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Chlorine in PDB 6bl3: Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate

Enzymatic activity of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate

All present enzymatic activity of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate:
1.14.99.1;

Protein crystallography data

The structure of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate, PDB code: 6bl3 was solved by S.Xu, M.J.Uddin, S.Banerjee, L.J.Marnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.44 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.474, 121.776, 134.800, 90.00, 123.48, 90.00
R / Rfree (%) 20.5 / 22.9

Other elements in 6bl3:

The structure of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate (pdb code 6bl3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate, PDB code: 6bl3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6bl3

Go back to Chlorine Binding Sites List in 6bl3
Chlorine binding site 1 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:46.6
occ:1.00
 CLAV A:L7M706 0.0 46.6 1.0
CAS A:L7M706 1.7 41.3 1.0
CAR A:L7M706 2.7 37.6 1.0
CAT A:L7M706 2.7 38.7 1.0
CZ2 A:TRP387 3.5 36.3 1.0
SD A:MET522 3.6 40.4 1.0
CD2 A:LEU384 3.8 56.1 1.0
CAQ A:L7M706 4.0 37.8 1.0
CAU A:L7M706 4.0 36.5 1.0
CB A:LEU384 4.0 45.5 1.0
CA A:GLY526 4.0 31.9 1.0
NE1 A:TRP387 4.1 33.9 1.0
CE2 A:TRP387 4.1 37.9 1.0
O A:LEU384 4.2 50.6 1.0
CG A:MET522 4.2 37.5 1.0
O A:MET522 4.2 30.3 1.0
C A:LEU384 4.2 42.0 1.0
CG A:LEU384 4.3 48.1 1.0
CD2 A:TYR385 4.3 43.1 1.0
CE1 A:PHE381 4.4 32.9 1.0
N A:TYR385 4.4 36.7 1.0
CH2 A:TRP387 4.5 31.9 1.0
CAP A:L7M706 4.5 37.8 1.0
CE2 A:TYR385 4.5 42.2 1.0
CG A:TYR385 4.6 38.8 1.0
CA A:TYR385 4.6 31.1 1.0
C A:GLY526 4.8 35.9 1.0
CA A:LEU384 4.8 41.4 1.0
CD1 A:PHE381 4.8 35.5 1.0
CZ A:TYR385 4.9 41.9 1.0
N A:GLY526 4.9 32.9 1.0
CD1 A:TYR385 5.0 34.1 1.0

Chlorine binding site 2 out of 4 in 6bl3

Go back to Chlorine Binding Sites List in 6bl3
Chlorine binding site 2 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl706

b:41.8
occ:1.00
 CLAV B:L7M706 0.0 41.8 1.0
CAS B:L7M706 1.7 39.2 1.0
CAR B:L7M706 2.7 39.9 1.0
CAT B:L7M706 2.7 37.2 1.0
CZ2 B:TRP387 3.6 31.8 1.0
SD B:MET522 3.7 43.5 1.0
O B:LEU384 3.8 44.5 1.0
CA B:GLY526 4.0 38.8 1.0
CAQ B:L7M706 4.0 45.3 1.0
CB B:LEU384 4.0 53.5 1.0
CAU B:L7M706 4.0 39.1 1.0
C B:LEU384 4.1 41.2 1.0
CE1 B:PHE381 4.2 40.8 1.0
NE1 B:TRP387 4.2 27.4 1.0
CE2 B:TRP387 4.2 32.3 1.0
O B:MET522 4.3 34.8 1.0
CD2 B:TYR385 4.3 30.7 1.0
CG B:MET522 4.3 39.0 1.0
N B:TYR385 4.5 32.7 1.0
CD2 B:LEU384 4.5 60.2 1.0
CG B:TYR385 4.5 40.0 1.0
CAP B:L7M706 4.5 43.0 1.0
CE2 B:TYR385 4.5 31.7 1.0
CH2 B:TRP387 4.6 28.6 1.0
CA B:TYR385 4.6 33.0 1.0
CD1 B:PHE381 4.6 37.9 1.0
C B:GLY526 4.7 41.8 1.0
CA B:LEU384 4.8 47.7 1.0
CG B:LEU384 4.9 60.6 1.0
CD1 B:TYR385 4.9 32.7 1.0
N B:GLY526 4.9 41.1 1.0
CZ B:TYR385 4.9 34.9 1.0
O B:GLY526 4.9 46.0 1.0
CB B:TYR385 5.0 40.1 1.0

Chlorine binding site 3 out of 4 in 6bl3

Go back to Chlorine Binding Sites List in 6bl3
Chlorine binding site 3 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl706

b:42.7
occ:1.00
 CLAV C:L7M706 0.0 42.7 1.0
CAS C:L7M706 1.7 34.0 1.0
CAR C:L7M706 2.7 32.5 1.0
CAT C:L7M706 2.7 33.2 1.0
CD2 C:LEU384 3.4 65.2 1.0
CZ2 C:TRP387 3.6 35.0 1.0
SD C:MET522 3.6 46.4 1.0
O C:LEU384 3.9 48.9 1.0
CA C:GLY526 4.0 37.2 1.0
CAQ C:L7M706 4.0 32.7 1.0
CAU C:L7M706 4.0 35.2 1.0
CB C:LEU384 4.1 54.4 1.0
NE1 C:TRP387 4.1 35.5 1.0
C C:LEU384 4.2 43.6 1.0
CE2 C:TRP387 4.2 33.5 1.0
O C:MET522 4.2 34.0 1.0
CG C:MET522 4.2 41.4 1.0
CG C:LEU384 4.3 57.2 1.0
CD2 C:TYR385 4.3 42.2 1.0
CE1 C:PHE381 4.3 42.5 1.0
CE2 C:TYR385 4.5 44.9 1.0
CAP C:L7M706 4.5 34.2 1.0
N C:TYR385 4.5 34.9 1.0
CH2 C:TRP387 4.6 34.1 1.0
CG C:TYR385 4.6 38.6 1.0
CA C:TYR385 4.7 33.9 1.0
C C:GLY526 4.7 37.0 1.0
CD1 C:PHE381 4.7 42.9 1.0
CA C:LEU384 4.8 50.3 1.0
N C:GLY526 4.9 39.7 1.0
CZ C:TYR385 5.0 46.5 1.0
O C:GLY526 5.0 35.2 1.0

Chlorine binding site 4 out of 4 in 6bl3

Go back to Chlorine Binding Sites List in 6bl3
Chlorine binding site 4 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl706

b:40.0
occ:1.00
 CLAV D:L7M706 0.0 40.0 1.0
CAS D:L7M706 1.7 38.0 1.0
CAR D:L7M706 2.7 34.2 1.0
CAT D:L7M706 2.7 36.7 1.0
CZ2 D:TRP387 3.5 31.4 1.0
SD D:MET522 3.8 40.8 1.0
CB D:LEU384 4.0 48.8 1.0
O D:LEU384 4.0 40.5 1.0
CAU D:L7M706 4.0 38.4 1.0
CAQ D:L7M706 4.0 36.4 1.0
CA D:GLY526 4.0 31.6 1.0
NE1 D:TRP387 4.1 29.5 1.0
CE2 D:TRP387 4.1 30.4 1.0
C D:LEU384 4.2 36.9 1.0
CE1 D:PHE381 4.3 31.5 1.0
CD2 D:TYR385 4.3 33.5 1.0
CG D:MET522 4.4 32.2 1.0
O D:MET522 4.4 36.3 1.0
CG D:TYR385 4.4 33.5 1.0
N D:TYR385 4.4 32.7 1.0
CH2 D:TRP387 4.5 28.9 1.0
CAP D:L7M706 4.5 40.0 1.0
CE2 D:TYR385 4.5 29.4 1.0
CA D:TYR385 4.6 33.1 1.0
CD1 D:LEU384 4.6 68.7 1.0
CD1 D:PHE381 4.7 27.6 1.0
C D:GLY526 4.7 34.4 1.0
CD1 D:TYR385 4.7 22.1 1.0
CA D:LEU384 4.8 42.7 1.0
CZ D:TYR385 4.8 30.8 1.0
CG D:LEU384 4.9 55.2 1.0
CB D:TYR385 4.9 35.0 1.0
O D:GLY526 4.9 38.3 1.0
CE1 D:TYR385 4.9 26.6 1.0
N D:GLY526 5.0 34.0 1.0

Reference:

S.Xu, M.J.Uddin, S.Banerjee, K.Duggan, J.Musee, J.R.Kiefer, K.Ghebreselasie, C.A.Rouzer, L.J.Marnett. Fluorescent Indomethacin-Dansyl Conjugates Utilize the Membrane-Binding Domain of Cyclooxygenase-2 to Block the Opening to the Active Site. J.Biol.Chem. V. 294 8690 2019.
ISSN: ESSN 1083-351X
PubMed: 31000626
DOI: 10.1074/JBC.RA119.007405
Page generated: Fri Jul 26 22:51:06 2024

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