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Iron in PDB 3hok: X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode

Enzymatic activity of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode

All present enzymatic activity of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode:
1.14.99.3;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode, PDB code: 3hok was solved by M.N.Rahman, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.072, 54.592, 71.884, 90.00, 94.64, 90.00
R / Rfree (%) 22.2 / 28.9

Other elements in 3hok:

The structure of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode (pdb code 3hok). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode, PDB code: 3hok:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3hok

Go back to Iron Binding Sites List in 3hok
Iron binding site 1 out of 2 in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe300

b:54.5
occ:1.00
 FE A:HEM300 0.0 54.5 1.0
NC A:HEM300 2.0 54.1 1.0
NA A:HEM300 2.1 55.4 1.0
NB A:HEM300 2.1 54.7 1.0
ND A:HEM300 2.1 54.3 1.0
NE2 A:HIS25 2.3 57.3 1.0
C1C A:HEM300 3.0 54.1 1.0
C1A A:HEM300 3.1 55.5 1.0
C4D A:HEM300 3.1 54.5 1.0
C4C A:HEM300 3.1 53.9 1.0
C4B A:HEM300 3.1 55.0 1.0
C4A A:HEM300 3.1 55.7 1.0
C1D A:HEM300 3.1 54.0 1.0
CE1 A:HIS25 3.1 57.0 1.0
C1B A:HEM300 3.1 54.9 1.0
CD2 A:HIS25 3.3 56.9 1.0
CHA A:HEM300 3.4 54.9 1.0
CHC A:HEM300 3.4 54.3 1.0
CHD A:HEM300 3.5 54.1 1.0
CHB A:HEM300 3.5 55.4 1.0
O A:HOH297 4.2 45.8 1.0
C2C A:HEM300 4.2 54.1 1.0
ND1 A:HIS25 4.3 56.9 1.0
C3C A:HEM300 4.3 53.6 1.0
C2A A:HEM300 4.3 56.5 1.0
C3A A:HEM300 4.3 56.4 1.0
C3D A:HEM300 4.3 54.6 1.0
C3B A:HEM300 4.3 55.4 1.0
C2B A:HEM300 4.3 55.3 1.0
C2D A:HEM300 4.3 53.8 1.0
CG A:HIS25 4.4 56.9 1.0
OE2 A:GLU29 4.9 67.9 1.0

Iron binding site 2 out of 2 in 3hok

Go back to Iron Binding Sites List in 3hok
Iron binding site 2 out of 2 in the X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R, 4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H-Imidazol-1-Yl) Methyl]-4[((5-Trifluoromethylpyridin-2-Yl)Thio)Methyl]-1,3- Dioxolane: A Novel, Inducible Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe300

b:37.0
occ:1.00
 FE B:HEM300 0.0 37.0 1.0
NB B:HEM300 2.0 37.3 1.0
NC B:HEM300 2.0 36.8 1.0
NA B:HEM300 2.1 38.8 1.0
ND B:HEM300 2.1 36.4 1.0
NE2 B:HIS25 2.2 39.3 1.0
CE1 B:HIS25 2.6 39.0 1.0
NAN B:Q80301 2.7 47.4 1.0
CAM B:Q80301 2.8 47.9 1.0
C4C B:HEM300 3.0 35.9 1.0
C1B B:HEM300 3.0 38.2 1.0
C4B B:HEM300 3.1 37.1 1.0
C1C B:HEM300 3.1 36.9 1.0
C4A B:HEM300 3.1 39.2 1.0
C1D B:HEM300 3.1 35.8 1.0
C1A B:HEM300 3.1 38.8 1.0
C4D B:HEM300 3.1 36.5 1.0
CD2 B:HIS25 3.4 39.1 1.0
CHD B:HEM300 3.4 35.4 1.0
CHB B:HEM300 3.4 39.1 1.0
CHC B:HEM300 3.4 37.2 1.0
CHA B:HEM300 3.5 36.8 1.0
ND1 B:HIS25 3.8 39.0 1.0
CAO B:Q80301 4.0 48.1 1.0
CG B:HIS25 4.2 37.7 1.0
CAL B:Q80301 4.2 48.8 1.0
C3C B:HEM300 4.3 36.4 1.0
C2B B:HEM300 4.3 38.1 1.0
C2C B:HEM300 4.3 36.9 1.0
C3B B:HEM300 4.3 37.7 1.0
C3A B:HEM300 4.3 40.2 1.0
C2A B:HEM300 4.3 40.5 1.0
C2D B:HEM300 4.3 35.9 1.0
C3D B:HEM300 4.4 36.0 1.0
NAK B:Q80301 4.8 49.9 1.0

Reference:

M.N.Rahman, J.Z.Vlahakis, D.Vukomanovic, W.A.Szarek, K.Nakatsu, Z.Jia. X-Ray Crystal Structure of Human Heme Oxygenase-1 with (2R,4S)-2-[2-(4-Chlorophenyl)Ethyl]-2-[(1H- Imidazol-1-Yl)Methyl]-4[((5-Trifluoromethylpyridin- 2-Yl)Thio)Methyl]-1,3-Dioxolane: A Novel, Inducible Binding Mode. J.Med.Chem. V. 52 4946 2009.
ISSN: ISSN 0022-2623
PubMed: 19601578
DOI: 10.1021/JM900434F
Page generated: Sun Aug 4 11:42:54 2024

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