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Iron in PDB 4ejh: Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)

Enzymatic activity of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)

All present enzymatic activity of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk):
1.14.14.1;

Protein crystallography data

The structure of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk), PDB code: 4ejh was solved by N.M.Devore, E.E.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.77 / 2.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.678, 119.269, 153.665, 100.59, 101.86, 93.56
R / Rfree (%) 21.4 / 27.3

Iron Binding Sites:

The binding sites of Iron atom in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) (pdb code 4ejh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk), PDB code: 4ejh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4ejh

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Iron binding site 1 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:29.3
occ:1.00
FE A:HEM501 0.0 29.3 1.0
NA A:HEM501 2.0 30.3 1.0
NB A:HEM501 2.0 28.6 1.0
NC A:HEM501 2.1 28.7 1.0
ND A:HEM501 2.1 28.0 1.0
SG A:CYS439 2.3 29.8 1.0
O2 A:0QA502 2.5 58.9 1.0
N3 A:0QA502 2.8 58.8 1.0
C4A A:HEM501 2.9 27.2 1.0
C1B A:HEM501 3.0 26.1 1.0
C4C A:HEM501 3.0 27.4 1.0
C1D A:HEM501 3.1 24.3 1.0
C4B A:HEM501 3.1 27.4 1.0
C1A A:HEM501 3.1 28.1 1.0
C1C A:HEM501 3.1 29.8 1.0
C4D A:HEM501 3.1 27.7 1.0
CHB A:HEM501 3.3 27.1 1.0
CHD A:HEM501 3.4 23.3 1.0
CB A:CYS439 3.4 30.9 1.0
CHC A:HEM501 3.5 28.1 1.0
CHA A:HEM501 3.5 28.1 1.0
C3A A:HEM501 4.2 29.0 1.0
N2 A:0QA502 4.2 58.7 1.0
C2A A:HEM501 4.2 26.1 1.0
C2B A:HEM501 4.3 26.1 1.0
C3C A:HEM501 4.3 30.9 1.0
C3B A:HEM501 4.3 25.7 1.0
C2C A:HEM501 4.3 30.4 1.0
CA A:CYS439 4.3 29.6 1.0
C2D A:HEM501 4.3 31.0 1.0
C3D A:HEM501 4.4 26.6 1.0
C9 A:0QA502 4.6 57.6 1.0
CB A:ALA301 4.7 28.5 1.0
N A:GLY441 4.9 26.1 1.0

Iron binding site 2 out of 8 in 4ejh

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Iron binding site 2 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:26.2
occ:1.00
FE B:HEM501 0.0 26.2 1.0
NB B:HEM501 1.9 28.3 1.0
NC B:HEM501 2.0 29.1 1.0
NA B:HEM501 2.0 28.6 1.0
ND B:HEM501 2.1 25.9 1.0
SG B:CYS439 2.3 25.6 1.0
C4B B:HEM501 2.9 22.9 1.0
C1C B:HEM501 2.9 28.7 1.0
C1B B:HEM501 3.0 27.6 1.0
N3 B:0QA502 3.0 44.3 1.0
C1A B:HEM501 3.0 24.7 1.0
C4C B:HEM501 3.0 27.5 1.0
C4D B:HEM501 3.0 24.8 1.0
C4A B:HEM501 3.0 27.1 1.0
C1D B:HEM501 3.1 22.6 1.0
O2 B:0QA502 3.1 46.8 1.0
CHC B:HEM501 3.3 25.1 1.0
CHA B:HEM501 3.3 22.9 1.0
CB B:CYS439 3.4 26.7 1.0
CHB B:HEM501 3.4 29.7 1.0
CHD B:HEM501 3.4 23.6 1.0
C3B B:HEM501 4.2 24.5 1.0
C2B B:HEM501 4.2 25.5 1.0
C2C B:HEM501 4.2 29.4 1.0
C3C B:HEM501 4.2 28.0 1.0
C2A B:HEM501 4.3 25.9 1.0
C3A B:HEM501 4.3 25.1 1.0
N2 B:0QA502 4.3 45.8 1.0
C3D B:HEM501 4.3 23.8 1.0
CA B:CYS439 4.3 26.2 1.0
C2D B:HEM501 4.4 23.3 1.0
C9 B:0QA502 4.6 46.1 1.0
CB B:ALA301 4.7 31.2 1.0

Iron binding site 3 out of 8 in 4ejh

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Iron binding site 3 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:25.1
occ:1.00
FE C:HEM501 0.0 25.1 1.0
NA C:HEM501 2.0 25.1 1.0
NC C:HEM501 2.0 27.6 1.0
NB C:HEM501 2.1 24.8 1.0
C10 C:0QA502 2.1 48.0 1.0
ND C:HEM501 2.1 28.8 1.0
SG C:CYS439 2.3 26.5 1.0
C4A C:HEM501 3.0 21.4 1.0
C4C C:HEM501 3.0 24.0 1.0
C1A C:HEM501 3.0 24.4 1.0
C1C C:HEM501 3.0 25.9 1.0
C1B C:HEM501 3.1 23.0 1.0
C4B C:HEM501 3.1 23.8 1.0
C1D C:HEM501 3.1 22.9 1.0
C4D C:HEM501 3.1 23.0 1.0
CHD C:HEM501 3.4 20.2 1.0
CHB C:HEM501 3.4 22.0 1.0
CHC C:HEM501 3.4 25.5 1.0
CHA C:HEM501 3.4 23.2 1.0
O2 C:0QA502 3.5 67.1 1.0
CB C:CYS439 3.5 26.5 1.0
N2 C:0QA502 3.6 53.4 1.0
N3 C:0QA502 4.1 58.2 1.0
C3C C:HEM501 4.2 25.7 1.0
C3A C:HEM501 4.2 22.4 1.0
C2A C:HEM501 4.2 23.5 1.0
C2C C:HEM501 4.2 23.6 1.0
C2B C:HEM501 4.3 21.3 1.0
C3B C:HEM501 4.3 23.6 1.0
C2D C:HEM501 4.3 24.9 1.0
C3D C:HEM501 4.4 23.6 1.0
C9 C:0QA502 4.4 54.1 1.0
CA C:CYS439 4.4 27.1 1.0
CB C:ALA301 4.7 27.8 1.0
N C:GLY441 5.0 25.6 1.0

Iron binding site 4 out of 8 in 4ejh

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Iron binding site 4 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:27.0
occ:1.00
FE D:HEM501 0.0 27.0 1.0
NA D:HEM501 2.0 27.5 1.0
NB D:HEM501 2.0 29.0 1.0
NC D:HEM501 2.1 30.8 1.0
ND D:HEM501 2.1 25.2 1.0
C10 D:0QA502 2.2 48.0 1.0
SG D:CYS439 2.2 24.6 1.0
C1A D:HEM501 3.0 26.1 1.0
C4B D:HEM501 3.0 27.4 1.0
C4A D:HEM501 3.0 25.5 1.0
C4D D:HEM501 3.1 25.5 1.0
C1C D:HEM501 3.1 30.1 1.0
C1D D:HEM501 3.1 22.3 1.0
C4C D:HEM501 3.1 28.9 1.0
C1B D:HEM501 3.1 26.4 1.0
CB D:CYS439 3.3 26.6 1.0
CHA D:HEM501 3.3 24.9 1.0
CHC D:HEM501 3.4 27.9 1.0
CHD D:HEM501 3.4 27.7 1.0
CHB D:HEM501 3.4 23.6 1.0
O2 D:0QA502 3.6 67.1 1.0
N2 D:0QA502 3.7 53.4 1.0
N3 D:0QA502 4.2 58.2 1.0
C2A D:HEM501 4.2 24.2 1.0
C3A D:HEM501 4.2 26.2 1.0
CA D:CYS439 4.2 26.9 1.0
C3B D:HEM501 4.3 28.1 1.0
C3C D:HEM501 4.3 28.1 1.0
C2C D:HEM501 4.3 28.3 1.0
C2B D:HEM501 4.3 26.7 1.0
C2D D:HEM501 4.3 27.4 1.0
C3D D:HEM501 4.3 21.1 1.0
C9 D:0QA502 4.5 54.1 1.0
CB D:ALA301 4.7 27.9 1.0

Iron binding site 5 out of 8 in 4ejh

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Iron binding site 5 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:35.7
occ:1.00
FE E:HEM501 0.0 35.7 1.0
NC E:HEM501 2.0 36.5 1.0
NA E:HEM501 2.0 35.2 1.0
ND E:HEM501 2.0 34.6 1.0
NB E:HEM501 2.1 34.4 1.0
O2 E:0QA502 2.1 71.8 1.0
SG E:CYS439 2.3 35.4 1.0
C1C E:HEM501 3.0 36.9 1.0
C4B E:HEM501 3.0 37.1 1.0
C1A E:HEM501 3.0 36.5 1.0
C4D E:HEM501 3.0 35.5 1.0
C1D E:HEM501 3.0 34.4 1.0
C4C E:HEM501 3.1 36.0 1.0
C4A E:HEM501 3.1 34.8 1.0
C1B E:HEM501 3.1 34.6 1.0
N3 E:0QA502 3.3 72.9 1.0
CHC E:HEM501 3.3 37.9 1.0
CHA E:HEM501 3.4 35.2 1.0
CHD E:HEM501 3.4 35.0 1.0
CB E:CYS439 3.4 38.0 1.0
CHB E:HEM501 3.5 34.8 1.0
C2C E:HEM501 4.2 37.2 1.0
N2 E:0QA502 4.2 74.7 1.0
C3C E:HEM501 4.3 37.0 1.0
C2A E:HEM501 4.3 35.2 1.0
C3B E:HEM501 4.3 39.4 1.0
C2D E:HEM501 4.3 37.4 1.0
C3A E:HEM501 4.3 34.9 1.0
C3D E:HEM501 4.3 37.2 1.0
C2B E:HEM501 4.3 37.4 1.0
CA E:CYS439 4.4 38.3 1.0
CB E:ALA301 4.7 42.0 1.0
CA E:GLY441 5.0 38.0 1.0

Iron binding site 6 out of 8 in 4ejh

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Iron binding site 6 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:51.3
occ:1.00
FE F:HEM501 0.0 51.3 1.0
NC F:HEM501 2.0 53.5 1.0
NA F:HEM501 2.0 48.3 1.0
NB F:HEM501 2.1 50.0 1.0
ND F:HEM501 2.1 50.0 1.0
O2 F:0QA502 2.2 86.8 1.0
SG F:CYS439 2.3 50.2 1.0
C4C F:HEM501 3.0 54.9 1.0
C4A F:HEM501 3.0 47.4 1.0
C10 F:0QA502 3.0 85.8 1.0
C1A F:HEM501 3.0 49.0 1.0
C1C F:HEM501 3.1 52.9 1.0
C1B F:HEM501 3.1 48.8 1.0
C1D F:HEM501 3.1 51.5 1.0
C4B F:HEM501 3.1 50.8 1.0
C4D F:HEM501 3.1 49.6 1.0
N3 F:0QA502 3.3 87.2 1.0
CHD F:HEM501 3.3 52.1 1.0
CHB F:HEM501 3.4 50.0 1.0
CB F:CYS439 3.4 50.6 1.0
CHA F:HEM501 3.4 50.7 1.0
CHC F:HEM501 3.5 51.8 1.0
N2 F:0QA502 3.8 86.3 1.0
C3C F:HEM501 4.2 55.7 1.0
C3A F:HEM501 4.2 46.9 1.0
C2C F:HEM501 4.2 53.9 1.0
C2A F:HEM501 4.3 47.9 1.0
C2B F:HEM501 4.3 49.1 1.0
C3B F:HEM501 4.3 49.4 1.0
CA F:CYS439 4.3 50.8 1.0
C2D F:HEM501 4.4 50.7 1.0
C3D F:HEM501 4.4 49.0 1.0
C9 F:0QA502 4.7 85.5 1.0
CB F:ALA301 4.9 55.5 1.0
C F:CYS439 5.0 51.2 1.0

Iron binding site 7 out of 8 in 4ejh

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Iron binding site 7 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:38.6
occ:1.00
FE G:HEM501 0.0 38.6 1.0
NC G:HEM501 1.9 37.7 1.0
NA G:HEM501 2.0 37.4 1.0
ND G:HEM501 2.1 36.7 1.0
NB G:HEM501 2.2 37.6 1.0
SG G:CYS439 2.4 37.5 1.0
C1C G:HEM501 3.0 40.2 1.0
C4C G:HEM501 3.0 41.2 1.0
C4A G:HEM501 3.1 39.4 1.0
C1A G:HEM501 3.1 38.0 1.0
C1D G:HEM501 3.1 37.6 1.0
C4D G:HEM501 3.1 36.4 1.0
C4B G:HEM501 3.1 38.5 1.0
C1B G:HEM501 3.2 37.2 1.0
CB G:CYS439 3.3 40.1 1.0
CHC G:HEM501 3.4 38.4 1.0
CHD G:HEM501 3.4 40.8 1.0
CHA G:HEM501 3.5 36.0 1.0
CHB G:HEM501 3.5 40.7 1.0
C2C G:HEM501 4.1 41.7 1.0
CB G:ALA301 4.2 62.9 1.0
C3C G:HEM501 4.2 40.1 1.0
CA G:CYS439 4.2 40.7 1.0
C3A G:HEM501 4.3 39.4 1.0
C2A G:HEM501 4.3 38.7 1.0
C2D G:HEM501 4.3 39.0 1.0
C3D G:HEM501 4.4 35.7 1.0
C2B G:HEM501 4.4 40.5 1.0
C3B G:HEM501 4.4 40.5 1.0
O G:ALA301 4.5 64.1 1.0
N G:GLY441 4.9 40.2 1.0
CA G:ALA301 4.9 63.6 1.0
CA G:GLY441 5.0 40.7 1.0
C G:ALA301 5.0 63.8 1.0

Iron binding site 8 out of 8 in 4ejh

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Iron binding site 8 out of 8 in the Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Human Cytochrome P450 2A13 in Complex with 4-(Methylnitrosamino)-1-(3- Pyridyl)-1-Butanone (Nnk) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:55.0
occ:1.00
FE H:HEM501 0.0 55.0 1.0
NA H:HEM501 1.9 53.0 1.0
NB H:HEM501 2.0 51.0 1.0
NC H:HEM501 2.0 51.4 1.0
ND H:HEM501 2.1 52.8 1.0
SG H:CYS439 2.7 59.3 1.0
C1A H:HEM501 3.0 54.3 1.0
C4A H:HEM501 3.0 52.4 1.0
C1B H:HEM501 3.0 51.1 1.0
C4C H:HEM501 3.0 52.2 1.0
C4B H:HEM501 3.0 51.9 1.0
C1C H:HEM501 3.1 52.0 1.0
C4D H:HEM501 3.1 53.6 1.0
C1D H:HEM501 3.1 51.5 1.0
CHB H:HEM501 3.4 51.7 1.0
CHA H:HEM501 3.4 53.5 1.0
CHC H:HEM501 3.4 51.7 1.0
CHD H:HEM501 3.4 51.7 1.0
CB H:CYS439 3.7 61.6 1.0
C2A H:HEM501 4.2 54.0 1.0
C3A H:HEM501 4.2 51.0 1.0
C3C H:HEM501 4.2 50.7 1.0
CB H:ALA301 4.2 60.1 1.0
C2B H:HEM501 4.2 51.7 1.0
C3B H:HEM501 4.3 52.3 1.0
C2C H:HEM501 4.3 50.4 1.0
O H:ALA301 4.3 61.6 1.0
C3D H:HEM501 4.3 53.9 1.0
C2D H:HEM501 4.3 52.9 1.0
CA H:CYS439 4.5 61.7 1.0
C H:ALA301 4.8 61.7 1.0
CA H:ALA301 4.9 60.9 1.0

Reference:

N.M.Devore, E.E.Scott. Nicotine and 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanone Binding and Access Channel in Human Cytochrome P450 2A6 and 2A13 Enzymes. J.Biol.Chem. V. 287 26576 2012.
ISSN: ISSN 0021-9258
PubMed: 22700965
DOI: 10.1074/JBC.M112.372813
Page generated: Mon Aug 5 01:39:45 2024

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