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Iron 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:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Butyldiamine- Dansyl Conjugate, PDB code: 6bl3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6bl3

Go back to Iron Binding Sites List in 6bl3
Iron 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 Iron with other atoms in the Fe 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:Fe705

b:36.4
occ:1.00
 FE A:HEM705 0.0 36.4 1.0
NC A:HEM705 2.0 34.2 1.0
NA A:HEM705 2.0 33.4 1.0
NB A:HEM705 2.0 38.1 1.0
ND A:HEM705 2.1 38.4 1.0
NE2 A:HIS388 2.6 43.6 1.0
C4B A:HEM705 3.0 34.7 1.0
C1A A:HEM705 3.0 39.1 1.0
C1C A:HEM705 3.0 28.9 1.0
C4C A:HEM705 3.1 31.5 1.0
O A:HOH941 3.1 41.8 1.0
C4A A:HEM705 3.1 41.3 1.0
C1B A:HEM705 3.1 38.0 1.0
C4D A:HEM705 3.1 38.7 1.0
C1D A:HEM705 3.1 31.1 1.0
CD2 A:HIS388 3.3 44.1 1.0
CHC A:HEM705 3.4 32.2 1.0
CHA A:HEM705 3.4 37.2 1.0
CHB A:HEM705 3.4 38.6 1.0
CHD A:HEM705 3.5 29.7 1.0
CE1 A:HIS388 3.7 46.4 1.0
NE2 A:GLN203 4.1 34.4 1.0
C3B A:HEM705 4.2 36.3 1.0
C2A A:HEM705 4.3 39.5 1.0
C2B A:HEM705 4.3 36.1 1.0
C3D A:HEM705 4.3 40.2 1.0
C3C A:HEM705 4.3 30.3 1.0
C3A A:HEM705 4.3 37.2 1.0
C2C A:HEM705 4.3 30.9 1.0
C2D A:HEM705 4.3 35.0 1.0
NE2 A:HIS207 4.3 42.1 1.0
CG A:HIS388 4.5 44.2 1.0
CE1 A:HIS207 4.5 43.3 1.0
ND1 A:HIS388 4.7 43.3 1.0
CD A:GLN203 4.9 28.0 1.0
CG A:GLN203 4.9 25.1 1.0

Iron binding site 2 out of 4 in 6bl3

Go back to Iron Binding Sites List in 6bl3
Iron 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 Iron with other atoms in the Fe 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:Fe705

b:38.9
occ:1.00
 FE B:HEM705 0.0 38.9 1.0
NC B:HEM705 2.0 35.3 1.0
NA B:HEM705 2.0 32.2 1.0
NB B:HEM705 2.0 36.3 1.0
ND B:HEM705 2.1 39.4 1.0
NE2 B:HIS388 2.6 50.5 1.0
C4B B:HEM705 3.0 28.7 1.0
C4C B:HEM705 3.0 31.2 1.0
C1C B:HEM705 3.0 33.2 1.0
C1B B:HEM705 3.0 32.1 1.0
C4A B:HEM705 3.1 33.9 1.0
C1A B:HEM705 3.1 38.9 1.0
C1D B:HEM705 3.1 33.4 1.0
C4D B:HEM705 3.1 38.8 1.0
CD2 B:HIS388 3.3 49.8 1.0
CHC B:HEM705 3.4 26.0 1.0
CHB B:HEM705 3.4 32.6 1.0
CHD B:HEM705 3.4 28.9 1.0
CHA B:HEM705 3.5 37.7 1.0
CE1 B:HIS388 3.7 51.4 1.0
C3B B:HEM705 4.2 35.7 1.0
C2B B:HEM705 4.3 32.9 1.0
C3C B:HEM705 4.3 34.7 1.0
C2A B:HEM705 4.3 40.6 1.0
C2C B:HEM705 4.3 36.8 1.0
C3A B:HEM705 4.3 38.2 1.0
NE2 B:GLN203 4.3 33.3 1.0
C2D B:HEM705 4.3 36.8 1.0
C3D B:HEM705 4.3 41.5 1.0
NE2 B:HIS207 4.4 40.2 1.0
CG B:HIS388 4.5 49.1 1.0
CE1 B:HIS207 4.6 42.5 1.0
ND1 B:HIS388 4.6 50.2 1.0
CD B:GLN203 5.0 35.5 1.0
CG B:GLN203 5.0 31.7 1.0

Iron binding site 3 out of 4 in 6bl3

Go back to Iron Binding Sites List in 6bl3
Iron 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 Iron with other atoms in the Fe 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:Fe705

b:38.4
occ:1.00
 FE C:HEM705 0.0 38.4 1.0
NC C:HEM705 2.0 30.3 1.0
NB C:HEM705 2.0 35.3 1.0
NA C:HEM705 2.0 37.6 1.0
ND C:HEM705 2.1 40.8 1.0
NE2 C:HIS388 2.6 51.0 1.0
O C:HOH877 2.7 43.7 1.0
C4B C:HEM705 3.0 30.8 1.0
C1C C:HEM705 3.0 32.9 1.0
C1A C:HEM705 3.0 40.5 1.0
C4C C:HEM705 3.1 32.1 1.0
C1B C:HEM705 3.1 41.0 1.0
C4A C:HEM705 3.1 41.5 1.0
C4D C:HEM705 3.1 32.9 1.0
C1D C:HEM705 3.1 31.5 1.0
CD2 C:HIS388 3.3 49.7 1.0
CHC C:HEM705 3.4 29.8 1.0
CHA C:HEM705 3.4 35.7 1.0
CHB C:HEM705 3.4 41.6 1.0
CHD C:HEM705 3.5 36.4 1.0
CE1 C:HIS388 3.7 51.8 1.0
NE2 C:GLN203 4.1 34.6 1.0
C3B C:HEM705 4.2 39.6 1.0
C2B C:HEM705 4.3 41.1 1.0
C2A C:HEM705 4.3 41.4 1.0
C3C C:HEM705 4.3 35.1 1.0
C2C C:HEM705 4.3 31.4 1.0
C3A C:HEM705 4.3 42.5 1.0
C3D C:HEM705 4.3 36.8 1.0
C2D C:HEM705 4.3 31.4 1.0
NE2 C:HIS207 4.3 41.1 1.0
CG C:HIS388 4.5 49.0 1.0
CE1 C:HIS207 4.5 43.0 1.0
ND1 C:HIS388 4.7 51.1 1.0
CD C:GLN203 4.8 35.6 1.0
CG C:GLN203 4.9 31.2 1.0

Iron binding site 4 out of 4 in 6bl3

Go back to Iron Binding Sites List in 6bl3
Iron 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 Iron with other atoms in the Fe 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:Fe705

b:37.8
occ:1.00
 FE D:HEM705 0.0 37.8 1.0
NA D:HEM705 2.0 34.2 1.0
NC D:HEM705 2.0 32.2 1.0
NB D:HEM705 2.0 36.0 1.0
ND D:HEM705 2.1 35.5 1.0
NE2 D:HIS388 2.6 43.8 1.0
O D:HOH858 2.9 35.1 1.0
C4B D:HEM705 3.0 31.5 1.0
C1A D:HEM705 3.0 37.9 1.0
C4A D:HEM705 3.1 36.2 1.0
C1B D:HEM705 3.1 36.5 1.0
C1C D:HEM705 3.1 26.8 1.0
C4C D:HEM705 3.1 32.5 1.0
C4D D:HEM705 3.1 35.9 1.0
C1D D:HEM705 3.1 31.2 1.0
CD2 D:HIS388 3.3 43.7 1.0
CHC D:HEM705 3.4 22.8 1.0
CHB D:HEM705 3.4 36.5 1.0
CHA D:HEM705 3.4 35.2 1.0
CHD D:HEM705 3.4 31.2 1.0
CE1 D:HIS388 3.7 45.6 1.0
NE2 D:GLN203 4.2 33.7 1.0
C3B D:HEM705 4.2 35.8 1.0
C2B D:HEM705 4.2 38.2 1.0
C2A D:HEM705 4.3 34.0 1.0
C3A D:HEM705 4.3 35.2 1.0
C3C D:HEM705 4.3 28.4 1.0
C2C D:HEM705 4.3 32.9 1.0
C3D D:HEM705 4.3 34.7 1.0
C2D D:HEM705 4.3 35.7 1.0
NE2 D:HIS207 4.4 40.5 1.0
CG D:HIS388 4.5 44.2 1.0
CE1 D:HIS207 4.5 43.4 1.0
ND1 D:HIS388 4.7 44.1 1.0
CD D:GLN203 4.9 33.5 1.0
CG D:GLN203 4.9 33.4 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: Tue Aug 6 14:17:21 2024

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