Calcium in PDB 5kva: Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt)

The structure of Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt), PDB code: 5kva was solved by A.M.Walker, S.A.Sattler, M.Regner, J.P.Jones, J.Ralph, W.Vermerris, S.E.Sattler, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.64 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.531, 91.562, 55.783, 90.00, 90.69, 90.00
R / Rfree (%)	15.9 / 19.3

The binding sites of Calcium atom in the Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt) (pdb code 5kva). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt), PDB code: 5kva:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt)


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 Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:19.3 occ:1.00 OD2 A:ASP203 2.3 17.6 1.0 OD1 A:ASP177 2.3 21.5 1.0 O A:HOH600 2.3 20.1 1.0 O A:HOH559 2.4 15.0 1.0 OD1 A:ASN204 2.4 17.6 1.0 O A:HOH598 2.5 16.6 1.0 OD2 A:ASP177 2.6 18.1 1.0 CG A:ASP177 2.7 15.9 1.0 CG A:ASP203 3.4 16.3 1.0 CG A:ASN204 3.4 21.1 1.0 ND2 A:ASN204 3.8 16.1 1.0 CB A:ASP203 3.9 15.4 1.0 CE A:SAM301 4.0 20.2 1.0 CB A:ASP177 4.1 16.4 1.0 O A:HOH434 4.4 23.7 1.0 OD1 A:ASP203 4.4 17.5 1.0 O A:HOH516 4.4 18.3 1.0 O A:HOH422 4.4 30.9 1.0 OG1 A:THR77 4.5 18.6 1.0 O A:MET75 4.6 18.8 1.0 O A:HOH630 4.6 32.5 1.0 CB A:ASN204 4.8 16.4 1.0 CB A:SAM301 4.8 17.7 1.0 O A:HOH613 4.8 24.9 1.0 O A:HOH523 4.9 20.6 1.0 N A:ASN204 4.9 13.9 1.0 CA A:ASP177 4.9 14.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt)


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 Sorghum Caffeoyl-Coa O-Methyltransferase (Ccoaomt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.4 occ:1.00 OD2 B:ASP203 2.3 16.6 1.0 O B:HOH587 2.4 15.9 1.0 OD1 B:ASP177 2.4 17.9 1.0 OD1 B:ASN204 2.4 17.0 1.0 O B:HOH608 2.4 17.6 1.0 O B:HOH550 2.4 17.2 1.0 OD2 B:ASP177 2.6 18.4 1.0 CG B:ASP177 2.8 19.0 1.0 CG B:ASP203 3.4 19.4 1.0 CG B:ASN204 3.4 24.2 1.0 ND2 B:ASN204 3.8 20.4 1.0 CB B:ASP203 3.9 12.9 1.0 O B:HOH521 4.1 31.9 1.0 CE B:SAM301 4.1 18.5 1.0 CB B:ASP177 4.2 15.3 1.0 O B:HOH459 4.3 23.9 1.0 OD1 B:ASP203 4.4 19.0 1.0 O B:HOH537 4.4 19.6 1.0 OG1 B:THR77 4.5 14.7 1.0 O B:HOH623 4.5 29.5 1.0 O B:MET75 4.6 17.7 1.0 O B:HOH595 4.7 26.8 1.0 CB B:ASN204 4.8 16.1 1.0 O B:HOH482 4.9 17.6 1.0 CB B:SAM301 4.9 13.5 1.0 N B:ASN204 4.9 14.1 1.0 CA B:ASP177 5.0 18.2 1.0

A.M.Walker, S.A.Sattler, M.Regner, J.P.Jones, J.Ralph, W.Vermerris, S.E.Sattler, C.Kang. The Structure and Catalytic Mechanism of Sorghum Bicolor Caffeoyl-Coa O-Methyltransferase. Plant Physiol. V. 172 78 2016.
ISSN: ESSN 1532-2548
PubMed: 27457122
DOI: 10.1104/PP.16.00845