Calcium in PDB 6p73: Cytochrome-C-Nitrite Reductase

All present enzymatic activity of Cytochrome-C-Nitrite Reductase:
1.7.2.2;

The structure of Cytochrome-C-Nitrite Reductase, PDB code: 6p73 was solved by M.Schmidt, A.Pacheco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.78 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.180, 96.070, 222.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.2

The structure of Cytochrome-C-Nitrite Reductase also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Calcium atom in the Cytochrome-C-Nitrite Reductase (pdb code 6p73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cytochrome-C-Nitrite Reductase, PDB code: 6p73:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the 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 Cytochrome-C-Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:20.5 occ:1.00 O A:TYR206 2.4 12.7 1.0 O A:LYS254 2.4 12.8 1.0 OE2 A:GLU205 2.4 15.1 1.0 O A:HOH687 2.5 18.0 1.0 OE1 A:GLU205 2.6 13.4 1.0 OE1 A:GLN256 2.6 22.5 1.0 O A:HOH844 2.6 22.0 1.0 CD A:GLU205 2.8 15.1 1.0 C A:LYS254 3.6 13.8 1.0 C A:TYR206 3.6 13.4 1.0 CD A:GLN256 3.7 22.2 1.0 OH A:TYR235 3.8 13.1 1.0 N A:TYR206 4.1 13.6 1.0 NE2 A:GLN256 4.1 22.9 1.0 CA A:ALA255 4.2 13.5 1.0 OD2 A:ASP242 4.3 16.9 1.0 CG A:GLU205 4.3 16.3 1.0 N A:ALA255 4.3 12.6 1.0 N A:GLN256 4.4 14.3 1.0 C A:ALA255 4.5 15.0 1.0 N A:TYR207 4.5 13.4 1.0 CA A:TYR206 4.5 12.7 1.0 CA A:TYR207 4.6 13.5 1.0 CB A:TYR207 4.6 14.0 1.0 CA A:LYS254 4.6 14.0 1.0 CZ A:TYR235 4.7 12.9 1.0 CB A:LYS254 4.8 13.6 1.0 OD1 A:ASP242 4.9 21.3 1.0 N A:LYS254 4.9 12.6 1.0 CZ3 A:TRP372 4.9 12.4 1.0 CG A:GLN256 4.9 18.5 1.0 CG A:ASP242 4.9 17.9 1.0

Calcium binding site 2 out of 2 in the 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 Cytochrome-C-Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:20.3 occ:1.00 O B:LYS254 2.4 11.1 1.0 O B:TYR206 2.4 9.3 1.0 O B:HOH938 2.4 21.1 1.0 OE2 B:GLU205 2.5 13.3 1.0 O B:HOH677 2.5 16.1 1.0 OE1 B:GLU205 2.5 12.3 1.0 OE1 B:GLN256 2.6 24.1 1.0 CD B:GLU205 2.8 14.7 1.0 C B:LYS254 3.6 13.6 1.0 C B:TYR206 3.6 11.4 1.0 CD B:GLN256 3.7 23.1 1.0 OH B:TYR235 3.8 11.7 1.0 N B:TYR206 4.1 9.3 1.0 CA B:ALA255 4.2 12.2 1.0 OD2 B:ASP242 4.2 12.7 1.0 NE2 B:GLN256 4.3 21.0 1.0 CG B:GLU205 4.3 13.1 1.0 N B:ALA255 4.3 12.6 1.0 N B:GLN256 4.4 13.3 1.0 C B:ALA255 4.5 14.4 1.0 N B:TYR207 4.5 8.7 1.0 CA B:TYR206 4.5 12.4 1.0 CB B:TYR207 4.6 9.1 1.0 CA B:TYR207 4.6 9.5 1.0 CA B:LYS254 4.6 12.3 1.0 OD1 B:ASP242 4.7 17.4 1.0 CZ B:TYR235 4.7 11.6 1.0 CB B:LYS254 4.8 13.1 1.0 CZ3 B:TRP372 4.8 10.8 1.0 CG B:ASP242 4.8 15.2 1.0 N B:LYS254 4.8 15.2 1.0 CB B:GLN256 4.9 13.9 1.0 CG B:GLN256 4.9 16.6 1.0

M.Ali, N.Stein, Y.Mao, S.Shahid, M.Schmidt, B.Bennett, A.A.Pacheco. Trapping of A Putative Intermediate in the Cytochromecnitrite Reductase (Ccnir)-Catalyzed Reduction of Nitrite: Implications For the Ccnir Reaction Mechanism. J.Am.Chem.Soc. V. 141 13358 2019.
ISSN: ESSN 1520-5126
PubMed: 31381304
DOI: 10.1021/JACS.9B03036