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Fluorine in PDB 1rf4: Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State

Enzymatic activity of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State

All present enzymatic activity of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State:
2.5.1.19;

Protein crystallography data

The structure of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State, PDB code: 1rf4 was solved by H.Park, J.L.Hilsenbeck, H.J.Kim, W.A.Shuttleworth, Y.H.Park, J.N.Evans, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.495, 149.705, 88.011, 90.00, 91.22, 90.00
R / Rfree (%) 19.6 / 23.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State (pdb code 1rf4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State, PDB code: 1rf4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1rf4

Go back to Fluorine Binding Sites List in 1rf4
Fluorine binding site 1 out of 4 in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1451

b:14.2
occ:1.00
 F A:SPQ1451 0.0 14.2 1.0
C10 A:SPQ1451 1.4 14.4 1.0
C9 A:SPQ1451 2.5 14.0 1.0
O9 A:SPQ1451 2.9 11.2 1.0
C8 A:SPQ1451 2.9 15.8 1.0
O5P A:SPQ1451 3.0 18.3 1.0
O10 A:SPQ1451 3.1 15.5 1.0
P2 A:SPQ1451 3.2 15.8 1.0
O4P A:SPQ1451 3.3 11.6 1.0
NH2 A:ARG120 3.3 15.3 1.0
CG A:GLU340 3.4 16.9 1.0
NH2 A:ARG343 3.6 8.0 1.0
OE1 A:GLU340 3.7 18.5 1.0
O3 A:SPQ1451 3.7 17.6 1.0
NH1 A:ARG343 3.7 9.6 1.0
CD A:LYS339 3.7 11.2 1.0
CZ A:ARG343 3.9 10.4 1.0
CD A:GLU340 3.9 18.6 1.0
O2' A:SPQ1451 3.9 16.1 1.0
CZ A:ARG120 3.9 15.0 1.0
N A:GLU340 4.0 12.7 1.0
NH1 A:ARG120 4.0 13.3 1.0
CB A:LYS339 4.1 13.9 1.0
C5 A:SPQ1451 4.4 18.8 1.0
O2 A:SPQ1451 4.4 19.0 1.0
CG A:LYS339 4.4 10.2 1.0
OD1 A:ASP312 4.5 14.7 1.0
CA A:LYS339 4.5 12.5 1.0
CB A:GLU340 4.5 14.0 1.0
O A:HOH1581 4.6 13.6 1.0
C A:LYS339 4.7 12.9 1.0
O6P A:SPQ1451 4.8 13.3 1.0
CE A:LYS339 4.8 11.8 1.0
CA A:GLU340 4.8 14.1 1.0
NE A:ARG343 4.9 10.1 1.0
NZ A:LYS339 4.9 8.0 1.0

Fluorine binding site 2 out of 4 in 1rf4

Go back to Fluorine Binding Sites List in 1rf4
Fluorine binding site 2 out of 4 in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1551

b:16.8
occ:1.00
 F B:SPQ1551 0.0 16.8 1.0
C10 B:SPQ1551 1.4 14.1 1.0
C9 B:SPQ1551 2.5 13.8 1.0
C8 B:SPQ1551 3.0 13.9 1.0
O10 B:SPQ1551 3.0 13.4 1.0
O9 B:SPQ1551 3.1 15.3 1.0
OE1 B:GLU340 3.1 31.0 1.0
P2 B:SPQ1551 3.2 11.9 1.0
O4P B:SPQ1551 3.2 15.1 1.0
O5P B:SPQ1551 3.3 11.9 1.0
NH2 B:ARG120 3.4 16.0 1.0
NH1 B:ARG343 3.6 9.8 1.0
CD B:GLU340 3.6 26.7 1.0
OE2 B:GLU340 3.7 25.0 1.0
CD B:LYS339 3.7 11.8 1.0
O3 B:SPQ1551 3.7 14.5 1.0
NH2 B:ARG343 3.8 7.5 1.0
N B:GLU340 3.9 13.7 1.0
O2' B:SPQ1551 3.9 13.5 1.0
CZ B:ARG343 4.0 9.6 1.0
CZ B:ARG120 4.0 13.4 1.0
CB B:LYS339 4.0 10.8 1.0
NH1 B:ARG120 4.0 12.7 1.0
O2 B:SPQ1551 4.2 16.6 1.0
C5 B:SPQ1551 4.3 16.9 1.0
CG B:LYS339 4.4 11.2 1.0
CA B:LYS339 4.4 13.3 1.0
O B:HOH1682 4.4 19.8 1.0
OD1 B:ASP312 4.5 15.2 1.0
C B:LYS339 4.7 13.4 1.0
CB B:GLU340 4.7 19.3 1.0
CG B:GLU340 4.7 23.7 1.0
CE B:LYS339 4.8 11.8 1.0
CA B:GLU340 4.8 14.7 1.0
O6P B:SPQ1551 4.8 11.5 1.0
NZ B:LYS339 4.9 11.8 1.0
C4 B:SPQ1551 4.9 16.5 1.0

Fluorine binding site 3 out of 4 in 1rf4

Go back to Fluorine Binding Sites List in 1rf4
Fluorine binding site 3 out of 4 in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1651

b:18.4
occ:1.00
 F C:SPQ1651 0.0 18.4 1.0
C10 C:SPQ1651 1.4 17.5 1.0
C9 C:SPQ1651 2.5 17.3 1.0
C8 C:SPQ1651 2.9 21.6 1.0
O5P C:SPQ1651 2.9 17.3 1.0
O9 C:SPQ1651 3.0 20.2 1.0
O10 C:SPQ1651 3.2 18.2 1.0
P2 C:SPQ1651 3.2 15.5 1.0
O4P C:SPQ1651 3.3 14.0 1.0
OE2 C:GLU340 3.4 21.9 1.0
NH2 C:ARG343 3.5 13.2 1.0
NH2 C:ARG120 3.6 10.3 1.0
NH1 C:ARG343 3.6 13.5 1.0
O3 C:SPQ1651 3.7 17.0 1.0
CG C:GLU340 3.7 21.7 1.0
CZ C:ARG343 3.8 15.1 1.0
O2' C:SPQ1651 3.8 22.7 1.0
CD C:LYS339 3.9 14.3 1.0
N C:GLU340 3.9 20.3 1.0
CD C:GLU340 4.0 23.5 1.0
NH1 C:ARG120 4.0 14.4 1.0
CZ C:ARG120 4.1 15.0 1.0
CB C:LYS339 4.1 15.0 1.0
CB C:GLU340 4.4 19.7 1.0
C5 C:SPQ1651 4.4 18.1 1.0
CG C:LYS339 4.5 15.1 1.0
OD1 C:ASP312 4.5 21.0 1.0
CA C:LYS339 4.5 18.0 1.0
O2 C:SPQ1651 4.6 19.4 1.0
C C:LYS339 4.7 18.8 1.0
CA C:GLU340 4.7 21.2 1.0
NE C:ARG343 4.8 13.9 1.0
O6P C:SPQ1651 4.8 15.4 1.0
CE C:LYS339 4.9 15.2 1.0
NZ C:LYS339 5.0 13.7 1.0

Fluorine binding site 4 out of 4 in 1rf4

Go back to Fluorine Binding Sites List in 1rf4
Fluorine binding site 4 out of 4 in the Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Studies of Streptococcus Pneumoniae Epsp Synthase, Tetrahedral Intermediate Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1751

b:25.6
occ:1.00
 F D:SPQ1751 0.0 25.6 1.0
C10 D:SPQ1751 1.4 18.9 1.0
C9 D:SPQ1751 2.4 20.2 1.0
O3 D:SPQ1751 2.7 19.5 1.0
O2 D:SPQ1751 3.1 21.2 1.0
O9 D:SPQ1751 3.1 17.7 1.0
CD D:LYS339 3.2 18.8 1.0
NH1 D:ARG343 3.2 21.2 1.0
C8 D:SPQ1751 3.2 19.0 1.0
OD1 D:ASP312 3.4 21.0 1.0
C5 D:SPQ1751 3.5 20.2 1.0
O10 D:SPQ1751 3.6 19.3 1.0
NZ D:LYS339 3.8 16.4 1.0
CZ D:ARG343 3.9 20.6 1.0
C4 D:SPQ1751 3.9 20.6 1.0
CE D:LYS339 3.9 18.4 1.0
NH2 D:ARG120 3.9 17.6 1.0
CG D:LYS339 3.9 19.8 1.0
O D:HOH1900 3.9 18.9 1.0
CB D:LYS339 4.0 20.3 1.0
O4P D:SPQ1751 4.0 17.8 1.0
NH2 D:ARG343 4.0 18.5 1.0
P2 D:SPQ1751 4.1 17.4 1.0
O D:HOH1776 4.2 12.1 1.0
O5P D:SPQ1751 4.3 19.5 1.0
CG D:ASP312 4.4 20.1 1.0
O2' D:SPQ1751 4.4 21.8 1.0
CA D:LYS339 4.6 20.6 1.0
N D:GLU340 4.7 20.3 1.0
CG D:GLU340 4.7 19.7 1.0
OD2 D:ASP312 4.8 20.2 1.0
CZ D:ARG120 4.8 19.8 1.0
NE D:ARG343 4.9 17.5 1.0
C6 D:SPQ1751 4.9 19.1 1.0
OE1 D:GLU340 4.9 21.2 1.0

Reference:

H.Park, J.L.Hilsenbeck, H.J.Kim, W.A.Shuttleworth, Y.H.Park, J.N.Evans, C.Kang. Structural Studies of Streptococcus Pneumoniae Epsp Synthase in Unliganded State, Tetrahedral Intermediate-Bound State and S3P-Glp-Bound State. Mol.Microbiol. V. 51 963 2004.
ISSN: ISSN 0950-382X
PubMed: 14763973
DOI: 10.1046/J.1365-2958.2003.03885.X
Page generated: Wed Jul 31 12:36:57 2024

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