Calcium in PDB 2ix0: Rnase II

All present enzymatic activity of Rnase II:
3.1.13.1;

The structure of Rnase II, PDB code: 2ix0 was solved by C.Frazao, C.E.Mcvey, M.Amblar, A.Barbas, C.Vonrhein, C.M.Arraiano, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.87 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.836, 125.719, 66.244, 90.00, 111.91, 90.00
R / Rfree (%)	18.7 / 23.6

The structure of Rnase II also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Rnase II (pdb code 2ix0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Rnase II, PDB code: 2ix0:

Calcium binding site 1 out of 1 in the Rnase II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rnase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1647 b:62.6 occ:1.00 O A:LEU106 2.3 33.4 1.0 O A:HIS103 2.4 32.7 1.0 O A:PRO101 2.5 32.6 1.0 O A:HOH2020 2.7 54.5 1.0 O A:HOH2021 2.9 55.1 1.0 O A:HOH2004 2.9 45.9 1.0 C A:LEU106 3.3 31.4 1.0 C A:HIS103 3.4 31.7 1.0 C A:PRO101 3.6 29.5 1.0 CG1 A:VAL100 3.8 20.9 1.0 C A:ASP102 3.9 30.1 1.0 O A:ASP102 4.0 29.9 1.0 N A:LEU106 4.1 31.8 1.0 CA A:LEU106 4.1 30.2 1.0 CA A:HIS103 4.1 29.4 1.0 N A:HIS103 4.2 30.9 1.0 N A:LYS107 4.2 32.9 1.0 N A:PRO104 4.3 33.2 1.0 CA A:ASP102 4.3 29.6 1.0 CA A:LYS107 4.3 34.4 1.0 CA A:PRO104 4.3 30.7 1.0 O A:PRO104 4.3 34.0 1.0 C A:PRO104 4.4 31.5 1.0 CB A:LEU106 4.4 29.0 1.0 N A:ASP102 4.4 31.1 1.0 CA A:PRO101 4.6 29.7 1.0 N A:PRO101 4.6 28.9 1.0 CB A:PRO101 4.8 32.9 1.0 CD A:PRO101 5.0 27.3 1.0 C A:VAL100 5.0 27.6 1.0

C.Frazao, C.E.Mcvey, M.Amblar, A.Barbas, C.Vonrhein, C.M.Arraiano, M.A.Carrondo. Unravelling the Dynamics of Rna Degradation By Ribonuclease II and Its Rna-Bound Complex Nature V. 7 443 2006.
ISSN: ISSN 0028-0836
PubMed: 16957732
DOI: 10.1038/NATURE05080