Calcium in PDB 6zk4: Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine

The structure of Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine, PDB code: 6zk4 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)	42.86 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.64, 148.18, 88.41, 90, 102.71, 90
R / Rfree (%)	17.5 / 20.3

The binding sites of Calcium atom in the Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine (pdb code 6zk4). 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 with A Bound Adenine, PDB code: 6zk4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine


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 with A Bound Adenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:31.5 occ:1.00 O A:LEU133 2.3 26.6 1.0 OD1 A:ASP23 2.4 30.9 1.0 OD2 A:ASP23 2.5 34.2 1.0 OD1 A:ASP18 2.5 35.3 1.0 O A:HOH511 2.5 29.7 1.0 OD2 A:ASP250 2.6 40.5 1.0 O A:HOH560 2.6 33.8 1.0 O A:HOH512 2.6 34.9 1.0 CG A:ASP23 2.7 30.4 1.0 C A:LEU133 3.4 30.0 1.0 ND2 A:ASN47 3.5 25.3 1.0 CG A:ASP250 3.5 40.7 1.0 CG A:ASP18 3.6 34.9 1.0 OD1 A:ASP250 3.8 40.8 1.0 CB A:LEU133 4.0 26.7 1.0 OD2 A:ASP18 4.1 39.8 1.0 CB A:ASP23 4.2 30.9 1.0 CA A:LEU133 4.2 26.6 1.0 O A:HOH662 4.3 48.8 1.0 N A:GLY134 4.3 27.5 1.0 OD1 A:ASP22 4.4 39.3 1.0 CA A:GLY134 4.4 27.3 1.0 OD1 A:ASN176 4.5 28.9 1.0 CG A:ASN47 4.5 39.6 1.0 ND2 A:ASN176 4.6 33.0 1.0 N A:ASP18 4.6 30.9 1.0 O A:ASP18 4.6 33.6 1.0 O A:HOH591 4.6 33.9 1.0 OD1 A:ASN47 4.8 32.8 1.0 CA A:ASP23 4.9 29.0 1.0 CB A:ASP18 4.9 34.3 1.0 OD2 A:ASP22 4.9 43.7 1.0 N A:ASP23 4.9 29.5 1.0 CB A:ASP250 4.9 31.0 1.0 CG A:ASP22 4.9 40.5 1.0 C A:ASP18 5.0 34.6 1.0

Calcium binding site 2 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine


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 with A Bound Adenine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:39.2 occ:1.00 O B:LEU133 2.3 38.0 1.0 O B:HOH526 2.4 37.8 1.0 OD1 B:ASP23 2.5 35.4 1.0 OD2 B:ASP250 2.5 48.2 1.0 OD2 B:ASP23 2.6 32.3 1.0 OD1 B:ASP18 2.6 35.3 1.0 O B:HOH519 2.6 30.6 1.0 O B:HOH517 2.7 38.5 1.0 CG B:ASP23 2.8 35.3 1.0 C B:LEU133 3.5 35.6 1.0 CG B:ASP250 3.5 46.9 1.0 ND2 B:ASN47 3.5 33.1 1.0 CG B:ASP18 3.7 36.6 1.0 OD1 B:ASP250 3.7 49.9 1.0 CB B:LEU133 4.1 30.7 1.0 OD2 B:ASP18 4.1 43.3 1.0 CB B:ASP23 4.3 31.8 1.0 CA B:LEU133 4.3 30.8 1.0 OD1 B:ASP22 4.3 45.6 1.0 N B:GLY134 4.4 32.2 1.0 O B:HOH627 4.4 41.8 1.0 CA B:GLY134 4.5 32.3 1.0 O B:HOH554 4.5 45.7 1.0 OD1 B:ASN176 4.5 35.6 1.0 CG B:ASN47 4.5 40.8 1.0 ND2 B:ASN176 4.5 25.9 1.0 O B:ASP18 4.7 35.6 1.0 N B:ASP18 4.7 33.6 1.0 OD2 B:ASP22 4.8 43.2 1.0 OD1 B:ASN47 4.8 38.1 1.0 CB B:ASP250 4.9 34.8 1.0 CA B:ASP23 4.9 31.6 1.0 CG B:ASP22 4.9 45.0 1.0 N B:ASP23 4.9 32.5 1.0 CB B:ASP18 5.0 34.0 1.0 CG B:ASN176 5.0 32.7 1.0

Calcium binding site 3 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine


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 with A Bound Adenine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:41.6 occ:1.00 O C:LEU133 2.3 43.0 1.0 OD2 C:ASP23 2.4 43.0 1.0 OD1 C:ASP18 2.4 46.2 1.0 OD1 C:ASP23 2.5 42.8 1.0 O C:HOH501 2.5 44.4 1.0 O C:HOH526 2.6 36.4 1.0 OD2 C:ASP250 2.6 46.2 1.0 O C:HOH507 2.7 40.1 1.0 CG C:ASP23 2.7 43.5 1.0 C C:LEU133 3.4 42.6 1.0 ND2 C:ASN47 3.5 32.6 1.0 CG C:ASP18 3.6 45.0 1.0 CG C:ASP250 3.6 49.4 1.0 OD1 C:ASP250 3.8 49.8 1.0 OD2 C:ASP18 4.0 42.0 1.0 CB C:LEU133 4.0 40.0 1.0 CB C:ASP23 4.2 39.8 1.0 CA C:LEU133 4.3 38.6 1.0 N C:GLY134 4.3 38.8 1.0 O C:HOH553 4.4 41.5 1.0 O C:HOH592 4.4 39.8 1.0 CA C:GLY134 4.4 37.7 1.0 OD1 C:ASP22 4.4 41.7 1.0 CG C:ASN47 4.5 44.2 1.0 O C:ASP18 4.5 41.2 1.0 N C:ASP18 4.6 36.8 1.0 OD1 C:ASN176 4.6 38.6 1.0 ND2 C:ASN176 4.6 44.4 1.0 CB C:ASP18 4.8 35.8 1.0 OD1 C:ASN47 4.8 36.3 1.0 CA C:ASP23 4.9 39.3 1.0 C C:ASP18 4.9 42.0 1.0 N C:ASP23 4.9 38.7 1.0 OD2 C:ASP22 4.9 46.4 1.0 CB C:ASP250 5.0 41.3 1.0

Calcium binding site 4 out of 4 in the Plant Nucleoside Hydrolase - ZMNRH2B with A Bound Adenine


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 with A Bound Adenine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:40.5 occ:1.00 O D:LEU133 2.3 39.8 1.0 O D:HOH516 2.4 38.6 1.0 OD1 D:ASP18 2.5 40.1 1.0 OD2 D:ASP23 2.5 43.1 1.0 OD1 D:ASP23 2.5 48.4 1.0 OD2 D:ASP250 2.6 52.6 1.0 O D:HOH512 2.7 49.1 1.0 O D:HOH520 2.8 49.2 1.0 CG D:ASP23 2.8 46.4 1.0 C D:LEU133 3.4 38.0 1.0 ND2 D:ASN47 3.5 40.5 1.0 CG D:ASP250 3.6 50.6 1.0 CG D:ASP18 3.6 44.3 1.0 OD1 D:ASP250 3.7 52.9 1.0 OD2 D:ASP18 4.0 44.5 1.0 CB D:LEU133 4.0 34.2 1.0 CA D:LEU133 4.3 34.0 1.0 N D:GLY134 4.3 34.9 1.0 CB D:ASP23 4.3 39.5 1.0 CA D:GLY134 4.4 34.4 1.0 OD1 D:ASN176 4.4 40.3 1.0 OD1 D:ASP22 4.4 55.6 1.0 O D:HOH574 4.5 53.0 1.0 ND2 D:ASN176 4.5 28.3 1.0 CG D:ASN47 4.6 53.3 1.0 O D:ASP18 4.6 45.5 1.0 N D:ASP18 4.6 40.8 1.0 OD1 D:ASN47 4.9 47.1 1.0 CB D:ASP18 4.9 41.6 1.0 OD2 D:ASP22 4.9 57.5 1.0 CA D:ASP23 4.9 39.4 1.0 CG D:ASN176 5.0 41.8 1.0 CB D:ASP250 5.0 41.8 1.0 N D:ASP23 5.0 40.3 1.0 CG D:ASP22 5.0 53.2 1.0 C D:ASP18 5.0 46.4 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 Schwartzenbarg, D.Kopecny, S.Morera. Plant Nucleoside N-Ribohydrolases: Substrate Binding and Role in Nitrogen Storage Mobilization To Be Published.