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Fluorine in PDB 3kk6: Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib

Enzymatic activity of Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib

All present enzymatic activity of Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib:
1.14.99.1;

Protein crystallography data

The structure of Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib, PDB code: 3kk6 was solved by R.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.42 / 2.75
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 181.035, 181.035, 102.698, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 24.2

Other elements in 3kk6:

The structure of Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib (pdb code 3kk6). 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 Cyclooxygenase-1 in Complex with Celecoxib, PDB code: 3kk6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 1 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:99.3
occ:1.00
 F3 A:CEL701 0.0 99.3 1.0
C4 A:CEL701 1.3 92.8 1.0
F1 A:CEL701 2.1 92.3 1.0
F2 A:CEL701 2.2 90.1 1.0
C1 A:CEL701 2.3 83.8 1.0
HG11 A:VAL349 2.7 81.4 0.0
HC2 A:CEL701 2.9 77.3 0.0
HD22 A:LEU359 2.9 29.4 0.0
C2 A:CEL701 2.9 73.2 1.0
HD12 A:LEU359 2.9 29.4 0.0
HD21 A:LEU531 3.1 76.5 0.0
HD21 A:LEU359 3.4 29.4 0.0
HD13 A:LEU359 3.4 29.4 0.0
HG12 A:VAL349 3.4 81.4 0.0
HG11 A:VAL116 3.4 28.1 0.0
CG1 A:VAL349 3.5 81.4 1.0
N1 A:CEL701 3.5 79.6 1.0
CD2 A:LEU359 3.5 65.7 1.0
CD1 A:LEU359 3.5 61.6 1.0
HD11 A:LEU531 3.7 76.5 0.0
CD2 A:LEU531 4.0 54.4 1.0
HG13 A:VAL349 4.1 81.4 0.0
CG A:LEU359 4.1 51.7 1.0
C3 A:CEL701 4.2 66.7 1.0
CG1 A:VAL116 4.2 46.1 1.0
HB A:VAL349 4.3 81.4 0.0
HG12 A:VAL116 4.3 28.1 0.0
HD23 A:LEU359 4.3 29.4 0.0
HD11 A:LEU359 4.4 29.4 0.0
HD22 A:LEU531 4.4 76.5 0.0
N2 A:CEL701 4.4 78.5 1.0
HB3 A:LEU359 4.5 29.4 0.0
CB A:VAL349 4.5 78.9 1.0
HD23 A:LEU531 4.5 76.5 0.0
CD1 A:LEU531 4.5 60.6 1.0
HG13 A:VAL116 4.6 28.1 0.0
HG21 A:VAL349 4.6 81.4 0.0
HG A:LEU531 4.6 76.5 0.0
CG A:LEU531 4.7 65.0 1.0
HD13 A:LEU531 4.9 76.5 0.0
HG A:LEU359 4.9 29.4 0.0
CB A:LEU359 4.9 53.5 1.0
H10C A:CEL701 4.9 77.3 0.0
HE2 A:MET113 5.0 43.0 0.0

Fluorine binding site 2 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 2 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:90.1
occ:1.00
 F2 A:CEL701 0.0 90.1 1.0
C4 A:CEL701 1.3 92.8 1.0
F1 A:CEL701 2.1 92.3 1.0
F3 A:CEL701 2.2 99.3 1.0
C1 A:CEL701 2.3 83.8 1.0
HG11 A:VAL116 2.3 28.1 0.0
HG13 A:VAL116 2.8 28.1 0.0
CG1 A:VAL116 2.9 46.1 1.0
HD11 A:LEU531 2.9 76.5 0.0
C2 A:CEL701 3.0 73.2 1.0
HC2 A:CEL701 3.2 77.3 0.0
HG12 A:VAL116 3.2 28.1 0.0
N1 A:CEL701 3.3 79.6 1.0
HD21 A:LEU531 3.8 76.5 0.0
CD1 A:LEU531 3.9 60.6 1.0
HB1 A:ALA527 4.0 3.3 0.0
HE A:ARG120 4.0 65.6 0.0
HD22 A:LEU359 4.1 29.4 0.0
HG21 A:VAL116 4.1 28.1 0.0
HG3 A:ARG120 4.1 65.6 0.0
HD21 A:LEU359 4.2 29.4 0.0
HD13 A:LEU531 4.2 76.5 0.0
C3 A:CEL701 4.2 66.7 1.0
CB A:VAL116 4.3 63.0 1.0
N2 A:CEL701 4.3 78.5 1.0
HD12 A:LEU531 4.3 76.5 0.0
HG11 A:VAL349 4.4 81.4 0.0
HE2 A:TYR355 4.5 20.4 0.0
HG22 A:VAL116 4.5 28.1 0.0
CG2 A:VAL116 4.5 74.3 1.0
HH21 A:ARG120 4.6 65.6 0.0
NE A:ARG120 4.6 0.6 1.0
HB A:VAL116 4.6 28.1 0.0
CD2 A:LEU531 4.6 54.4 1.0
CD2 A:LEU359 4.6 65.7 1.0
CG A:LEU531 4.7 65.0 1.0
HG A:LEU531 4.7 76.5 0.0
CB A:ALA527 4.8 78.9 1.0
HB2 A:ALA527 4.8 3.3 0.0
HD22 A:LEU531 4.9 76.5 0.0
HD12 A:LEU359 4.9 29.4 0.0
HD13 A:LEU359 5.0 29.4 0.0
HG12 A:VAL349 5.0 81.4 0.0
NH2 A:ARG120 5.0 0.9 1.0

Fluorine binding site 3 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 3 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:92.3
occ:1.00
 F1 A:CEL701 0.0 92.3 1.0
C4 A:CEL701 1.3 92.8 1.0
F3 A:CEL701 2.1 99.3 1.0
F2 A:CEL701 2.1 90.1 1.0
C1 A:CEL701 2.3 83.8 1.0
HD21 A:LEU359 2.3 29.4 0.0
N1 A:CEL701 2.7 79.6 1.0
HD22 A:LEU359 2.9 29.4 0.0
CD2 A:LEU359 3.0 65.7 1.0
HD13 A:LEU359 3.2 29.4 0.0
HD2 A:TYR355 3.4 20.4 0.0
HG11 A:VAL116 3.4 28.1 0.0
C2 A:CEL701 3.5 73.2 1.0
HD12 A:LEU359 3.6 29.4 0.0
HD23 A:LEU359 3.7 29.4 0.0
CD1 A:LEU359 3.7 61.6 1.0
HE2 A:TYR355 3.8 20.4 0.0
HG12 A:VAL349 3.8 81.4 0.0
HG11 A:VAL349 3.9 81.4 0.0
CG A:LEU359 4.0 51.7 1.0
CD2 A:TYR355 4.0 59.2 1.0
HC2 A:CEL701 4.1 77.3 0.0
N2 A:CEL701 4.1 78.5 1.0
CE2 A:TYR355 4.2 63.6 1.0
HB2 A:SER353 4.3 7.7 0.0
CG1 A:VAL349 4.3 81.4 1.0
CG1 A:VAL116 4.3 46.1 1.0
HG21 A:VAL116 4.4 28.1 0.0
HG A:LEU359 4.4 29.4 0.0
C3 A:CEL701 4.4 66.7 1.0
HG13 A:VAL116 4.5 28.1 0.0
CB A:SER353 4.6 65.8 1.0
HD11 A:LEU359 4.6 29.4 0.0
HG13 A:VAL349 4.8 81.4 0.0
H17C A:CEL701 4.8 77.3 0.0
HG12 A:VAL116 4.8 28.1 0.0
HG A:SER353 4.9 7.7 0.0
HD11 A:LEU531 4.9 76.5 0.0
OG A:SER353 4.9 71.3 1.0
HB2 A:TYR355 4.9 20.4 0.0

Fluorine binding site 4 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 4 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1701

b:58.3
occ:0.50
 F3 B:CEL1701 0.0 58.3 0.5
C4 B:CEL1701 1.3 50.6 0.5
F1 B:CEL1701 2.1 66.5 0.5
F2 B:CEL1701 2.2 55.4 0.5
C1 B:CEL1701 2.3 34.1 0.5
HG11 B:VAL349 2.8 48.7 0.0
HC2 B:CEL1701 2.9 65.8 0.0
HD22 B:LEU359 2.9 70.6 0.0
C2 B:CEL1701 2.9 29.2 0.5
HD13 B:LEU359 2.9 70.6 0.0
HD21 B:LEU531 3.1 71.8 0.0
HD21 B:LEU359 3.4 70.6 0.0
HD11 B:LEU359 3.4 70.6 0.0
HG12 B:VAL349 3.4 48.7 0.0
HG11 B:VAL116 3.4 28.7 0.0
N1 B:CEL1701 3.5 37.8 0.5
CD2 B:LEU359 3.5 70.0 1.0
CG1 B:VAL349 3.5 82.7 1.0
CD1 B:LEU359 3.5 64.2 1.0
HD11 B:LEU531 3.7 71.8 0.0
CD2 B:LEU531 4.0 51.1 1.0
HG13 B:VAL349 4.1 48.7 0.0
CG B:LEU359 4.1 55.2 1.0
C3 B:CEL1701 4.2 30.9 0.5
CG1 B:VAL116 4.2 44.4 1.0
HG12 B:VAL116 4.3 28.7 0.0
HD23 B:LEU359 4.3 70.6 0.0
HD12 B:LEU359 4.4 70.6 0.0
HD22 B:LEU531 4.4 71.8 0.0
HB B:VAL349 4.4 48.7 0.0
N2 B:CEL1701 4.4 45.9 0.5
HB3 B:LEU359 4.5 70.6 0.0
HD23 B:LEU531 4.5 71.8 0.0
CD1 B:LEU531 4.5 57.3 1.0
CB B:VAL349 4.5 75.6 1.0
HG21 B:VAL349 4.6 48.7 0.0
HE2 B:TYR355 4.6 90.7 0.0
HG13 B:VAL116 4.6 28.7 0.0
HG B:LEU531 4.6 71.8 0.0
CG B:LEU531 4.7 61.8 1.0
HB3 B:SER353 4.8 0.8 0.0
HD13 B:LEU531 4.9 71.8 0.0
HG B:LEU359 4.9 70.6 0.0
CB B:LEU359 4.9 56.4 1.0
H10C B:CEL1701 4.9 65.8 0.0
HE1 B:MET113 5.0 0.0 0.0

Fluorine binding site 5 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 5 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1701

b:55.4
occ:0.50
 F2 B:CEL1701 0.0 55.4 0.5
C4 B:CEL1701 1.3 50.6 0.5
F1 B:CEL1701 2.1 66.5 0.5
F3 B:CEL1701 2.2 58.3 0.5
HG11 B:VAL116 2.3 28.7 0.0
C1 B:CEL1701 2.3 34.1 0.5
HG13 B:VAL116 2.8 28.7 0.0
CG1 B:VAL116 2.9 44.4 1.0
HD11 B:LEU531 2.9 71.8 0.0
C2 B:CEL1701 3.0 29.2 0.5
HC2 B:CEL1701 3.2 65.8 0.0
HG12 B:VAL116 3.2 28.7 0.0
N1 B:CEL1701 3.3 37.8 0.5
HE2 B:TYR355 3.8 90.7 0.0
HD21 B:LEU531 3.8 71.8 0.0
CD1 B:LEU531 3.9 57.3 1.0
HB1 B:ALA527 4.0 0.7 0.0
HD22 B:LEU359 4.1 70.6 0.0
HG21 B:VAL116 4.1 28.7 0.0
HE B:ARG120 4.1 80.7 0.0
HE B:ARG120 4.2 80.7 0.0
HD13 B:LEU531 4.2 71.8 0.0
HD21 B:LEU359 4.2 70.6 0.0
C3 B:CEL1701 4.2 30.9 0.5
CB B:VAL116 4.2 63.8 1.0
N2 B:CEL1701 4.3 45.9 0.5
HG3 B:ARG120 4.3 80.7 0.0
HG3 B:ARG120 4.3 80.7 0.0
HD12 B:LEU531 4.3 71.8 0.0
HH21 B:ARG120 4.4 80.7 0.0
HH21 B:ARG120 4.5 80.7 0.0
HG11 B:VAL349 4.5 48.7 0.0
HG22 B:VAL116 4.5 28.7 0.0
CG2 B:VAL116 4.5 70.2 1.0
HB B:VAL116 4.6 28.7 0.0
CD2 B:LEU531 4.6 51.1 1.0
CD2 B:LEU359 4.6 70.0 1.0
CE2 B:TYR355 4.7 67.9 1.0
CG B:LEU531 4.7 61.8 1.0
HG B:LEU531 4.7 71.8 0.0
NE B:ARG120 4.7 81.3 0.5
NE B:ARG120 4.8 81.4 0.5
CB B:ALA527 4.8 79.9 1.0
HB2 B:ALA527 4.9 0.7 0.0
HD22 B:LEU531 4.9 71.8 0.0
HD13 B:LEU359 4.9 70.6 0.0
HD11 B:LEU359 5.0 70.6 0.0

Fluorine binding site 6 out of 6 in 3kk6

Go back to Fluorine Binding Sites List in 3kk6
Fluorine binding site 6 out of 6 in the Crystal Structure of Cyclooxygenase-1 in Complex with Celecoxib


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 Cyclooxygenase-1 in Complex with Celecoxib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1701

b:66.5
occ:0.50
 F1 B:CEL1701 0.0 66.5 0.5
C4 B:CEL1701 1.3 50.6 0.5
F3 B:CEL1701 2.1 58.3 0.5
F2 B:CEL1701 2.1 55.4 0.5
C1 B:CEL1701 2.3 34.1 0.5
HD21 B:LEU359 2.3 70.6 0.0
HE2 B:TYR355 2.6 90.7 0.0
N1 B:CEL1701 2.7 37.8 0.5
HD22 B:LEU359 2.9 70.6 0.0
CD2 B:LEU359 3.0 70.0 1.0
HD2 B:TYR355 3.1 90.7 0.0
HD11 B:LEU359 3.2 70.6 0.0
CE2 B:TYR355 3.4 67.9 1.0
HG11 B:VAL116 3.4 28.7 0.0
C2 B:CEL1701 3.5 29.2 0.5
CD2 B:TYR355 3.6 57.2 1.0
HD13 B:LEU359 3.6 70.6 0.0
HD23 B:LEU359 3.7 70.6 0.0
CD1 B:LEU359 3.7 64.2 1.0
HB3 B:SER353 3.8 0.8 0.0
HG12 B:VAL349 3.8 48.7 0.0
CG B:LEU359 4.0 55.2 1.0
HG11 B:VAL349 4.0 48.7 0.0
HC2 B:CEL1701 4.1 65.8 0.0
N2 B:CEL1701 4.1 45.9 0.5
CG1 B:VAL116 4.3 44.4 1.0
CG1 B:VAL349 4.4 82.7 1.0
HG21 B:VAL116 4.4 28.7 0.0
HG B:LEU359 4.4 70.6 0.0
C3 B:CEL1701 4.4 30.9 0.5
HB2 B:SER353 4.5 0.8 0.0
HG13 B:VAL116 4.5 28.7 0.0
CB B:SER353 4.5 71.6 1.0
CZ B:TYR355 4.6 83.9 1.0
HD12 B:LEU359 4.6 70.6 0.0
HG13 B:VAL349 4.8 48.7 0.0
H17C B:CEL1701 4.8 65.8 0.0
HG12 B:VAL116 4.8 28.7 0.0
HD11 B:LEU531 4.9 71.8 0.0
HG B:SER353 4.9 0.8 0.0
HH B:TYR355 4.9 90.7 0.0
CG B:TYR355 4.9 73.5 1.0
OG B:SER353 5.0 81.4 1.0

Reference:

G.Rimon, R.S.Sidhu, D.A.Lauver, J.Y.Lee, N.P.Sharma, C.Yuan, R.A.Frieler, R.C.Trievel, B.R.Lucchesi, W.L.Smith. Coxibs Interfere with the Action of Aspirin By Binding Tightly to One Monomer of Cyclooxygenase-1. Proc.Natl.Acad.Sci.Usa V. 107 28 2010.
ISSN: ISSN 0027-8424
PubMed: 19955429
DOI: 10.1073/PNAS.0909765106
Page generated: Wed Jul 31 19:55:20 2024

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