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Fluorine in PDB 5yig: Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor

Enzymatic activity of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor

All present enzymatic activity of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor, PDB code: 5yig was solved by J.Cherian, Y.Tan, J.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.93 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.394, 61.980, 84.824, 90.00, 99.03, 90.00
R / Rfree (%) 20.6 / 25.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor (pdb code 5yig). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor, PDB code: 5yig:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 1 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


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 Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:25.1
occ:1.00
 FBL A:54B301 0.0 25.1 1.0
CBK A:54B301 1.3 34.7 1.0
FBM A:54B301 2.2 27.9 1.0
FBN A:54B301 2.2 38.5 1.0
CBJ A:54B301 2.3 34.5 1.0
CBI A:54B301 2.7 35.1 1.0
CG2 A:ILE98 3.3 15.1 1.0
NBO A:54B301 3.6 35.3 1.0
CG1 A:ILE98 3.6 14.2 1.0
CD1 A:ILE98 3.7 19.4 1.0
CB A:ILE98 4.0 10.4 1.0
SBP A:54B301 4.3 45.1 1.0
CBH A:54B301 4.5 29.0 1.0
CE A:MET83 4.6 32.6 1.0
CA A:ILE98 4.8 14.1 1.0

Fluorine binding site 2 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 2 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


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 Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:27.9
occ:1.00
 FBM A:54B301 0.0 27.9 1.0
CBK A:54B301 1.3 34.7 1.0
FBL A:54B301 2.2 25.1 1.0
FBN A:54B301 2.2 38.5 1.0
CBJ A:54B301 2.3 34.5 1.0
NBO A:54B301 3.1 35.3 1.0
CBI A:54B301 3.2 35.1 1.0
CAD A:54B301 3.6 27.7 1.0
CBG A:54B301 3.7 22.2 1.0
NAE A:54B301 4.2 20.9 1.0
CBH A:54B301 4.3 29.0 1.0
SBP A:54B301 4.5 45.1 1.0
OD1 A:ASN51 4.6 11.8 1.0
CAF A:54B301 4.7 25.0 1.0
CAC A:54B301 4.8 24.1 1.0

Fluorine binding site 3 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 3 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


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 Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:38.5
occ:1.00
 FBN A:54B301 0.0 38.5 1.0
CBK A:54B301 1.4 34.7 1.0
FBL A:54B301 2.2 25.1 1.0
FBM A:54B301 2.2 27.9 1.0
CBJ A:54B301 2.4 34.5 1.0
NBO A:54B301 2.8 35.3 1.0
OG A:SER124 3.2 24.6 1.0
CG2 A:ILE98 3.4 15.1 1.0
CBI A:54B301 3.5 35.1 1.0
CE A:MET83 3.7 32.6 1.0
CBH A:54B301 4.1 29.0 1.0
CB A:SER124 4.2 19.9 1.0
ND2 A:ASN51 4.2 14.1 1.0
CG A:ASN51 4.5 11.2 1.0
OD1 A:ASN51 4.5 11.8 1.0
CD1 A:ILE98 4.6 19.4 1.0
SBP A:54B301 4.7 45.1 1.0
CB A:ILE98 4.7 10.4 1.0
CG1 A:ILE98 4.8 14.2 1.0
CBG A:54B301 4.9 22.2 1.0

Fluorine binding site 4 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 4 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:24.1
occ:1.00
 FBL B:54B301 0.0 24.1 1.0
CBK B:54B301 1.4 39.2 1.0
FBN B:54B301 2.2 49.2 1.0
FBM B:54B301 2.2 27.9 1.0
CBJ B:54B301 2.4 25.8 1.0
CBI B:54B301 2.7 22.9 1.0
CG2 B:ILE98 3.4 22.7 1.0
CG1 B:ILE98 3.6 20.5 1.0
NBO B:54B301 3.6 29.3 1.0
CD1 B:ILE98 3.7 24.2 1.0
CB B:ILE98 4.1 16.7 1.0
SBP B:54B301 4.3 31.4 1.0
CE B:MET83 4.5 21.3 1.0
CBH B:54B301 4.6 28.3 1.0
CA B:GLY121 4.8 61.5 1.0
CA B:ILE98 4.9 18.9 1.0
O B:GLY121 4.9 42.5 1.0
CAD B:54B301 5.0 29.8 1.0

Fluorine binding site 5 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 5 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:27.9
occ:1.00
 FBM B:54B301 0.0 27.9 1.0
CBK B:54B301 1.4 39.2 1.0
FBN B:54B301 2.2 49.2 1.0
FBL B:54B301 2.2 24.1 1.0
CBJ B:54B301 2.4 25.8 1.0
NBO B:54B301 3.1 29.3 1.0
CBI B:54B301 3.3 22.9 1.0
CAD B:54B301 3.3 29.8 1.0
CBG B:54B301 3.5 26.6 1.0
CA B:GLY121 3.8 61.5 1.0
NAE B:54B301 4.0 26.1 1.0
CBH B:54B301 4.3 28.3 1.0
SBP B:54B301 4.6 31.4 1.0
CAC B:54B301 4.6 25.0 1.0
OD1 B:ASN51 4.7 39.0 1.0
C B:GLY121 4.7 46.5 1.0
N B:GLY121 4.9 55.7 1.0
CAF B:54B301 4.9 28.6 1.0
O B:GLY121 5.0 42.5 1.0

Fluorine binding site 6 out of 6 in 5yig

Go back to Fluorine Binding Sites List in 5yig
Fluorine binding site 6 out of 6 in the Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Streptococcus Pneumonia Pare with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:49.2
occ:1.00
 FBN B:54B301 0.0 49.2 1.0
CBK B:54B301 1.4 39.2 1.0
FBL B:54B301 2.2 24.1 1.0
FBM B:54B301 2.2 27.9 1.0
CBJ B:54B301 2.4 25.8 1.0
NBO B:54B301 2.9 29.3 1.0
CG2 B:ILE98 3.4 22.7 1.0
OG B:SER124 3.4 37.6 1.0
CBI B:54B301 3.5 22.9 1.0
CE B:MET83 3.6 21.3 1.0
CBH B:54B301 4.2 28.3 1.0
CB B:SER124 4.2 22.1 1.0
ND2 B:ASN51 4.2 28.4 1.0
CG B:ASN51 4.5 32.3 1.0
OD1 B:ASN51 4.6 39.0 1.0
CD1 B:ILE98 4.6 24.2 1.0
CBG B:54B301 4.6 26.6 1.0
CB B:ILE98 4.6 16.7 1.0
SBP B:54B301 4.7 31.4 1.0
CG1 B:ILE98 4.7 20.5 1.0
CAD B:54B301 4.8 29.8 1.0

Reference:

S.Y.Ho, W.Wang, F.M.Ng, Y.X.Wong, Z.Y.Poh, S.W.E.Tan, S.H.Ang, S.S.Liew, Y.S.Joyner Wong, Y.Tan, A.Poulsen, V.Pendharkar, K.Sangthongpitag, J.Manchester, G.Basarab, J.Hill, T.H.Keller, J.Cherian. Discovery of Dual Gyrb/Pare Inhibitors Active Against Gram-Negative Bacteria. Eur J Med Chem V. 157 610 2018.
ISSN: ISSN 1768-3254
PubMed: 30125722
DOI: 10.1016/J.EJMECH.2018.08.025
Page generated: Thu Aug 1 17:19:40 2024

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