Calcium in PDB 1qdb: Cytochrome C Nitrite Reductase

The structure of Cytochrome C Nitrite Reductase, PDB code: 1qdb was solved by O.Einsle, A.Messerschmidt, P.Stach, R.Huber, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.484, 185.344, 92.192, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22

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

Iron

(Fe)

15 atoms

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

Calcium binding site 1 out of 3 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:Ca520 b:2.1 occ:1.00 O A:TYR217 2.5 24.0 1.0 O A:LYS279 2.5 23.2 1.0 OE1 A:GLN281 2.5 29.6 1.0 O A:HOH1564 2.6 32.6 1.0 OE2 A:GLU216 2.7 21.6 1.0 OE1 A:GLU216 2.7 19.6 1.0 O A:HOH1534 2.7 27.8 1.0 CD A:GLU216 3.0 21.6 1.0 C A:LYS279 3.6 24.4 1.0 CD A:GLN281 3.6 28.1 1.0 C A:TYR217 3.6 27.5 1.0 OH A:TYR260 4.0 24.3 1.0 N A:TYR217 4.2 25.2 1.0 CA A:ALA280 4.2 24.4 1.0 NE2 A:GLN281 4.2 30.3 1.0 N A:GLN281 4.3 21.9 1.0 N A:ALA280 4.3 23.8 1.0 OD2 A:ASP267 4.4 29.8 1.0 C A:ALA280 4.4 22.3 1.0 N A:TYR218 4.5 26.2 1.0 CG A:GLU216 4.5 18.5 1.0 OD1 A:ASP267 4.5 28.3 1.0 CA A:TYR217 4.5 26.5 1.0 CA A:TYR218 4.6 27.8 1.0 CA A:LYS279 4.6 22.1 1.0 CB A:LYS279 4.6 21.3 1.0 CB A:TYR218 4.6 28.6 1.0 N A:LYS279 4.8 21.1 1.0 CB A:GLN281 4.8 24.5 1.0 CG A:GLN281 4.8 28.6 1.0 CG A:ASP267 4.8 31.5 1.0 CZ A:TYR260 5.0 24.1 1.0 O A:HOH1678 5.0 41.8 1.0

Calcium binding site 2 out of 3 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:Ca520 b:2.1 occ:1.00 O B:TYR217 2.5 13.9 1.0 O B:LYS279 2.5 16.9 1.0 OE1 B:GLN281 2.5 22.2 1.0 O B:HOH1535 2.6 19.0 1.0 O B:HOH1610 2.6 25.3 1.0 OE2 B:GLU216 2.6 17.9 1.0 OE1 B:GLU216 2.6 14.8 1.0 CD B:GLU216 3.0 19.0 1.0 CD B:GLN281 3.6 24.1 1.0 C B:TYR217 3.6 15.8 1.0 C B:LYS279 3.6 18.1 1.0 OH B:TYR260 3.9 17.2 1.0 N B:TYR217 4.1 16.1 1.0 NE2 B:GLN281 4.2 25.6 1.0 CA B:ALA280 4.3 15.5 1.0 OD2 B:ASP267 4.3 20.1 1.0 N B:GLN281 4.3 15.6 1.0 N B:ALA280 4.4 15.3 1.0 CG B:GLU216 4.5 14.9 1.0 C B:ALA280 4.5 16.2 1.0 N B:TYR218 4.5 17.2 1.0 CA B:TYR218 4.5 18.1 1.0 CA B:TYR217 4.5 16.5 1.0 CB B:TYR218 4.6 17.9 1.0 CA B:LYS279 4.6 15.7 1.0 OD1 B:ASP267 4.6 18.8 1.0 CB B:LYS279 4.7 17.8 1.0 N B:LYS279 4.8 17.1 1.0 CB B:GLN281 4.8 18.7 1.0 CG B:GLN281 4.8 21.1 1.0 CG B:ASP267 4.8 20.2 1.0 CZ B:TYR260 4.8 18.2 1.0 CE1 B:PHE397 4.9 15.9 1.0

Calcium binding site 3 out of 3 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 3 of Cytochrome C Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca520 b:2.1 occ:1.00 O C:LYS279 2.4 9.3 1.0 O C:TYR217 2.5 12.9 1.0 OE1 C:GLN281 2.5 17.1 1.0 O C:HOH1546 2.6 12.6 1.0 O C:HOH1543 2.6 13.6 1.0 OE2 C:GLU216 2.6 13.6 1.0 OE1 C:GLU216 2.6 13.3 1.0 CD C:GLU216 3.0 15.0 1.0 C C:LYS279 3.6 13.6 1.0 CD C:GLN281 3.6 18.3 1.0 C C:TYR217 3.6 15.7 1.0 OH C:TYR260 3.9 13.3 1.0 N C:TYR217 4.2 13.3 1.0 NE2 C:GLN281 4.2 21.7 1.0 CA C:ALA280 4.2 13.4 1.0 N C:GLN281 4.3 13.2 1.0 OD2 C:ASP267 4.3 16.2 1.0 N C:ALA280 4.4 13.4 1.0 C C:ALA280 4.4 14.2 1.0 CG C:GLU216 4.5 9.7 1.0 N C:TYR218 4.5 15.7 1.0 CA C:TYR218 4.5 14.0 1.0 CA C:TYR217 4.6 14.5 1.0 CB C:TYR218 4.6 12.1 1.0 CA C:LYS279 4.6 12.2 1.0 OD1 C:ASP267 4.6 13.7 1.0 CB C:LYS279 4.7 11.7 1.0 N C:LYS279 4.7 10.8 1.0 CB C:GLN281 4.8 17.1 1.0 CG C:GLN281 4.8 17.2 1.0 CG C:ASP267 4.8 15.1 1.0 CE1 C:PHE397 4.8 12.5 1.0 CZ C:TYR260 4.9 13.4 1.0 O C:HOH1699 4.9 29.7 1.0

O.Einsle, A.Messerschmidt, P.Stach, G.P.Bourenkov, H.D.Bartunik, R.Huber, P.M.Kroneck. Structure of Cytochrome C Nitrite Reductase. Nature V. 400 476 1999.
ISSN: ISSN 0028-0836
PubMed: 10440380
DOI: 10.1038/22802