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

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

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

Iron

(Fe)

5 atoms

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution, PDB code: 3a4z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca2501 b:39.2 occ:1.00 O1 A:GOL3002 2.4 36.9 1.0 O A:HOH601 2.5 25.2 1.0 O A:HOH768 2.5 32.4 1.0 OD1 A:ASP204 2.6 31.7 1.0 O A:HOH580 2.6 33.2 1.0 O A:HOH582 2.7 34.2 1.0 O2 A:GOL3002 2.9 39.8 1.0 C2 A:GOL3002 3.2 39.5 1.0 C1 A:GOL3002 3.3 36.2 1.0 CG A:ASP204 3.8 33.3 1.0 O A:ASP203 4.2 31.8 1.0 O A:HOH552 4.4 29.6 1.0 OD2 A:ASP204 4.5 34.8 1.0 O A:HOH769 4.5 31.6 1.0 C3 A:GOL3002 4.6 39.0 1.0 C A:ASP203 4.7 32.6 1.0 CA A:ASP204 4.7 31.8 1.0 O A:HOH526 4.7 31.6 1.0 CB A:ASP204 4.8 31.9 1.0 O A:HOH789 4.9 46.4 1.0 O3 A:GOL3002 4.9 45.2 1.0 O A:HOH635 5.0 30.0 1.0 N A:ASP204 5.0 32.3 1.0

Calcium binding site 2 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca2505 b:37.0 occ:1.00 O A:HOH690 2.3 29.1 1.0 O A:GLY128 2.3 30.3 1.0 O A:HOH796 2.3 46.5 1.0 O A:HOH795 2.4 31.6 1.0 O A:HOH610 2.5 35.3 1.0 C A:GLY128 3.5 31.0 1.0 CA A:GLY128 4.3 30.4 1.0 N A:LEU129 4.6 31.6 1.0 O A:HOH436 4.7 34.1 1.0 CA A:LEU129 4.7 32.2 1.0 CD A:PRO130 4.8 33.3 1.0

Calcium binding site 3 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca2506 b:50.1 occ:1.00 O A:ASP320 2.6 27.3 1.0 O D:ASP320 2.8 38.5 1.0 C A:ASP320 3.7 27.5 1.0 C D:ASP320 3.7 37.8 1.0 CA D:ASP320 4.0 37.6 1.0 CB D:ASP320 4.1 38.0 1.0 CA A:ASP320 4.3 28.1 1.0 OD2 D:ASP320 4.4 43.0 1.0 O A:HOH706 4.4 31.5 1.0 CB A:ASP320 4.5 29.5 1.0 CG D:ASP320 4.6 40.3 1.0 N A:TRP321 4.7 26.6 1.0 N D:TRP321 5.0 37.6 1.0 CA A:TRP321 5.0 26.5 1.0

Calcium binding site 4 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 C:Ca2503 b:43.0 occ:1.00 O C:HOH428 2.4 30.0 1.0 O C:HOH466 2.6 40.4 1.0 OD1 C:ASP204 2.6 41.2 1.0 O C:HOH436 2.6 36.3 1.0 O C:HOH429 2.7 18.5 1.0 O C:ACT4004 2.8 50.4 1.0 OXT C:ACT4004 3.0 50.0 1.0 C C:ACT4004 3.2 50.7 1.0 CG C:ASP204 3.8 38.6 1.0 CH3 C:ACT4004 4.4 50.4 1.0 O C:ASP203 4.4 34.2 1.0 OD2 C:ASP204 4.4 40.3 1.0 O C:HOH477 4.5 31.7 1.0 O C:HOH762 4.7 44.6 1.0 O C:HOH761 4.8 32.3 1.0 CA C:ASP204 4.9 35.1 1.0 C C:ASP203 4.9 34.5 1.0 CB C:ASP204 4.9 35.7 1.0

Calcium binding site 5 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 D:Ca2502 b:44.1 occ:1.00 OD1 D:ASP204 2.3 41.3 1.0 CG D:ASP204 3.5 42.4 1.0 OD2 D:ASP204 4.3 45.0 1.0 O D:ASP203 4.3 41.9 1.0 CB D:ASP204 4.5 41.3 1.0 CA D:ASP204 4.6 40.2 1.0 C D:ASP203 4.9 42.3 1.0

Calcium binding site 6 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca2504 b:43.4 occ:1.00 O E:HOH458 2.4 23.0 1.0 O E:HOH792 2.6 50.8 1.0 OD1 E:ASP204 2.8 37.4 1.0 O E:ACT4005 3.0 47.9 1.0 OXT E:ACT4005 3.2 48.1 1.0 C E:ACT4005 3.4 48.6 1.0 CG E:ASP204 4.0 37.9 1.0 O E:ASP203 4.2 34.0 1.0 CH3 E:ACT4005 4.6 48.4 1.0 C E:ASP203 4.6 34.1 1.0 O E:HOH747 4.7 30.4 1.0 OD2 E:ASP204 4.8 43.8 1.0 O E:HOH749 4.8 29.9 1.0 CA E:ASP204 4.9 32.5 1.0 N E:ASP204 5.0 33.1 1.0

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