Calcium in PDB 3odt: Crystal Structure of WD40 Beta Propeller Domain of DOA1

The structure of Crystal Structure of WD40 Beta Propeller Domain of DOA1, PDB code: 3odt was solved by N.Pashkova, L.Gakhar, S.C.Winistorfer, L.Yu, S.Ramaswamy, R.C.Piper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.85 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.656, 87.996, 92.265, 90.00, 96.73, 90.00
R / Rfree (%)	13.6 / 17.6

The binding sites of Calcium atom in the Crystal Structure of WD40 Beta Propeller Domain of DOA1 (pdb code 3odt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of WD40 Beta Propeller Domain of DOA1, PDB code: 3odt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of WD40 Beta Propeller Domain of DOA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of WD40 Beta Propeller Domain of DOA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca309 b:7.8 occ:1.00 OD2 B:ASP24 2.3 10.5 1.0 O A:HOH869 2.4 10.6 1.0 O A:HOH349 2.4 9.0 1.0 CG B:ASP24 3.5 10.6 1.0 OG B:SER271 3.8 10.5 1.0 OD1 B:ASP24 4.2 10.9 1.0 CB B:ASP24 4.4 10.2 1.0 O2S A:MES311 4.5 19.9 1.0 O A:HOH438 4.6 19.3 1.0 O A:HOH494 4.6 12.2 1.0 CB B:ASN272 4.7 9.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of WD40 Beta Propeller Domain of DOA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of WD40 Beta Propeller Domain of DOA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca310 b:12.1 occ:1.00 O B:SER280 2.3 9.8 1.0 O A:HOH620 2.3 22.0 1.0 O A:HOH557 2.4 25.8 1.0 OD1 B:ASP15 2.4 12.7 1.0 O A:HOH949 2.4 27.0 1.0 O A:HOH837 2.4 21.5 1.0 OD1 B:ASN282 2.5 8.4 1.0 CG B:ASN282 3.5 11.3 1.0 C B:SER280 3.5 8.8 1.0 CG B:ASP15 3.6 9.3 1.0 ND2 B:ASN282 3.9 15.2 1.0 N B:ASP15 3.9 8.6 1.0 CA B:ASP15 4.3 7.4 1.0 O A:HOH466 4.3 15.9 1.0 CA B:SER280 4.3 8.8 1.0 OD2 B:ASP15 4.4 9.7 1.0 O A:HOH478 4.4 20.4 1.0 C B:GLN14 4.4 7.8 1.0 N B:ASP281 4.5 7.1 1.0 N B:ASN282 4.5 7.3 1.0 CA B:ASP281 4.5 8.8 1.0 CB B:ASP15 4.5 8.7 1.0 OE1 B:GLN14 4.6 13.9 1.0 CA B:GLN14 4.6 7.0 1.0 C B:ASP281 4.6 8.3 1.0 O A:HOH378 4.7 25.6 1.0 CB B:SER280 4.7 9.5 1.0 CB B:ASN282 4.8 10.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of WD40 Beta Propeller Domain of DOA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of WD40 Beta Propeller Domain of DOA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca309 b:6.4 occ:1.00 OD2 A:ASP24 2.3 9.1 1.0 O B:HOH318 2.3 10.6 1.0 O B:HOH342 2.4 8.8 1.0 CG A:ASP24 3.5 8.1 1.0 OG A:SER271 3.9 9.0 1.0 OD1 A:ASP24 4.2 10.0 1.0 CB A:ASP24 4.5 8.8 1.0 O B:HOH378 4.6 18.9 1.0 CB A:ASN272 4.7 11.2 1.0 O B:HOH317 4.8 11.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of WD40 Beta Propeller Domain of DOA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of WD40 Beta Propeller Domain of DOA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca310 b:12.0 occ:1.00 O A:SER280 2.3 10.1 1.0 OD1 A:ASP15 2.4 15.4 1.0 O B:HOH341 2.4 20.3 1.0 O B:HOH389 2.4 20.3 1.0 O B:HOH684 2.4 31.4 1.0 OD1 A:ASN282 2.5 10.3 1.0 O B:HOH951 2.5 30.4 1.0 O B:HOH669 2.6 29.1 1.0 CG A:ASN282 3.5 8.9 1.0 C A:SER280 3.5 8.7 1.0 CG A:ASP15 3.6 10.1 1.0 ND2 A:ASN282 3.8 14.6 1.0 N A:ASP15 3.9 7.7 1.0 CA A:ASP15 4.2 7.5 1.0 O B:HOH415 4.3 17.9 1.0 OD2 A:ASP15 4.3 8.9 1.0 CA A:SER280 4.3 6.7 1.0 O B:HOH560 4.3 20.0 1.0 C A:GLN14 4.4 7.5 1.0 OE1 A:GLN14 4.5 15.9 1.0 O B:HOH950 4.5 26.8 1.0 N A:ASP281 4.5 8.3 1.0 CB A:ASP15 4.5 7.5 1.0 N A:ASN282 4.5 8.6 1.0 CA A:ASP281 4.6 11.3 1.0 CA A:GLN14 4.6 7.4 1.0 CB A:SER280 4.6 8.4 1.0 C A:ASP281 4.7 11.3 1.0 CB A:ASN282 4.9 9.3 1.0 O B:HOH641 4.9 29.9 1.0

N.Pashkova, L.Gakhar, S.C.Winistorfer, L.Yu, S.Ramaswamy, R.C.Piper. WD40 Repeat Propellers Define A Ubiquitin-Binding Domain That Regulates Turnover of F Box Proteins. Mol.Cell V. 40 433 2010.
ISSN: ISSN 1097-2765
PubMed: 21070969
DOI: 10.1016/J.MOLCEL.2010.10.018