Calcium in PDB 6zk5: Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine

The structure of Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine, PDB code: 6zk5 was solved by S.Morera, A.Vigouroux, D.Kopecny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.61 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.54, 79.27, 85.22, 90, 90, 90
R / Rfree (%)	17 / 19.3

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine (pdb code 6zk5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine, PDB code: 6zk5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:24.9 occ:1.00 O A:LEU123 2.4 23.7 1.0 O3' A:IMH402 2.4 23.9 1.0 OD1 A:ASP13 2.4 23.7 1.0 OD2 A:ASP240 2.5 28.2 1.0 O2' A:IMH402 2.5 25.0 1.0 OD1 A:ASP8 2.5 27.9 1.0 OD2 A:ASP13 2.6 29.2 1.0 O A:HOH506 2.6 20.9 1.0 CG A:ASP13 2.8 26.9 1.0 CG A:ASP240 3.4 28.5 1.0 C A:LEU123 3.5 24.6 1.0 C3' A:IMH402 3.5 24.0 1.0 ND2 A:ASN37 3.5 21.9 1.0 C2' A:IMH402 3.5 23.6 1.0 CG A:ASP8 3.6 28.3 1.0 OD1 A:ASP240 3.7 27.3 1.0 OD2 A:ASP8 3.9 29.6 1.0 CB A:LEU123 4.1 22.1 1.0 C1' A:IMH402 4.3 24.6 1.0 CB A:ASP13 4.3 27.1 1.0 CA A:LEU123 4.3 22.9 1.0 N A:GLY124 4.3 23.1 1.0 CA A:GLY124 4.4 22.6 1.0 N4' A:IMH402 4.4 27.2 1.0 C4' A:IMH402 4.5 25.1 1.0 OD1 A:ASP12 4.5 27.5 1.0 CG A:ASN37 4.5 27.7 1.0 ND2 A:ASN166 4.6 22.6 1.0 OD1 A:ASN166 4.6 21.6 1.0 O A:ASP8 4.6 26.3 1.0 N A:ASP8 4.7 23.4 1.0 CB A:ASP240 4.8 23.5 1.0 OD1 A:ASN37 4.8 25.5 1.0 CB A:ASP8 4.9 23.2 1.0 CA A:ASP13 4.9 25.0 1.0 N A:ASP13 4.9 25.1 1.0 OD2 A:ASP12 4.9 26.9 1.0

Calcium binding site 2 out of 2 in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Plant Nucleoside Hydrolase - ZMNRH3 Enzyme in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:25.3 occ:1.00 O B:LEU123 2.3 25.5 1.0 OD1 B:ASP8 2.4 28.4 1.0 O3' B:IMH401 2.4 26.8 1.0 OD1 B:ASP13 2.5 28.5 1.0 O B:HOH527 2.5 22.6 1.0 O2' B:IMH401 2.5 25.6 1.0 OD2 B:ASP240 2.5 24.4 1.0 OD2 B:ASP13 2.6 25.4 1.0 CG B:ASP13 2.8 26.1 1.0 C B:LEU123 3.4 27.6 1.0 C3' B:IMH401 3.5 24.2 1.0 CG B:ASP8 3.5 29.9 1.0 CG B:ASP240 3.5 26.0 1.0 ND2 B:ASN37 3.5 24.8 1.0 C2' B:IMH401 3.5 26.6 1.0 OD1 B:ASP240 3.7 25.6 1.0 OD2 B:ASP8 3.9 34.3 1.0 CB B:LEU123 4.0 20.9 1.0 C1' B:IMH401 4.2 25.8 1.0 CA B:LEU123 4.2 22.2 1.0 N B:GLY124 4.3 25.0 1.0 CB B:ASP13 4.3 24.2 1.0 CA B:GLY124 4.4 24.2 1.0 N4' B:IMH401 4.4 26.2 1.0 C4' B:IMH401 4.4 25.6 1.0 CG B:ASN37 4.5 37.3 1.0 ND2 B:ASN166 4.5 21.9 1.0 OD1 B:ASP12 4.5 28.8 1.0 OD1 B:ASN166 4.6 23.2 1.0 O B:ASP8 4.6 29.2 1.0 N B:ASP8 4.7 24.0 1.0 CB B:ASP8 4.8 24.9 1.0 OD1 B:ASN37 4.8 26.7 1.0 CB B:ASP240 4.9 24.4 1.0 CA B:ASP13 4.9 23.4 1.0 N B:ASP13 5.0 24.7 1.0 OD2 B:ASP12 5.0 29.0 1.0

E.Luptakova, A.Vigouroux, R.Koncitikova, M.Kopecny, D.Zalabak, O.Novak, N.De Diego, S.C.Zeljkovic, O.Plihal, M.Strnad, K.Von Schwartzenberg, D.Kopecny, S.Morera. Plant Nucleoside N-Ribohydrolases: Substrate Binding and Role in Nitrogen Storage Mobilization To Be Published.