Calcium in PDB 6zk2: Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine

The structure of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine, PDB code: 6zk2 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)	30.12 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.92, 148.98, 88.51, 90, 102.4, 90
R / Rfree (%)	19.1 / 22.9

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine (pdb code 6zk2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine, PDB code: 6zk2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B 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 - ZMNRH2B in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:24.8 occ:1.00 O A:LEU133 2.3 25.8 1.0 OD1 A:ASP18 2.5 26.1 1.0 O2' A:IMH402 2.5 27.6 1.0 OD1 A:ASP23 2.5 32.5 1.0 OD2 A:ASP23 2.5 30.0 1.0 OD2 A:ASP250 2.6 23.1 1.0 O3' A:IMH402 2.7 29.2 1.0 O A:HOH501 2.8 18.6 1.0 CG A:ASP23 2.9 28.5 1.0 C A:LEU133 3.4 23.7 1.0 ND2 A:ASN47 3.5 13.0 1.0 C2' A:IMH402 3.6 26.5 1.0 CG A:ASP18 3.6 25.8 1.0 CG A:ASP250 3.6 23.6 1.0 C3' A:IMH402 3.6 26.7 1.0 OD1 A:ASP250 3.8 24.5 1.0 OD2 A:ASP18 4.0 30.5 1.0 CB A:LEU133 4.0 18.5 1.0 CA A:LEU133 4.2 20.1 1.0 N A:GLY134 4.2 19.2 1.0 CB A:ASP23 4.3 23.1 1.0 C1' A:IMH402 4.3 25.5 1.0 CA A:GLY134 4.4 16.7 1.0 N4' A:IMH402 4.5 26.1 1.0 OD1 A:ASP22 4.5 24.1 1.0 OD1 A:ASN176 4.5 19.0 1.0 CG A:ASN47 4.5 21.0 1.0 C4' A:IMH402 4.5 23.2 1.0 ND2 A:ASN176 4.6 20.2 1.0 O A:ASP18 4.6 24.3 1.0 N A:ASP18 4.7 22.9 1.0 OD1 A:ASN47 4.8 22.5 1.0 CB A:ASP18 4.9 22.4 1.0 CB A:ASP250 5.0 19.1 1.0 OD2 A:ASP22 5.0 25.1 1.0

Calcium binding site 2 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B 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 - ZMNRH2B in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:26.4 occ:1.00 O B:LEU133 2.4 27.0 1.0 O2' B:IMH402 2.4 32.0 1.0 OD2 B:ASP250 2.5 29.4 1.0 OD1 B:ASP23 2.6 28.1 1.0 O3' B:IMH402 2.6 29.8 1.0 OD1 B:ASP18 2.6 31.9 1.0 OD2 B:ASP23 2.6 29.7 1.0 O B:HOH506 2.6 24.4 1.0 CG B:ASP23 2.9 30.4 1.0 C2' B:IMH402 3.4 29.3 1.0 C B:LEU133 3.5 26.6 1.0 ND2 B:ASN47 3.5 20.0 1.0 CG B:ASP250 3.5 30.6 1.0 C3' B:IMH402 3.5 26.7 1.0 CG B:ASP18 3.7 28.7 1.0 OD1 B:ASP250 3.7 29.0 1.0 OD2 B:ASP18 4.0 31.8 1.0 CB B:LEU133 4.1 23.2 1.0 C1' B:IMH402 4.3 27.9 1.0 CA B:LEU133 4.3 23.6 1.0 OD1 B:ASP22 4.3 26.6 1.0 N B:GLY134 4.4 21.1 1.0 N4' B:IMH402 4.4 28.4 1.0 CB B:ASP23 4.4 25.8 1.0 C4' B:IMH402 4.4 27.0 1.0 CG B:ASN47 4.5 31.9 1.0 CA B:GLY134 4.5 20.0 1.0 OD1 B:ASN176 4.5 30.1 1.0 ND2 B:ASN176 4.5 19.3 1.0 O B:ASP18 4.7 27.0 1.0 OD1 B:ASN47 4.7 26.9 1.0 N B:ASP18 4.8 25.7 1.0 CB B:ASP250 4.9 29.6 1.0 OD2 B:ASP22 4.9 34.2 1.0 CB B:ASP18 4.9 26.6 1.0 CG B:ASP22 5.0 29.3 1.0 CA B:ASP23 5.0 25.9 1.0 CG B:ASN176 5.0 33.2 1.0

Calcium binding site 3 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:36.4 occ:1.00 O C:LEU133 2.4 41.8 1.0 O2' C:IMH402 2.4 38.8 1.0 OD1 C:ASP23 2.4 40.2 1.0 OD2 C:ASP23 2.5 41.2 1.0 OD1 C:ASP18 2.5 42.7 1.0 OD2 C:ASP250 2.6 42.7 1.0 O3' C:IMH402 2.7 35.9 1.0 CG C:ASP23 2.8 40.5 1.0 O C:HOH501 2.9 28.9 1.0 C C:LEU133 3.5 41.2 1.0 C2' C:IMH402 3.5 35.7 1.0 CG C:ASP18 3.6 40.9 1.0 CG C:ASP250 3.6 41.4 1.0 C3' C:IMH402 3.6 35.4 1.0 ND2 C:ASN47 3.6 33.0 1.0 OD1 C:ASP250 3.9 38.1 1.0 OD2 C:ASP18 4.0 44.6 1.0 CB C:LEU133 4.1 39.2 1.0 CB C:ASP23 4.3 36.2 1.0 C1' C:IMH402 4.3 33.0 1.0 CA C:LEU133 4.3 38.4 1.0 N C:GLY134 4.4 36.7 1.0 N4' C:IMH402 4.4 31.8 1.0 CA C:GLY134 4.5 35.0 1.0 C4' C:IMH402 4.5 30.6 1.0 O C:ASP18 4.5 36.3 1.0 CG C:ASN47 4.6 40.6 1.0 OD1 C:ASP22 4.6 31.9 1.0 OD1 C:ASN176 4.6 32.9 1.0 N C:ASP18 4.6 36.2 1.0 ND2 C:ASN176 4.7 40.0 1.0 CB C:ASP18 4.9 35.0 1.0 OD1 C:ASN47 4.9 37.8 1.0 CA C:ASP23 4.9 36.6 1.0 C C:ASP18 4.9 39.0 1.0 CB C:ASP250 5.0 43.5 1.0 N C:ASP23 5.0 35.7 1.0

Calcium binding site 4 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Plant Nucleoside Hydrolase - ZMNRH2B in Complex with Forodesine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:37.1 occ:1.00 O D:LEU133 2.4 34.6 1.0 O2' D:IMH402 2.4 38.4 1.0 OD1 D:ASP23 2.6 39.0 1.0 OD1 D:ASP18 2.6 37.8 1.0 OD2 D:ASP23 2.6 35.8 1.0 O3' D:IMH402 2.6 29.7 1.0 OD2 D:ASP250 2.6 35.8 1.0 CG D:ASP23 2.9 37.8 1.0 C2' D:IMH402 3.4 35.9 1.0 C D:LEU133 3.5 32.2 1.0 C3' D:IMH402 3.5 31.3 1.0 ND2 D:ASN47 3.5 33.9 1.0 CG D:ASP250 3.6 35.6 1.0 CG D:ASP18 3.6 38.5 1.0 OD1 D:ASP250 3.8 34.1 1.0 OD2 D:ASP18 4.0 44.1 1.0 CB D:LEU133 4.1 28.0 1.0 C1' D:IMH402 4.2 35.3 1.0 CA D:LEU133 4.3 27.1 1.0 N D:GLY134 4.3 27.6 1.0 N4' D:IMH402 4.3 34.0 1.0 CB D:ASP23 4.4 30.6 1.0 C4' D:IMH402 4.4 31.3 1.0 CA D:GLY134 4.4 27.8 1.0 OD1 D:ASN176 4.5 32.3 1.0 OD1 D:ASP22 4.5 35.6 1.0 CG D:ASN47 4.5 44.0 1.0 ND2 D:ASN176 4.5 28.7 1.0 O D:ASP18 4.6 37.4 1.0 N D:ASP18 4.8 30.4 1.0 OD1 D:ASN47 4.8 35.3 1.0 CB D:ASP18 4.9 33.6 1.0 CB D:ASP250 5.0 34.8 1.0 CG D:ASN176 5.0 37.4 1.0 CA D:ASP23 5.0 29.5 1.0

E.Luptakova, A.Vigouroux, R.Koncitikova, M.Kopecna, D.Zalabak, O.Novak, N.De Diego, S.Cavar Zelkovic, 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.