Atomistry » Calcium » PDB 3a4u-3aas » 3a51
Atomistry »
  Calcium »
    PDB 3a4u-3aas »
      3a51 »

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 Dec 12 04:02:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy