Calcium in PDB 5why: Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides

The structure of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides, PDB code: 5why was solved by T.L.Grove, P.Himes, A.Bowers, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.68 / 2.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.929, 59.357, 81.363, 83.09, 73.31, 66.63
R / Rfree (%)	22.5 / 28.1

The structure of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides also contains other interesting chemical elements:

Iron

(Fe)

24 atoms

The binding sites of Calcium atom in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides (pdb code 5why). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides, PDB code: 5why:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:90.1 occ:1.00 ND2 A:ASN180 2.7 76.7 1.0 OE1 A:GLU174 3.2 77.9 1.0 OE2 A:GLU174 3.2 76.8 1.0 CD A:GLU174 3.6 77.5 1.0 O A:PHE181 3.9 71.7 1.0 CG A:ASN180 4.0 77.2 1.0 NE A:ARG171 4.3 74.4 1.0 N A:PHE181 4.4 73.0 1.0 OE1 B:GLU66 4.5 91.7 1.0 CD A:ARG171 4.8 74.4 1.0 OD1 A:ASN180 4.8 77.2 1.0 CB A:ASN180 4.8 77.8 1.0 CA A:ASN180 4.9 78.2 1.0 C A:PHE181 4.9 71.8 1.0

Calcium binding site 2 out of 5 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:89.5 occ:1.00 OD1 B:ASP28 2.6 94.1 1.0 O B:GLY11 3.1 82.8 1.0 CG B:ASP28 3.3 91.9 1.0 OD2 B:ASP28 3.3 89.5 1.0 C B:GLY11 4.0 82.3 1.0 CA B:GLY11 4.1 85.2 1.0 ND2 B:ASN13 4.3 86.0 1.0 OD1 B:ASN13 4.6 81.5 1.0 CB B:ASP28 4.7 92.5 1.0 CG B:ASN13 4.9 83.2 1.0

Calcium binding site 3 out of 5 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:82.2 occ:1.00 OD2 B:ASP103 2.7 73.6 1.0 OD1 B:ASP103 2.7 73.0 1.0 CG B:ASP103 3.0 73.1 1.0 NH2 B:ARG107 3.7 66.7 1.0 O B:CYS104 4.1 68.6 1.0 CB B:ASP103 4.5 72.7 1.0 CZ B:ARG107 4.9 66.4 1.0 N B:CYS104 5.0 67.7 1.0 C B:CYS104 5.0 68.5 1.0

Calcium binding site 4 out of 5 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:0.6 occ:1.00 ND2 B:ASN180 3.8 90.7 1.0 OE1 A:GLU66 4.0 0.5 1.0 OD1 B:ASN180 4.3 90.4 1.0 CG B:ASN180 4.4 90.9 1.0 CD A:GLU66 5.0 97.4 1.0

Calcium binding site 5 out of 5 in the Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca508 b:85.7 occ:1.00 OE1 B:GLU306 2.6 74.8 1.0 CD B:GLU306 3.5 74.7 1.0 OE2 B:GLU306 3.6 75.3 1.0 NZ B:LYS437 4.5 72.2 1.0 CB B:PHE302 4.8 73.2 1.0 CG B:GLU306 4.9 74.0 1.0

T.L.Grove, P.M.Himes, S.Hwang, H.Yumerefendi, J.B.Bonanno, B.Kuhlman, S.C.Almo, A.A.Bowers. Structural Insights Into Thioether Bond Formation in the Biosynthesis of Sactipeptides. J. Am. Chem. Soc. V. 139 11734 2017.
ISSN: ESSN 1520-5126
PubMed: 28704043
DOI: 10.1021/JACS.7B01283