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Calcium in PDB 3a50: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3

Protein crystallography data

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3, PDB code: 3a50 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) 49.09 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.384, 172.266, 189.063, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24

Other elements in 3a50:

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3 also contains other interesting chemical elements:

Iron (Fe) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3 (pdb code 3a50). 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 with Bound Vitamin D3, PDB code: 3a50:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 1 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2501

b:29.3
occ:1.00
 O A:HOH601 2.4 19.0 1.0
O1 A:GOL3002 2.5 29.2 1.0
OD1 A:ASP204 2.5 23.7 1.0
O A:HOH572 2.6 28.0 1.0
O A:HOH596 2.6 26.5 1.0
O2 A:GOL3002 2.9 33.4 1.0
C2 A:GOL3002 3.2 32.9 1.0
C1 A:GOL3002 3.3 29.8 1.0
CG A:ASP204 3.7 25.3 1.0
O A:ASP203 4.1 24.0 1.0
O A:HOH662 4.4 23.8 1.0
O A:HOH988 4.4 33.4 1.0
OD2 A:ASP204 4.4 25.8 1.0
O A:HOH882 4.5 23.1 1.0
O A:HOH989 4.5 37.2 1.0
C3 A:GOL3002 4.6 33.1 1.0
C A:ASP203 4.6 24.7 1.0
CA A:ASP204 4.7 24.2 1.0
O A:HOH496 4.8 24.2 1.0
CB A:ASP204 4.8 24.4 1.0
O A:HOH674 4.9 23.5 1.0
N A:ASP204 4.9 24.3 1.0

Calcium binding site 2 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 2 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2505

b:27.3
occ:1.00
 O A:HOH1027 2.3 36.9 1.0
O A:GLY128 2.3 22.9 1.0
O A:HOH818 2.4 29.9 1.0
O A:HOH993 2.4 32.3 1.0
C A:GLY128 3.5 22.9 1.0
CA A:GLY128 4.2 23.0 1.0
N A:LEU129 4.5 23.7 1.0
O A:HOH563 4.6 31.9 1.0
CA A:LEU129 4.6 24.3 1.0
O A:HOH826 4.7 28.5 1.0
CD A:PRO130 4.7 26.1 1.0
O A:HOH519 4.9 22.9 1.0
N A:PRO130 5.0 26.7 1.0
C A:LEU129 5.0 25.1 1.0

Calcium binding site 3 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 3 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2506

b:41.4
occ:1.00
 O D:HOH892 2.4 40.7 1.0
O A:ASP320 2.5 22.8 1.0
O D:ASP320 2.8 34.8 1.0
C A:ASP320 3.7 22.7 1.0
C D:ASP320 3.8 33.6 1.0
CA D:ASP320 4.0 33.4 1.0
CB D:ASP320 4.1 33.6 1.0
CA A:ASP320 4.3 22.8 1.0
O A:HOH722 4.3 32.2 1.0
CB A:ASP320 4.5 23.5 1.0
CG D:ASP320 4.7 35.9 1.0
OD2 D:ASP320 4.7 39.6 1.0
N A:TRP321 4.7 21.9 1.0
CA A:TRP321 5.0 21.6 1.0

Calcium binding site 4 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 4 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2503

b:33.5
occ:1.00
 OD1 C:ASP204 2.5 32.0 1.0
O C:HOH470 2.5 32.5 1.0
O C:HOH437 2.6 27.3 1.0
O C:ACT4004 2.8 43.6 1.0
OXT C:ACT4004 2.9 43.5 1.0
C C:ACT4004 3.1 43.9 1.0
CG C:ASP204 3.7 30.0 1.0
OD2 C:ASP204 4.3 33.2 1.0
O C:ASP203 4.4 26.2 1.0
CH3 C:ACT4004 4.4 43.7 1.0
O C:HOH648 4.4 32.6 1.0
O C:HOH885 4.8 51.5 1.0
CB C:ASP204 4.8 27.3 1.0
CA C:ASP204 4.9 26.6 1.0
C C:ASP203 4.9 26.2 1.0

Calcium binding site 5 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 5 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2502

b:35.6
occ:1.00
 OD1 D:ASP204 2.3 34.1 1.0
O D:HOH884 2.4 30.5 1.0
O D:HOH883 2.5 28.7 1.0
CG D:ASP204 3.6 34.0 1.0
O D:ASP203 4.3 33.8 1.0
OD2 D:ASP204 4.4 37.1 1.0
CA D:ASP204 4.5 32.2 1.0
CB D:ASP204 4.5 33.0 1.0
C D:ASP203 4.8 34.3 1.0
N D:ASP204 4.9 33.1 1.0

Calcium binding site 6 out of 6 in 3a50

Go back to Calcium Binding Sites List in 3a50
Calcium binding site 6 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3


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 with Bound Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2504

b:35.8
occ:1.00
 O E:HOH887 2.3 21.8 1.0
O E:HOH886 2.3 38.6 1.0
OD1 E:ASP204 2.7 34.0 1.0
O E:ACT4005 3.0 42.1 1.0
OXT E:ACT4005 3.1 42.3 1.0
C E:ACT4005 3.3 42.7 1.0
CG E:ASP204 3.9 31.7 1.0
O E:ASP203 4.3 29.9 1.0
OD2 E:ASP204 4.4 36.3 1.0
CH3 E:ACT4005 4.5 42.4 1.0
O E:HOH888 4.6 24.6 1.0
O E:HOH890 4.6 26.4 1.0
C E:ASP203 4.7 29.7 1.0
O E:HOH889 5.0 21.7 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: Tue Jul 8 10:23:37 2025

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