Atomistry » Iron » PDB 3a0g-3ae5 » 3a4z
Atomistry »
  Iron »
    PDB 3a0g-3ae5 »
      3a4z »

Iron in PDB 3a4z: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution

Protein crystallography data

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution, PDB code: 3a4z was solved by Y.Yasutake, Y.Fujii, W.K.Cheon, A.Arisawa, T.Tamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.378, 172.467, 189.873, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.4

Other elements in 3a4z:

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution (pdb code 3a4z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution, PDB code: 3a4z:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 1 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe412

b:18.3
occ:1.00
 FE A:HEM412 0.0 18.3 1.0
NC A:HEM412 2.1 20.0 1.0
NB A:HEM412 2.1 19.9 1.0
NA A:HEM412 2.1 19.1 1.0
ND A:HEM412 2.1 20.0 1.0
SG A:CYS347 2.2 18.1 1.0
C4C A:HEM412 3.1 20.6 1.0
C1C A:HEM412 3.1 18.6 1.0
C4B A:HEM412 3.1 20.0 1.0
C1D A:HEM412 3.1 20.2 1.0
C1A A:HEM412 3.2 19.2 1.0
C4A A:HEM412 3.2 20.4 1.0
C4D A:HEM412 3.2 20.5 1.0
C1B A:HEM412 3.2 18.5 1.0
CB A:CYS347 3.4 16.6 1.0
CHD A:HEM412 3.4 19.2 1.0
CHC A:HEM412 3.4 18.0 1.0
CHA A:HEM412 3.5 18.9 1.0
CHB A:HEM412 3.5 17.6 1.0
CA A:CYS347 3.9 17.6 1.0
C3C A:HEM412 4.3 19.7 1.0
C2C A:HEM412 4.3 19.8 1.0
C3B A:HEM412 4.3 18.1 1.0
C2A A:HEM412 4.4 19.9 1.0
C2D A:HEM412 4.4 21.4 1.0
C3A A:HEM412 4.4 20.0 1.0
C3D A:HEM412 4.4 17.7 1.0
C2B A:HEM412 4.4 19.1 1.0
N A:LEU348 4.5 17.1 1.0
N A:GLY349 4.5 16.7 1.0
C A:CYS347 4.6 17.4 1.0

Iron binding site 2 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 2 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe412

b:31.6
occ:1.00
 FE B:HEM412 0.0 31.6 1.0
NC B:HEM412 2.1 33.8 1.0
NA B:HEM412 2.1 32.5 1.0
NB B:HEM412 2.1 32.2 1.0
ND B:HEM412 2.1 33.6 1.0
SG B:CYS347 2.2 30.3 1.0
C1A B:HEM412 3.1 32.8 1.0
C1C B:HEM412 3.1 33.6 1.0
C4C B:HEM412 3.1 33.7 1.0
C4B B:HEM412 3.1 33.3 1.0
C4D B:HEM412 3.1 33.6 1.0
C4A B:HEM412 3.1 31.4 1.0
C1D B:HEM412 3.1 35.5 1.0
C1B B:HEM412 3.2 32.2 1.0
CB B:CYS347 3.3 32.8 1.0
CHA B:HEM412 3.4 32.2 1.0
CHC B:HEM412 3.4 32.6 1.0
CHD B:HEM412 3.5 33.5 1.0
CHB B:HEM412 3.5 30.9 1.0
CA B:CYS347 3.9 32.9 1.0
C3C B:HEM412 4.3 34.5 1.0
C2A B:HEM412 4.3 31.5 1.0
C2C B:HEM412 4.3 34.5 1.0
C3A B:HEM412 4.3 31.5 1.0
C3B B:HEM412 4.3 31.6 1.0
C2B B:HEM412 4.4 30.8 1.0
C3D B:HEM412 4.4 33.9 1.0
C2D B:HEM412 4.4 34.5 1.0
C B:CYS347 4.6 33.2 1.0
N B:LEU348 4.6 34.0 1.0
N B:GLY349 4.6 35.2 1.0

Iron binding site 3 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 3 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe412

b:22.4
occ:1.00
 FE C:HEM412 0.0 22.4 1.0
NC C:HEM412 2.1 22.4 1.0
NA C:HEM412 2.1 21.6 1.0
NB C:HEM412 2.1 23.3 1.0
ND C:HEM412 2.1 21.7 1.0
SG C:CYS347 2.4 24.0 1.0
C1C C:HEM412 3.1 21.2 1.0
C4B C:HEM412 3.1 24.1 1.0
C1A C:HEM412 3.1 22.5 1.0
C4C C:HEM412 3.1 22.9 1.0
C1D C:HEM412 3.1 21.6 1.0
C4D C:HEM412 3.1 21.1 1.0
C4A C:HEM412 3.1 22.5 1.0
C1B C:HEM412 3.2 22.9 1.0
CB C:CYS347 3.4 22.1 1.0
CHC C:HEM412 3.4 22.6 1.0
CHA C:HEM412 3.5 19.9 1.0
CHD C:HEM412 3.5 20.4 1.0
CHB C:HEM412 3.6 22.2 1.0
CA C:CYS347 3.9 22.8 1.0
C2A C:HEM412 4.3 20.5 1.0
C2C C:HEM412 4.3 20.7 1.0
C3A C:HEM412 4.3 21.6 1.0
C3B C:HEM412 4.3 24.6 1.0
C3C C:HEM412 4.3 22.6 1.0
C2D C:HEM412 4.3 19.3 1.0
C3D C:HEM412 4.4 18.4 1.0
C2B C:HEM412 4.4 23.7 1.0
N C:GLY349 4.5 26.2 1.0
N C:LEU348 4.5 24.6 1.0
C C:CYS347 4.6 23.4 1.0
CA C:GLY349 5.0 27.3 1.0

Iron binding site 4 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 4 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe412

b:22.0
occ:1.00
 FE D:HEM412 0.0 22.0 1.0
NA D:HEM412 2.1 23.1 1.0
ND D:HEM412 2.1 23.1 1.0
NB D:HEM412 2.1 22.9 1.0
NC D:HEM412 2.1 24.7 1.0
SG D:CYS347 2.4 22.1 1.0
C4D D:HEM412 3.1 23.6 1.0
C1A D:HEM412 3.1 21.2 1.0
C4B D:HEM412 3.1 21.1 1.0
C1C D:HEM412 3.1 23.1 1.0
C1D D:HEM412 3.1 23.4 1.0
C1B D:HEM412 3.1 22.2 1.0
C4A D:HEM412 3.1 23.0 1.0
C4C D:HEM412 3.2 22.7 1.0
CHA D:HEM412 3.4 20.7 1.0
CB D:CYS347 3.4 20.1 1.0
CHC D:HEM412 3.4 21.2 1.0
CHD D:HEM412 3.5 23.1 1.0
CHB D:HEM412 3.5 22.6 1.0
CA D:CYS347 3.9 20.9 1.0
C2A D:HEM412 4.3 21.1 1.0
C3B D:HEM412 4.3 21.2 1.0
C3D D:HEM412 4.3 21.8 1.0
C2B D:HEM412 4.3 21.6 1.0
C2C D:HEM412 4.3 22.8 1.0
C3A D:HEM412 4.3 23.0 1.0
C2D D:HEM412 4.4 22.8 1.0
C3C D:HEM412 4.4 22.7 1.0
N D:LEU348 4.5 21.4 1.0
C D:CYS347 4.5 21.2 1.0
N D:GLY349 4.6 21.3 1.0

Iron binding site 5 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 5 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe412

b:24.3
occ:1.00
 FE E:HEM412 0.0 24.3 1.0
NC E:HEM412 2.0 22.5 1.0
NB E:HEM412 2.1 22.7 1.0
ND E:HEM412 2.1 23.4 1.0
NA E:HEM412 2.2 23.6 1.0
SG E:CYS347 2.4 23.1 1.0
C4C E:HEM412 3.0 23.1 1.0
C1C E:HEM412 3.1 22.4 1.0
C1D E:HEM412 3.1 22.1 1.0
C4B E:HEM412 3.1 22.9 1.0
C1B E:HEM412 3.2 24.4 1.0
C4A E:HEM412 3.2 23.3 1.0
C1A E:HEM412 3.2 23.7 1.0
C4D E:HEM412 3.2 22.7 1.0
CHD E:HEM412 3.4 22.4 1.0
CB E:CYS347 3.4 22.5 1.0
CHC E:HEM412 3.4 22.9 1.0
CHA E:HEM412 3.5 21.7 1.0
CHB E:HEM412 3.5 23.6 1.0
CA E:CYS347 4.0 23.2 1.0
C3C E:HEM412 4.2 22.5 1.0
C2C E:HEM412 4.3 22.4 1.0
C2D E:HEM412 4.3 22.7 1.0
C3B E:HEM412 4.4 24.8 1.0
C2B E:HEM412 4.4 23.8 1.0
C3D E:HEM412 4.4 21.3 1.0
C3A E:HEM412 4.4 23.8 1.0
C2A E:HEM412 4.4 22.7 1.0
N E:GLY349 4.5 22.6 1.0
N E:LEU348 4.5 23.0 1.0
C E:CYS347 4.6 23.2 1.0

Reference:

Y.Yasutake, Y.Fujii, T.Nishioka, W.K.Cheon, A.Arisawa, T.Tamura. Structural Evidence For Enhancement of Sequential Vitamin D3 Hydroxylation Activities By Directed Evolution of Cytochrome P450 Vitamin D3 Hydroxylase J.Biol.Chem. V. 285 31193 2010.
ISSN: ISSN 0021-9258
PubMed: 20667833
DOI: 10.1074/JBC.M110.147009
Page generated: Sun Aug 4 06:40:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy