Calcium in PDB 6dyo: C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine

The structure of C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine, PDB code: 6dyo was solved by T.Izore, J.Tailhades, M.H.Hansen, J.A.Kaczmarski, C.J.Jackson, M.J.Cryle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.07 / 2.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.967, 57.195, 50.427, 90.00, 114.00, 90.00
R / Rfree (%)	20 / 25.9

The binding sites of Calcium atom in the C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine (pdb code 6dyo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine, PDB code: 6dyo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:50.0 occ:1.00 N A:GLN782 2.7 29.3 1.0 OD1 A:ASP744 2.7 33.2 1.0 N A:ILE783 2.9 26.9 1.0 O A:GLY779 3.1 38.4 1.0 N A:ASN781 3.2 33.8 1.0 CA A:GLN782 3.4 33.1 1.0 C A:LEU780 3.5 35.2 1.0 CB A:GLN782 3.5 35.7 1.0 CA A:LEU780 3.6 38.0 1.0 C A:GLN782 3.6 32.5 1.0 CG A:ARG746 3.7 34.8 1.0 CG A:ASP744 3.7 34.6 1.0 C A:ASN781 3.7 32.5 1.0 O A:ILE783 3.9 28.6 1.0 CA A:ASN781 3.9 34.1 1.0 CA A:ILE783 3.9 30.2 1.0 OD2 A:ASP744 3.9 33.9 1.0 CB A:ARG746 3.9 37.5 1.0 C A:GLY779 4.1 41.0 1.0 CB A:ILE783 4.1 32.2 1.0 N A:ARG746 4.2 30.4 1.0 CG1 A:ILE783 4.2 31.6 1.0 C A:ILE783 4.2 30.9 1.0 O A:LEU780 4.3 35.7 1.0 CG A:GLN782 4.3 35.7 1.0 CD A:ARG746 4.3 32.3 1.0 N A:LEU780 4.3 41.2 1.0 CE2 A:PHE820 4.6 31.2 1.0 N A:ALA745 4.7 29.2 1.0 CA A:ARG746 4.7 34.4 1.0 CB A:LEU780 4.7 38.1 1.0 O A:GLN782 4.8 31.3 1.0 NE A:ARG746 4.8 37.4 1.0 O A:ASN781 4.9 37.4 1.0 CD1 A:ILE783 4.9 29.9 1.0 CD2 A:PHE820 5.0 30.5 1.0

Calcium binding site 2 out of 2 in the C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Terminal Condensation Domain of Ebony in Complex with L-Dopamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:51.2 occ:1.00 O A:MET788 2.7 32.2 1.0 OD1 A:ASN742 2.8 28.1 1.0 OG A:SER786 2.8 40.3 1.0 O A:LEU741 3.1 30.1 1.0 CG A:MET789 3.5 40.3 1.0 C A:MET788 3.5 32.4 1.0 N A:LEU741 3.7 28.5 1.0 CB A:ALA740 3.8 26.8 1.0 CG A:ASN742 3.8 25.0 1.0 CB A:SER786 3.8 32.2 1.0 N A:MET788 3.9 35.1 1.0 CA A:ALA740 3.9 31.0 1.0 C A:LEU741 3.9 28.3 1.0 CA A:SER786 3.9 32.9 1.0 N A:PHE787 3.9 33.4 1.0 C A:ALA740 3.9 29.6 1.0 C A:SER786 4.0 34.3 1.0 CE A:MET789 4.2 43.3 1.0 N A:MET789 4.3 41.0 1.0 CB A:MET789 4.3 37.3 1.0 CA A:MET788 4.3 30.9 1.0 ND2 A:ASN742 4.4 25.7 1.0 CA A:LEU741 4.4 28.2 1.0 CA A:MET789 4.5 35.1 1.0 C A:PHE787 4.6 36.3 1.0 O A:ALA740 4.7 31.0 1.0 SD A:MET789 4.7 48.1 1.0 N A:ASN742 4.7 27.0 1.0 CA A:PHE787 4.8 34.1 1.0 O A:SER786 4.8 34.6 1.0 CG2 A:VAL811 4.8 38.8 1.0 CB A:ASN742 5.0 27.3 1.0 CA A:ASN742 5.0 29.9 1.0

T.Izore, J.Tailhades, M.H.Hansen, J.A.Kaczmarski, C.J.Jackson, M.J.Cryle. Drosophila Melanogasternonribosomal Peptide Synthetase Ebony Encodes An Atypical Condensation Domain. Proc. Natl. Acad. Sci. V. 116 2913 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30705105
DOI: 10.1073/PNAS.1811194116