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Iron in PDB 6bl4: Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- Dansyl Conjugate

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

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

Protein crystallography data

The structure of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- Dansyl Conjugate, PDB code: 6bl4 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) 111.96 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.795, 120.414, 134.417, 90.00, 123.60, 90.00
R / Rfree (%) 18.9 / 22

Other elements in 6bl4:

The structure of Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- 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-Ethylenediamine- Dansyl Conjugate (pdb code 6bl4). 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-Ethylenediamine- Dansyl Conjugate, PDB code: 6bl4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6bl4

Go back to Iron Binding Sites List in 6bl4
Iron binding site 1 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- 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-Ethylenediamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:28.7
occ:1.00
 FE A:HEM701 0.0 28.7 1.0
NC A:HEM701 2.0 28.5 1.0
NA A:HEM701 2.0 27.2 1.0
ND A:HEM701 2.0 30.7 1.0
NB A:HEM701 2.1 30.3 1.0
NE2 A:HIS388 2.3 35.9 1.0
C1C A:HEM701 3.0 28.4 1.0
C1A A:HEM701 3.0 30.9 1.0
C4D A:HEM701 3.0 30.0 1.0
C1D A:HEM701 3.1 28.8 1.0
C4C A:HEM701 3.1 28.7 1.0
C4A A:HEM701 3.1 28.4 1.0
CD2 A:HIS388 3.1 35.6 1.0
C4B A:HEM701 3.1 29.3 1.0
C1B A:HEM701 3.1 30.3 1.0
CHA A:HEM701 3.4 28.1 1.0
CE1 A:HIS388 3.4 36.1 1.0
CHC A:HEM701 3.4 30.3 1.0
CHD A:HEM701 3.4 28.6 1.0
CHB A:HEM701 3.5 29.8 1.0
C2C A:HEM701 4.2 26.2 1.0
C3D A:HEM701 4.2 29.5 1.0
C2D A:HEM701 4.2 28.8 1.0
C2A A:HEM701 4.2 30.3 1.0
C3C A:HEM701 4.3 26.9 1.0
NE2 A:GLN203 4.3 25.0 1.0
CG A:HIS388 4.3 35.6 1.0
C3A A:HEM701 4.3 27.9 1.0
C3B A:HEM701 4.3 32.3 1.0
C2B A:HEM701 4.3 31.0 1.0
ND1 A:HIS388 4.4 36.7 1.0
NE2 A:HIS207 4.4 31.7 1.0
CE1 A:HIS207 4.6 31.5 1.0
CG A:GLN203 4.9 23.1 1.0
CD A:GLN203 4.9 25.8 1.0

Iron binding site 2 out of 4 in 6bl4

Go back to Iron Binding Sites List in 6bl4
Iron binding site 2 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- 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-Ethylenediamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:23.0
occ:1.00
 FE B:HEM701 0.0 23.0 1.0
ND B:HEM701 1.9 26.4 1.0
NA B:HEM701 1.9 26.0 1.0
NC B:HEM701 2.0 26.0 1.0
NB B:HEM701 2.1 30.0 1.0
NE2 B:HIS388 2.3 38.0 1.0
C4D B:HEM701 2.8 23.3 1.0
C1D B:HEM701 2.9 25.7 1.0
C1A B:HEM701 2.9 29.3 1.0
C4A B:HEM701 3.0 30.8 1.0
C4B B:HEM701 3.0 29.3 1.0
C1C B:HEM701 3.0 27.9 1.0
C1B B:HEM701 3.0 31.8 1.0
C4C B:HEM701 3.0 28.1 1.0
CD2 B:HIS388 3.1 39.2 1.0
CHA B:HEM701 3.3 26.8 1.0
O B:HOH934 3.3 44.0 1.0
CHD B:HEM701 3.4 26.6 1.0
CHC B:HEM701 3.4 27.1 1.0
CHB B:HEM701 3.4 30.3 1.0
CE1 B:HIS388 3.4 38.7 1.0
C2A B:HEM701 4.1 31.6 1.0
C3D B:HEM701 4.1 25.9 1.0
C2D B:HEM701 4.1 24.2 1.0
C3A B:HEM701 4.1 31.1 1.0
C2C B:HEM701 4.1 28.1 1.0
C3C B:HEM701 4.2 24.9 1.0
C2B B:HEM701 4.2 31.0 1.0
C3B B:HEM701 4.2 31.2 1.0
CG B:HIS388 4.3 38.7 1.0
NE2 B:GLN203 4.3 31.1 1.0
NE2 B:HIS207 4.3 33.9 1.0
ND1 B:HIS388 4.4 38.0 1.0
CE1 B:HIS207 4.5 34.7 1.0
CG B:GLN203 4.9 31.1 1.0
CD B:GLN203 4.9 33.5 1.0

Iron binding site 3 out of 4 in 6bl4

Go back to Iron Binding Sites List in 6bl4
Iron binding site 3 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- 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-Ethylenediamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe701

b:27.0
occ:1.00
 FE C:HEM701 0.0 27.0 1.0
ND C:HEM701 1.8 26.1 1.0
NA C:HEM701 1.9 30.0 1.0
NC C:HEM701 2.0 22.4 1.0
NB C:HEM701 2.1 27.3 1.0
NE2 C:HIS388 2.2 29.8 1.0
C4D C:HEM701 2.8 23.9 1.0
C1D C:HEM701 2.9 22.6 1.0
C1A C:HEM701 2.9 30.2 1.0
C4C C:HEM701 3.0 21.5 1.0
C4A C:HEM701 3.0 30.6 1.0
CD2 C:HIS388 3.0 30.2 1.0
C1B C:HEM701 3.0 27.5 1.0
C1C C:HEM701 3.1 23.5 1.0
C4B C:HEM701 3.1 25.2 1.0
CHA C:HEM701 3.3 28.2 1.0
CE1 C:HIS388 3.3 30.1 1.0
CHD C:HEM701 3.3 24.7 1.0
O C:HOH858 3.4 34.7 1.0
CHB C:HEM701 3.4 28.4 1.0
CHC C:HEM701 3.5 21.9 1.0
C3D C:HEM701 4.1 25.7 1.0
C2A C:HEM701 4.1 31.8 1.0
C2D C:HEM701 4.1 25.2 1.0
C3A C:HEM701 4.1 30.0 1.0
C3C C:HEM701 4.2 20.9 1.0
C2C C:HEM701 4.2 21.1 1.0
CG C:HIS388 4.2 30.9 1.0
C2B C:HEM701 4.2 29.2 1.0
C3B C:HEM701 4.3 29.8 1.0
ND1 C:HIS388 4.3 30.3 1.0
NE2 C:GLN203 4.3 20.7 1.0
NE2 C:HIS207 4.5 25.0 1.0
CE1 C:HIS207 4.6 25.1 1.0
CD C:GLN203 4.9 21.4 1.0
CG C:GLN203 4.9 21.2 1.0

Iron binding site 4 out of 4 in 6bl4

Go back to Iron Binding Sites List in 6bl4
Iron binding site 4 out of 4 in the Crystal Complex of Cyclooxygenase-2 with Indomethacin-Ethylenediamine- 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-Ethylenediamine- Dansyl Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe701

b:28.6
occ:1.00
 FE D:HEM701 0.0 28.6 1.0
NC D:HEM701 2.0 25.2 1.0
NA D:HEM701 2.0 31.6 1.0
ND D:HEM701 2.1 32.5 1.0
NB D:HEM701 2.1 32.4 1.0
NE2 D:HIS388 2.4 38.5 1.0
C1C D:HEM701 3.0 26.3 1.0
C1A D:HEM701 3.0 33.9 1.0
C4C D:HEM701 3.0 26.5 1.0
C4A D:HEM701 3.0 33.7 1.0
C4D D:HEM701 3.1 30.6 1.0
C1D D:HEM701 3.1 29.6 1.0
C4B D:HEM701 3.1 29.4 1.0
C1B D:HEM701 3.1 30.3 1.0
CD2 D:HIS388 3.1 39.3 1.0
CHD D:HEM701 3.4 27.7 1.0
CHA D:HEM701 3.4 31.3 1.0
O D:HOH974 3.4 34.1 1.0
CHC D:HEM701 3.4 26.8 1.0
CE1 D:HIS388 3.4 39.5 1.0
CHB D:HEM701 3.5 32.1 1.0
NE2 D:GLN203 4.2 32.3 1.0
C2C D:HEM701 4.2 23.3 1.0
C2A D:HEM701 4.2 36.2 1.0
C3C D:HEM701 4.2 22.5 1.0
C3A D:HEM701 4.2 32.3 1.0
C2D D:HEM701 4.3 30.6 1.0
C3D D:HEM701 4.3 32.6 1.0
CG D:HIS388 4.3 38.8 1.0
C3B D:HEM701 4.3 32.5 1.0
C2B D:HEM701 4.3 32.9 1.0
NE2 D:HIS207 4.4 35.4 1.0
ND1 D:HIS388 4.4 40.4 1.0
CE1 D:HIS207 4.6 35.3 1.0
CD D:GLN203 4.8 29.1 1.0
CG D:GLN203 4.9 26.9 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 14:17:23 2024

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