHA A:HEM202 3.3 15.4 0.5
CE A:MET52 3.3 16.5 1.0
CHB A:HEM202 3.4 17.8 0.5
CHD A:HEM202 3.4 18.0 0.5
CG A:MET52 3.5 13.4 1.0
CHB A:HEM202 3.5 17.2 0.5
CHD A:HEM202 3.5 17.5 0.5
CHC A:HEM202 3.5 16.6 0.5
CHC A:HEM202 3.5 16.7 0.5
CG B:MET52 3.6 13.4 1.0
C2A A:HEM202 4.1 18.4 0.5
C3A A:HEM202 4.1 18.2 0.5
C3D A:HEM202 4.1 18.4 0.5
C2D A:HEM202 4.1 18.2 0.5
CB A:MET52 4.2 13.4 1.0
C2A A:HEM202 4.2 16.0 0.5
C3D A:HEM202 4.2 16.1 0.5
C3A A:HEM202 4.2 16.3 0.5
C2D A:HEM202 4.2 16.3 0.5
C2B A:HEM202 4.2 17.1 0.5
C3C A:HEM202 4.3 17.2 0.5
CB B:MET52 4.3 13.6 1.0
C3B A:HEM202 4.3 17.3 0.5
C2C A:HEM202 4.3 17.2 0.5
C2B A:HEM202 4.3 18.4 0.5
C3B A:HEM202 4.4 18.1 0.5
C3C A:HEM202 4.4 18.5 0.5
C2C A:HEM202 4.4 18.1 0.5

Iron binding site 3 out of 4 in 6nlg

Go back to Iron Binding Sites List in 6nlg
Iron binding site 3 out of 4 in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:16.0
occ:0.50
 FE C:HEM202 0.0 16.0 0.5
NA C:HEM202 2.0 16.3 0.5
NC C:HEM202 2.0 14.1 0.5
NB C:HEM202 2.0 16.9 0.5
ND C:HEM202 2.0 16.0 0.5
SD C:MET52 2.2 15.3 1.0
C1A C:HEM202 3.0 17.2 0.5
C4A C:HEM202 3.0 17.1 0.5
C4C C:HEM202 3.0 17.7 0.5
C1C C:HEM202 3.0 17.0 0.5
C4D C:HEM202 3.0 17.3 0.5
C1B C:HEM202 3.1 15.2 0.5
C4B C:HEM202 3.1 15.2 0.5
C1D C:HEM202 3.1 17.5 0.5
CE C:MET52 3.3 17.0 1.0
CG C:MET52 3.4 14.6 1.0
CHA C:HEM202 3.4 16.8 0.5
CHB C:HEM202 3.4 17.0 0.5
CHD C:HEM202 3.4 18.3 0.5
CHC C:HEM202 3.4 16.0 0.5
CB C:MET52 4.1 14.5 1.0
C2A C:HEM202 4.2 17.8 0.5
C3A C:HEM202 4.2 18.0 0.5
C3C C:HEM202 4.2 16.3 0.5
C2C C:HEM202 4.2 16.8 0.5
C2D C:HEM202 4.3 16.6 0.5
C3D C:HEM202 4.3 17.8 0.5
C3B C:HEM202 4.3 15.6 0.5
C2B C:HEM202 4.3 15.2 0.5

Iron binding site 4 out of 4 in 6nlg

Go back to Iron Binding Sites List in 6nlg
Iron binding site 4 out of 4 in the 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.50 A Resolution Structure of Bfrb (C89S/K96C) From Pseudomonas Aeruginosa in Complex with A Small Molecule Fragment (Analog 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:16.1
occ:0.50
 FE D:HEM202 0.0 16.1 0.5
NB D:HEM202 2.0 16.5 0.5
NA D:HEM202 2.0 17.2 0.5
NC D:HEM202 2.0 15.4 0.5
ND D:HEM202 2.1 16.7 0.5
SD D:MET52 2.3 15.8 1.0
C1B D:HEM202 3.0 15.4 0.5
C1C D:HEM202 3.1 15.3 0.5
C4A D:HEM202 3.1 15.9 0.5
C1A D:HEM202 3.1 17.5 0.5
C4B D:HEM202 3.1 15.0 0.5
C4D D:HEM202 3.1 17.4 0.5
C4C D:HEM202 3.1 16.6 0.5
C1D D:HEM202 3.1 15.8 0.5
CE D:MET52 3.2 17.9 1.0
CHB D:HEM202 3.4 15.5 0.5
CHA D:HEM202 3.4 16.8 0.5
CHC D:HEM202 3.4 15.7 0.5
CHD D:HEM202 3.4 17.1 0.5
CG D:MET52 3.5 14.1 1.0
C2B D:HEM202 4.3 16.6 0.5
C3A D:HEM202 4.3 17.4 0.5
C2A D:HEM202 4.3 17.2 0.5
C3B D:HEM202 4.3 16.8 0.5
C2C D:HEM202 4.3 16.5 0.5
CB D:MET52 4.3 13.6 1.0
C3C D:HEM202 4.3 14.7 0.5
C3D D:HEM202 4.3 17.5 0.5
C2D D:HEM202 4.3 16.1 0.5

Reference:

A.N.D.Punchi Hewage, H.Yao, B.Nammalwar, K.K.Gnanasekaran, S.Lovell, R.A.Bunce, K.Eshelman, S.M.Phaniraj, M.M.Lee, B.R.Peterson, K.P.Battaile, A.B.Reitz, M.Rivera. Small Molecule Inhibitors of the Bfrb-Bfd Interaction Decrease Pseudomonas Aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J.Am.Chem.Soc. V. 141 8171 2019.
ISSN: ESSN 1520-5126
PubMed: 31038945
DOI: 10.1021/JACS.9B00394
Page generated: Wed Aug 7 03:29:05 2024

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