Calcium in PDB 3ubr: Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase

All present enzymatic activity of Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase:
1.7.2.2;

The structure of Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase, PDB code: 3ubr was solved by M.Youngblut, E.T.Judd, V.Srajer, B.Sayed, T.Goeltzner, S.Elliott, M.Schmidt, A.Pacheco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.56 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.500, 95.900, 223.800, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 28.5

The structure of Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Calcium atom in the Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase (pdb code 3ubr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase, PDB code: 3ubr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca476 b:18.7 occ:1.00 OE2 A:GLU205 2.4 14.5 1.0 OE1 A:GLN256 2.5 25.6 1.0 O A:LYS254 2.6 19.4 1.0 O A:TYR206 2.7 21.4 1.0 OE1 A:GLU205 2.9 17.3 1.0 CD A:GLU205 3.0 16.9 1.0 OH A:TYR235 3.4 18.1 1.0 CD A:GLN256 3.6 24.2 1.0 C A:LYS254 3.7 19.4 1.0 OD2 A:ASP242 3.8 16.9 1.0 C A:TYR206 3.9 21.6 1.0 CB A:TYR207 4.1 23.6 1.0 NE2 A:GLN256 4.2 23.4 1.0 CZ A:TYR235 4.3 18.3 1.0 OD1 A:ASP242 4.4 19.0 1.0 CG A:GLU205 4.4 17.9 1.0 CA A:TYR207 4.5 23.7 1.0 CG A:ASP242 4.5 16.6 1.0 N A:LYS254 4.5 18.8 1.0 CA A:LYS254 4.6 18.9 1.0 N A:TYR207 4.6 22.9 1.0 CB A:LYS254 4.6 18.7 1.0 N A:TYR206 4.7 20.1 1.0 N A:ALA255 4.7 20.2 1.0 CA A:ALA255 4.7 20.6 1.0 CE2 A:TYR235 4.7 17.9 1.0 CZ3 A:TRP372 4.8 9.5 1.0 CG A:GLN256 4.9 23.6 1.0 N A:GLN256 4.9 21.7 1.0 CA A:TYR206 4.9 21.0 1.0

Calcium binding site 2 out of 2 in the Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Laue Structure of Shewanella Oneidensis Cytochrome-C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca476 b:19.7 occ:1.00 O B:HOH483 2.2 15.6 1.0 OE2 B:GLU205 2.2 12.1 1.0 OE1 B:GLN256 2.3 24.1 1.0 O B:TYR206 2.3 17.3 1.0 O B:LYS254 2.4 13.5 1.0 CD B:GLU205 2.8 15.1 1.0 OE1 B:GLU205 2.9 15.9 1.0 CD B:GLN256 3.4 23.1 1.0 C B:TYR206 3.5 17.8 1.0 C B:LYS254 3.6 13.7 1.0 NE2 B:GLN256 3.8 24.2 1.0 OH B:TYR235 3.8 4.6 1.0 OD2 B:ASP242 3.9 17.7 1.0 N B:TYR206 4.2 16.6 1.0 CG B:GLU205 4.3 16.0 1.0 CA B:ALA255 4.4 14.7 1.0 N B:TYR207 4.4 18.9 1.0 CB B:TYR207 4.4 19.4 1.0 N B:ALA255 4.4 14.2 1.0 CA B:TYR207 4.5 19.6 1.0 N B:GLN256 4.5 16.7 1.0 CA B:TYR206 4.5 17.4 1.0 C B:ALA255 4.6 15.4 1.0 CA B:LYS254 4.6 13.5 1.0 CG B:GLN256 4.7 20.5 1.0 N B:LYS254 4.7 13.6 1.0 CZ B:TYR235 4.7 9.1 1.0 CG B:ASP242 4.8 16.4 1.0 CB B:LYS254 4.8 13.4 1.0 OD1 B:ASP242 4.8 19.1 1.0 CB B:GLN256 4.9 18.2 1.0

M.Youngblut, E.T.Judd, V.Srajer, B.Sayyed, T.Goelzer, S.J.Elliott, M.Schmidt, A.A.Pacheco. Laue Crystal Structure of Shewanella Oneidensis Cytochrome C Nitrite Reductase From A High-Yield Expression System. J.Biol.Inorg.Chem. V. 17 647 2012.
ISSN: ISSN 0949-8257
PubMed: 22382353
DOI: 10.1007/S00775-012-0885-0