Calcium in PDB 6zk1: Plant Nucleoside Hydrolase - ZMNRH2B Enzyme

The structure of Plant Nucleoside Hydrolase - ZMNRH2B Enzyme, PDB code: 6zk1 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)	28.99 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.79, 148.65, 88.58, 90, 102.24, 90
R / Rfree (%)	17.5 / 19.6

The structure of Plant Nucleoside Hydrolase - ZMNRH2B Enzyme also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH2B Enzyme (pdb code 6zk1). 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 Enzyme, PDB code: 6zk1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B 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 - ZMNRH2B Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:32.7 occ:1.00 O A:LEU133 2.2 27.0 1.0 O A:HOH525 2.4 39.1 1.0 OD2 A:ASP23 2.5 30.3 1.0 OD1 A:ASP18 2.5 32.0 1.0 OD2 A:ASP250 2.5 34.6 1.0 OD1 A:ASP23 2.5 34.1 1.0 O A:HOH508 2.7 35.0 1.0 O A:HOH521 2.8 40.0 1.0 CG A:ASP23 2.8 32.0 1.0 C A:LEU133 3.3 29.3 1.0 CG A:ASP250 3.5 38.4 1.0 ND2 A:ASN47 3.5 29.1 1.0 CG A:ASP18 3.6 32.8 1.0 OD1 A:ASP250 3.7 41.7 1.0 CB A:LEU133 4.0 25.9 1.0 OD2 A:ASP18 4.1 36.7 1.0 CA A:LEU133 4.2 26.8 1.0 CB A:ASP23 4.3 29.2 1.0 N A:GLY134 4.3 28.9 1.0 CA A:GLY134 4.4 28.7 1.0 OD1 A:ASN176 4.5 31.3 1.0 OD1 A:ASP22 4.5 36.5 1.0 CG A:ASN47 4.6 36.1 1.0 ND2 A:ASN176 4.6 32.9 1.0 O1 A:EDO406 4.6 60.0 1.0 N A:ASP18 4.6 29.5 1.0 O A:ASP18 4.8 31.4 1.0 CB A:ASP250 4.9 31.1 1.0 OD1 A:ASN47 4.9 32.8 1.0 CB A:ASP18 4.9 29.3 1.0 CA A:ASP23 4.9 28.3 1.0 OD2 A:ASP22 4.9 41.7 1.0 C1 A:EDO406 4.9 59.7 1.0 N A:ASP23 4.9 28.5 1.0

Calcium binding site 2 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B 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 - ZMNRH2B Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:34.2 occ:1.00 O B:LEU133 2.3 34.6 1.0 O B:HOH518 2.4 43.2 1.0 OD2 B:ASP250 2.5 43.3 1.0 OD1 B:ASP23 2.5 35.1 1.0 OD2 B:ASP23 2.6 28.2 1.0 OD1 B:ASP18 2.6 34.3 1.0 O B:HOH516 2.7 35.6 1.0 CG B:ASP23 2.8 32.8 1.0 O1 B:EDO407 2.9 57.4 1.0 C B:LEU133 3.4 34.5 1.0 CG B:ASP250 3.4 49.1 1.0 ND2 B:ASN47 3.4 27.5 1.0 CG B:ASP18 3.6 35.1 1.0 OD1 B:ASP250 3.6 54.9 1.0 CB B:LEU133 4.0 29.6 1.0 OD2 B:ASP18 4.0 36.0 1.0 C1 B:EDO407 4.2 56.4 1.0 CA B:LEU133 4.2 30.6 1.0 CB B:ASP23 4.3 31.0 1.0 N B:GLY134 4.3 29.8 1.0 CA B:GLY134 4.4 29.7 1.0 CG B:ASN47 4.5 39.7 1.0 C2 B:EDO407 4.5 55.8 1.0 OD1 B:ASN176 4.5 32.6 1.0 O2 B:EDO407 4.5 54.6 1.0 ND2 B:ASN176 4.6 27.1 1.0 N B:ASP18 4.6 30.2 1.0 O B:ASP18 4.7 32.9 1.0 OD1 B:ASP22 4.7 45.1 1.0 CB B:ASP250 4.8 34.7 1.0 OD2 B:ASP22 4.8 55.5 1.0 OD1 B:ASN47 4.8 37.0 1.0 CA B:ASP23 4.9 31.1 1.0 CB B:ASP18 4.9 30.1 1.0 N B:ASP23 4.9 32.5 1.0

Calcium binding site 3 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B Enzyme


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 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:41.1 occ:1.00 O C:LEU133 2.3 42.0 1.0 OD1 C:ASP18 2.4 42.5 1.0 OD2 C:ASP23 2.5 45.5 1.0 O C:HOH530 2.6 40.1 1.0 OD1 C:ASP23 2.6 42.9 1.0 OD2 C:ASP250 2.7 52.4 1.0 O C:HOH517 2.7 45.9 1.0 O C:HOH522 2.8 49.9 1.0 CG C:ASP23 2.8 43.0 1.0 C C:LEU133 3.4 41.9 1.0 CG C:ASP18 3.4 44.7 1.0 CG C:ASP250 3.6 53.0 1.0 ND2 C:ASN47 3.6 31.8 1.0 OD1 C:ASP250 3.8 55.8 1.0 OD2 C:ASP18 3.8 43.6 1.0 CB C:LEU133 4.0 39.7 1.0 N C:GLY134 4.3 37.2 1.0 CA C:LEU133 4.3 39.1 1.0 CB C:ASP23 4.3 37.1 1.0 CA C:GLY134 4.4 36.6 1.0 OD1 C:ASN176 4.5 39.3 1.0 OD1 C:ASP22 4.5 40.4 1.0 O C:ASP18 4.5 40.0 1.0 O C:HOH595 4.6 52.2 1.0 O C:HOH587 4.6 58.5 1.0 N C:ASP18 4.6 39.4 1.0 CG C:ASN47 4.6 44.4 1.0 ND2 C:ASN176 4.6 41.9 1.0 CB C:ASP18 4.8 37.2 1.0 OD2 C:ASP22 4.8 49.9 1.0 OD1 C:ASN47 4.9 37.8 1.0 C C:ASP18 4.9 41.7 1.0 N C:ASP23 5.0 36.1 1.0 CA C:ASP23 5.0 36.3 1.0 CG C:ASP22 5.0 41.6 1.0

Calcium binding site 4 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B Enzyme


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 Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:42.0 occ:1.00 O D:LEU133 2.2 40.2 1.0 OD1 D:ASP23 2.5 48.5 1.0 O D:HOH515 2.5 42.2 1.0 OD2 D:ASP23 2.6 49.1 1.0 OD2 D:ASP250 2.6 44.2 1.0 OD1 D:ASP18 2.6 40.4 1.0 O D:HOH503 2.7 40.8 1.0 CG D:ASP23 2.8 45.8 1.0 C D:LEU133 3.4 38.3 1.0 CG D:ASP250 3.5 49.1 1.0 ND2 D:ASN47 3.6 42.5 1.0 OD1 D:ASP250 3.7 51.5 1.0 CG D:ASP18 3.7 42.4 1.0 CB D:LEU133 4.0 33.6 1.0 OD2 D:ASP18 4.1 41.8 1.0 CA D:LEU133 4.2 32.7 1.0 N D:GLY134 4.3 33.1 1.0 CB D:ASP23 4.3 37.9 1.0 OD1 D:ASP22 4.4 58.6 1.0 CA D:GLY134 4.4 32.5 1.0 OD1 D:ASN176 4.4 35.5 1.0 ND2 D:ASN176 4.5 29.0 1.0 OD2 D:ASP22 4.5 62.5 1.0 CG D:ASN47 4.6 51.5 1.0 O D:HOH577 4.7 55.6 1.0 O D:ASP18 4.7 44.5 1.0 N D:ASP18 4.8 37.4 1.0 CG D:ASP22 4.8 57.3 1.0 OD1 D:ASN47 4.9 44.4 1.0 CB D:ASP250 4.9 43.6 1.0 CA D:ASP23 4.9 37.8 1.0 CG D:ASN176 5.0 39.2 1.0 N D:ASP23 5.0 38.9 1.0 CB D:ASP18 5.0 38.4 1.0

E.Luptakova, A.Vigouroux, R.Koncitikova, M.Kopecna, 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 and Role in Nitrogen Storage Mobilization To Be Published.