Calcium in PDB 6gp3: Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form

The structure of Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form, PDB code: 6gp3 was solved by V.Srinivas, H.Lebrette, D.Lundin, Y.Kutin, M.Sahlin, M.Lerche, J.Enrich, R.M.M.Branca, N.Cox, B.M.Sjoberg, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.71 / 1.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.193, 53.425, 79.133, 90.00, 108.53, 90.00
R / Rfree (%)	14.7 / 16.3

The binding sites of Calcium atom in the Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form (pdb code 6gp3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form, PDB code: 6gp3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.5 occ:0.69 O A:GLY266 2.2 24.2 1.0 O A:HOH548 2.3 38.9 1.0 OD2 A:ASP270 2.4 25.8 1.0 OD1 A:ASP269 2.4 26.1 1.0 O A:HOH647 2.5 38.2 1.0 O A:HOH846 2.5 47.1 1.0 CG A:ASP269 3.4 31.0 1.0 C A:GLY266 3.4 19.4 1.0 OD2 A:ASP269 3.6 38.7 1.0 CG A:ASP270 3.6 39.3 1.0 OD1 A:ASP270 4.1 36.1 1.0 O A:HOH534 4.1 38.1 1.0 CA A:GLY266 4.2 19.3 1.0 O A:HOH857 4.3 55.9 1.0 N A:LEU267 4.4 17.7 1.0 CA A:LEU267 4.4 16.4 1.0 O A:HOH908 4.5 59.1 1.0 O A:HOH623 4.6 39.2 1.0 O A:HOH775 4.7 55.3 1.0 N A:ASP270 4.7 20.0 1.0 C A:LEU267 4.7 17.8 1.0 CB A:ASP270 4.8 22.4 1.0 CB A:ASP269 4.8 24.6 1.0 N A:ASP269 4.9 18.6 1.0

Calcium binding site 2 out of 2 in the Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ribonucleotide Reductase Class Ie R2 From Mesoplasma Florum, Inactive Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:22.4 occ:0.47 OD1 B:ASP269 2.2 78.2 0.6 O B:GLY266 2.2 31.1 0.6 O B:GLY266 2.3 24.0 0.4 OD2 B:ASP270 2.3 24.7 0.4 O B:HOH562 2.4 48.7 1.0 O B:HOH745 2.5 55.3 1.0 OD1 B:ASP269 2.5 69.6 0.4 OD2 B:ASP269 2.8 26.5 0.4 CG B:ASP269 3.0 33.0 0.4 C B:GLY266 3.1 23.7 0.6 CG B:ASP269 3.3 49.3 0.6 CG B:ASP270 3.5 28.2 0.4 C B:GLY266 3.5 24.2 0.4 OD2 B:ASP269 3.7 52.4 0.6 CA B:GLY266 3.8 27.0 0.6 O B:HOH502 3.9 58.4 1.0 N B:LEU267 3.9 22.8 0.6 OD1 B:ASP270 4.0 30.9 0.4 OD2 B:ASP270 4.1 48.4 0.6 CA B:LEU267 4.2 20.7 0.6 CA B:GLY266 4.3 24.7 0.4 O B:HOH501 4.3 56.3 1.0 C B:LEU267 4.4 27.1 0.6 N B:ASP269 4.4 32.3 0.6 N B:LEU267 4.5 22.6 0.4 CB B:ASP269 4.5 28.2 0.4 N B:ALA268 4.5 22.8 0.6 O B:HOH755 4.5 53.0 1.0 CB B:ASP269 4.6 33.7 0.6 N B:ASP270 4.6 28.0 0.4 O B:HOH510 4.6 43.1 1.0 CA B:LEU267 4.6 24.0 0.4 CB B:ASP270 4.6 26.2 0.4 O B:HOH592 4.7 59.0 1.0 N B:ASP270 4.9 25.1 0.6 O B:HOH749 4.9 61.1 1.0 O B:LEU267 5.0 23.2 0.6 CA B:ASP269 5.0 31.3 0.6 CG B:ASP270 5.0 45.0 0.6

V.Srinivas, H.Lebrette, D.Lundin, Y.Kutin, M.Sahlin, M.Lerche, J.Eirich, R.M.M.Branca, N.Cox, B.M.Sjoberg, M.Hogbom. Metal-Free Ribonucleotide Reduction Powered By A Dopa Radical in Mycoplasma Pathogens. Nature V. 563 416 2018.
ISSN: ESSN 1476-4687
PubMed: 30429545
DOI: 10.1038/S41586-018-0653-6