Iron in PDB 4otj: The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide

Enzymatic activity of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide

All present enzymatic activity of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide:
1.14.99.1;

Protein crystallography data

The structure of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide, PDB code: 4otj 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) 50.11 / 2.11
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.712, 133.943, 122.223, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.9

Other elements in 4otj:

The structure of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide (pdb code 4otj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide, PDB code: 4otj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4otj

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Iron binding site 1 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe705

b:26.6
occ:1.00
 FE A:HEM705 0.0 26.6 1.0
NC A:HEM705 2.0 26.3 1.0
NA A:HEM705 2.1 27.2 1.0
ND A:HEM705 2.1 23.1 1.0
NB A:HEM705 2.1 28.7 1.0
O A:HOH860 2.2 33.6 1.0
NE2 A:HIS388 2.4 32.8 1.0
C1C A:HEM705 3.0 23.7 1.0
CD2 A:HIS388 3.0 31.7 1.0
C1A A:HEM705 3.1 31.0 1.0
C4D A:HEM705 3.1 26.6 1.0
C4C A:HEM705 3.1 26.6 1.0
C1D A:HEM705 3.1 22.9 1.0
C4A A:HEM705 3.1 30.6 1.0
C4B A:HEM705 3.1 27.9 1.0
C1B A:HEM705 3.1 29.6 1.0
CHA A:HEM705 3.4 29.6 1.0
CHC A:HEM705 3.4 22.2 1.0
CHD A:HEM705 3.4 25.8 1.0
CE1 A:HIS388 3.5 34.6 1.0
CHB A:HEM705 3.5 31.7 1.0
CG A:HIS388 4.3 32.0 1.0
C2C A:HEM705 4.3 25.8 1.0
NE2 A:GLN203 4.3 23.5 1.0
C3C A:HEM705 4.3 26.1 1.0
C2A A:HEM705 4.3 35.9 1.0
C3D A:HEM705 4.3 28.1 1.0
C2D A:HEM705 4.3 25.6 1.0
C3A A:HEM705 4.3 31.9 1.0
C2B A:HEM705 4.3 31.3 1.0
C3B A:HEM705 4.3 31.8 1.0
ND1 A:HIS388 4.4 32.6 1.0
NE2 A:HIS207 4.5 24.7 1.0
CE1 A:HIS207 4.7 23.8 1.0
CD A:GLN203 5.0 23.9 1.0
CG1 A:VAL447 5.0 26.4 1.0

Iron binding site 2 out of 4 in 4otj

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Iron binding site 2 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe706

b:30.1
occ:1.00
 FE B:HEM706 0.0 30.1 1.0
NC B:HEM706 2.0 31.8 1.0
NA B:HEM706 2.1 32.4 1.0
ND B:HEM706 2.1 27.5 1.0
NB B:HEM706 2.1 34.5 1.0
NE2 B:HIS388 2.4 35.9 1.0
O B:HOH822 2.5 32.3 1.0
C1C B:HEM706 3.0 29.4 1.0
C4C B:HEM706 3.0 31.8 1.0
C1D B:HEM706 3.1 26.6 1.0
C4B B:HEM706 3.1 32.3 1.0
CD2 B:HIS388 3.1 34.1 1.0
C1A B:HEM706 3.1 34.9 1.0
C4D B:HEM706 3.1 29.1 1.0
C1B B:HEM706 3.1 35.2 1.0
C4A B:HEM706 3.1 34.9 1.0
CHD B:HEM706 3.4 26.7 1.0
CHC B:HEM706 3.4 28.1 1.0
CHA B:HEM706 3.5 30.2 1.0
CHB B:HEM706 3.5 35.2 1.0
CE1 B:HIS388 3.5 37.4 1.0
C2C B:HEM706 4.2 30.9 1.0
C3C B:HEM706 4.2 31.8 1.0
NE2 B:GLN203 4.2 31.6 1.0
C2D B:HEM706 4.3 26.3 1.0
CG B:HIS388 4.3 33.9 1.0
C3B B:HEM706 4.3 34.1 1.0
C2B B:HEM706 4.3 36.6 1.0
C2A B:HEM706 4.3 39.2 1.0
C3D B:HEM706 4.3 30.4 1.0
C3A B:HEM706 4.3 35.4 1.0
NE2 B:HIS207 4.3 28.5 1.0
ND1 B:HIS388 4.5 36.2 1.0
CE1 B:HIS207 4.6 30.5 1.0
O B:HOH1000 4.8 47.0 1.0
CD B:GLN203 4.9 30.7 1.0
CG B:GLN203 5.0 29.5 1.0

Iron binding site 3 out of 4 in 4otj

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Iron binding site 3 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe705

b:25.4
occ:1.00
 FE C:HEM705 0.0 25.4 1.0
NC C:HEM705 2.0 18.0 1.0
NA C:HEM705 2.1 23.9 1.0
NB C:HEM705 2.1 27.2 1.0
ND C:HEM705 2.1 20.9 1.0
NE2 C:HIS388 2.4 27.7 1.0
O C:HOH1072 2.7 34.1 1.0
C1C C:HEM705 3.0 19.8 1.0
CD2 C:HIS388 3.0 28.2 1.0
C4C C:HEM705 3.0 21.1 1.0
C1A C:HEM705 3.1 24.2 1.0
C1D C:HEM705 3.1 19.9 1.0
C4D C:HEM705 3.1 22.2 1.0
C4B C:HEM705 3.1 25.0 1.0
C4A C:HEM705 3.1 25.5 1.0
C1B C:HEM705 3.1 24.4 1.0
CHC C:HEM705 3.4 22.6 1.0
CHD C:HEM705 3.4 21.2 1.0
CHA C:HEM705 3.4 22.9 1.0
CHB C:HEM705 3.5 25.6 1.0
CE1 C:HIS388 3.5 28.7 1.0
C2C C:HEM705 4.2 22.9 1.0
C3C C:HEM705 4.3 20.2 1.0
NE2 C:GLN203 4.3 20.6 1.0
CG C:HIS388 4.3 29.5 1.0
C2A C:HEM705 4.3 29.0 1.0
C3A C:HEM705 4.3 27.1 1.0
C2B C:HEM705 4.3 26.6 1.0
C3B C:HEM705 4.3 26.9 1.0
C2D C:HEM705 4.3 22.2 1.0
C3D C:HEM705 4.3 24.5 1.0
NE2 C:HIS207 4.4 25.6 1.0
ND1 C:HIS388 4.5 29.2 1.0
CE1 C:HIS207 4.7 24.0 1.0
O C:HOH1128 4.8 44.3 1.0
CG C:GLN203 4.9 23.5 1.0
CD C:GLN203 5.0 21.6 1.0

Iron binding site 4 out of 4 in 4otj

Go back to Iron Binding Sites List in 4otj
Iron binding site 4 out of 4 in the The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Complex of Murine Cyclooxygenase-2 with A Conjugate of Indomefathin and Podophyllotoxin, N-{(Succinylpodophyllotoxinyl)But- 4-Yl}-2-{1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1H-Indol-3- Yl}Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe705

b:26.8
occ:1.00
 FE D:HEM705 0.0 26.8 1.0
NC D:HEM705 2.0 21.2 1.0
NA D:HEM705 2.1 24.4 1.0
ND D:HEM705 2.1 23.8 1.0
NB D:HEM705 2.1 26.1 1.0
NE2 D:HIS388 2.4 28.8 1.0
O D:HOH815 2.6 31.6 1.0
C1C D:HEM705 3.0 23.2 1.0
C1A D:HEM705 3.1 29.1 1.0
C4C D:HEM705 3.1 20.9 1.0
C4D D:HEM705 3.1 22.3 1.0
CD2 D:HIS388 3.1 29.0 1.0
C1D D:HEM705 3.1 20.1 1.0
C4A D:HEM705 3.1 25.3 1.0
C1B D:HEM705 3.1 28.7 1.0
C4B D:HEM705 3.1 27.4 1.0
CE1 D:HIS388 3.4 31.6 1.0
CHA D:HEM705 3.4 23.9 1.0
CHD D:HEM705 3.4 20.7 1.0
CHC D:HEM705 3.4 25.6 1.0
CHB D:HEM705 3.5 27.7 1.0
NE2 D:GLN203 4.3 22.3 1.0
C2C D:HEM705 4.3 22.2 1.0
C3C D:HEM705 4.3 22.1 1.0
CG D:HIS388 4.3 30.8 1.0
C2A D:HEM705 4.3 30.8 1.0
C3A D:HEM705 4.3 26.9 1.0
C3D D:HEM705 4.3 23.1 1.0
C2D D:HEM705 4.3 20.6 1.0
C2B D:HEM705 4.3 30.6 1.0
C3B D:HEM705 4.3 28.4 1.0
ND1 D:HIS388 4.4 30.1 1.0
NE2 D:HIS207 4.4 26.4 1.0
O D:HOH1069 4.7 47.4 1.0
CE1 D:HIS207 4.7 26.3 1.0
CG1 D:VAL447 5.0 27.4 1.0
CD D:GLN203 5.0 24.8 1.0
CG D:GLN203 5.0 21.9 1.0

Reference:

M.J.Uddin, B.C.Crews, S.Xu, K.Ghebreselasie, S.Banerjee, C.K.Daniel, P.J.Kingsley, L.J.Marnett. Antitumor Activity of Cytotoxic Cyclooxygenase-2 Inhibitors To Be Published.
Page generated: Sun Dec 13 15:43:57 2020

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