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Calcium in PDB 3a51: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3

Protein crystallography data

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3, PDB code: 3a51 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) 45.60 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.173, 171.800, 189.143, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.4

Other elements in 3a51:

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 (pdb code 3a51). 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 25-Hydroxyvitamin D3, PDB code: 3a51:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 1 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2501

b:29.6
occ:1.00
 O2 A:GOL3002 2.4 30.7 1.0
O3 A:GOL3002 2.5 31.4 1.0
OD1 A:ASP204 2.5 26.6 1.0
O A:HOH926 2.5 30.5 1.0
O A:HOH579 2.6 27.9 1.0
O A:HOH528 2.6 30.0 1.0
C2 A:GOL3002 3.3 32.3 1.0
C3 A:GOL3002 3.3 30.7 1.0
CG A:ASP204 3.7 27.8 1.0
C1 A:GOL3002 3.8 34.7 1.0
O A:ASP203 4.2 26.1 1.0
O A:HOH506 4.4 24.8 1.0
OD2 A:ASP204 4.4 27.9 1.0
O A:HOH556 4.6 29.9 1.0
CA A:ASP204 4.6 25.6 1.0
C A:ASP203 4.7 26.4 1.0
CB A:ASP204 4.7 25.9 1.0
O A:HOH581 4.7 27.2 1.0
N A:ASP204 4.9 25.9 1.0

Calcium binding site 2 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 2 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2505

b:30.2
occ:1.00
 O A:GLY128 2.3 25.3 1.0
O A:HOH593 2.4 28.4 1.0
O A:HOH929 2.5 38.2 1.0
O A:HOH905 2.6 34.4 1.0
C A:GLY128 3.4 25.0 1.0
O A:HOH1294 3.9 31.7 1.0
CA A:GLY128 4.1 24.5 1.0
O A:HOH1190 4.4 44.6 1.0
N A:LEU129 4.5 25.8 1.0
CA A:LEU129 4.7 25.5 1.0
O A:HOH1147 4.7 34.9 1.0
O A:HOH529 4.7 30.2 1.0
CD A:PRO130 4.8 26.0 1.0
O A:HOH480 4.8 22.1 1.0

Calcium binding site 3 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 3 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2506

b:45.3
occ:1.00
 O D:HOH933 2.3 41.8 1.0
O A:ASP320 2.6 24.0 1.0
O D:ASP320 3.0 37.8 1.0
C A:ASP320 3.7 24.1 1.0
C D:ASP320 3.9 36.1 1.0
CA D:ASP320 4.1 35.7 1.0
O A:HOH664 4.2 29.0 1.0
O A:HOH1004 4.2 43.2 1.0
CB D:ASP320 4.2 36.2 1.0
CA A:ASP320 4.3 24.3 1.0
CB A:ASP320 4.5 25.0 1.0
OD2 D:ASP320 4.7 43.5 1.0
CG D:ASP320 4.7 38.0 1.0
O D:HOH834 4.7 31.0 1.0
N A:TRP321 4.8 23.3 1.0

Calcium binding site 4 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 4 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2503

b:32.5
occ:1.00
 OD1 C:ASP204 2.4 32.6 1.0
O C:HOH482 2.5 31.5 1.0
O C:ACT4004 2.5 40.1 1.0
O C:HOH703 2.6 32.0 1.0
OXT C:ACT4004 2.7 40.3 1.0
C C:ACT4004 3.0 41.2 1.0
CG C:ASP204 3.6 30.8 1.0
OD2 C:ASP204 4.2 35.8 1.0
CH3 C:ACT4004 4.3 41.2 1.0
O C:ASP203 4.4 27.2 1.0
O C:HOH725 4.4 32.0 1.0
CB C:ASP204 4.7 28.6 1.0
O C:HOH1009 4.8 40.2 1.0
CA C:ASP204 4.8 28.0 1.0
C C:ASP203 4.8 27.4 1.0

Calcium binding site 5 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 5 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2502

b:35.7
occ:1.00
 OD1 D:ASP204 2.3 36.0 1.0
O D:HOH601 2.5 30.8 1.0
CG D:ASP204 3.6 37.0 1.0
O D:ASP203 4.3 36.0 1.0
OD2 D:ASP204 4.3 40.3 1.0
CA D:ASP204 4.5 34.4 1.0
CB D:ASP204 4.5 35.3 1.0
C D:ASP203 4.8 36.8 1.0
N D:ASP204 5.0 35.2 1.0

Calcium binding site 6 out of 6 in 3a51

Go back to Calcium Binding Sites List in 3a51
Calcium binding site 6 out of 6 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin 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 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2504

b:35.6
occ:1.00
 O E:HOH576 2.4 24.1 1.0
O E:HOH565 2.4 23.2 1.0
O E:HOH652 2.5 30.6 1.0
OD1 E:ASP204 2.8 36.0 1.0
O E:ACT4005 2.9 41.6 1.0
OXT E:ACT4005 2.9 41.3 1.0
C E:ACT4005 3.2 42.3 1.0
CG E:ASP204 4.0 33.1 1.0
O E:ASP203 4.3 30.1 1.0
CH3 E:ACT4005 4.5 41.9 1.0
OD2 E:ASP204 4.5 37.8 1.0
O E:HOH448 4.6 29.5 1.0
C E:ASP203 4.7 30.2 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: Sat Jul 13 07:11:30 2024

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