Calcium in PDB 4kpo: Plant Nucleoside Hydrolase - ZMNRH3 Enzyme

The structure of Plant Nucleoside Hydrolase - ZMNRH3 Enzyme, PDB code: 4kpo 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)	43.69 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.440, 85.780, 87.390, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.5

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH3 Enzyme (pdb code 4kpo). 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, PDB code: 4kpo:
Jump to Calcium binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:57.9 occ:1.00 O A:LEU123 2.3 50.9 1.0 OD1 A:ASP13 2.5 58.3 1.0 OD2 A:ASP13 2.5 63.4 1.0 OD1 A:ASP8 2.6 57.3 1.0 O A:HOH507 2.7 45.3 1.0 OD2 A:ASP240 2.8 74.5 1.0 CG A:ASP13 2.8 58.2 1.0 ND2 A:ASN37 3.4 47.2 1.0 C A:LEU123 3.4 50.7 1.0 OD1 A:ASP240 3.5 72.8 1.0 CG A:ASP240 3.5 69.9 1.0 CG A:ASP8 3.6 57.0 1.0 OD2 A:ASP8 3.9 60.3 1.0 CB A:LEU123 4.2 48.8 1.0 N A:GLY124 4.2 46.1 1.0 CA A:GLY124 4.3 45.3 1.0 CB A:ASP13 4.3 49.8 1.0 CG A:ASN37 4.3 56.7 1.0 CA A:LEU123 4.3 48.2 1.0 OD1 A:ASN166 4.5 52.3 1.0 CD2 A:LEU149 4.5 58.7 1.0 ND2 A:ASN166 4.6 56.3 1.0 OD1 A:ASP12 4.6 72.8 1.0 OD1 A:ASN37 4.6 49.2 1.0 O A:ASP8 4.6 52.6 1.0 N A:ASP8 4.8 49.2 1.0 CB A:ASP8 4.9 50.5 1.0 CB A:ASP240 5.0 57.6 1.0 CG A:ASN166 5.0 61.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:62.9 occ:1.00 O B:LEU123 2.3 49.9 1.0 OD2 B:ASP13 2.5 65.1 1.0 OD1 B:ASP8 2.5 59.8 1.0 OD1 B:ASP13 2.5 64.7 1.0 OD2 B:ASP240 2.8 71.9 1.0 CG B:ASP13 2.9 63.4 1.0 C B:LEU123 3.4 49.2 1.0 ND2 B:ASN37 3.4 51.3 1.0 OD1 B:ASP240 3.5 70.3 1.0 CG B:ASP240 3.5 69.2 1.0 CG B:ASP8 3.5 59.6 1.0 OD2 B:ASP8 3.9 66.1 1.0 CB B:LEU123 4.2 45.8 1.0 N B:GLY124 4.2 45.9 1.0 CA B:GLY124 4.3 45.8 1.0 CG B:ASN37 4.3 61.6 1.0 CA B:LEU123 4.3 45.1 1.0 CB B:ASP13 4.4 55.9 1.0 CD2 B:LEU149 4.5 55.2 1.0 OD1 B:ASN166 4.5 48.1 1.0 OD1 B:ASN37 4.6 54.5 1.0 ND2 B:ASN166 4.6 47.3 1.0 O B:ASP8 4.6 53.6 1.0 OD1 B:ASP12 4.6 81.8 1.0 N B:ASP8 4.8 48.5 1.0 CB B:ASP8 4.9 50.2 1.0 CB B:ASP240 5.0 60.0 1.0

M.Kopecna, H.Blaschke, D.Kopecny, A.Vigouroux, R.Koncitikova, O.Novak, O.Kotland, M.Strnad, S.Morera, K.Von Schwartzenberg. Structure and Function of Nucleoside Hydrolases From Physcomitrella Patens and Maize Catalyzing the Hydrolysis of Purine, Pyrimidine, and Cytokinin Ribosides. Plant Physiol. V. 163 1568 2013.
ISSN: ISSN 0032-0889
PubMed: 24170203
DOI: 10.1104/PP.113.228775