Sodium in PDB 2czs: Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2

The structure of Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2, PDB code: 2czs was solved by D.Heitmann, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.12 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.645, 55.679, 39.637, 90.00, 105.91, 90.00
R / Rfree (%)	22.1 / 27.2

The structure of Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2 (pdb code 2czs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2, PDB code: 2czs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:22.8 occ:1.00 OD2 A:ASP56 2.9 19.9 1.0 O A:HOH511 3.1 36.7 1.0 O A:HOH558 3.1 46.3 1.0 N A:PHE89 3.5 21.0 1.0 NE A:ARG86 3.6 32.3 1.0 CB A:ARG86 3.7 23.1 1.0 CG A:ASP56 3.8 18.8 1.0 CB A:PHE89 3.9 22.4 1.0 CB A:LYS52 3.9 25.6 1.0 OD1 A:ASP56 3.9 19.4 1.0 C A:LEU88 4.0 21.1 1.0 N A:LEU88 4.0 18.5 1.0 CA A:ARG86 4.0 20.7 1.0 C A:ARG86 4.1 20.5 1.0 CB A:LEU88 4.1 19.4 1.0 CA A:PHE89 4.1 22.4 1.0 NH2 A:ARG86 4.2 33.8 1.0 CG A:ARG86 4.2 24.6 1.0 CA A:LEU88 4.2 20.2 1.0 O A:ARG86 4.2 20.4 1.0 CZ A:ARG86 4.4 33.0 1.0 O A:LYS52 4.5 22.3 1.0 C A:LYS52 4.5 24.2 1.0 CD A:ARG86 4.5 29.6 1.0 N A:CYS87 4.6 19.2 1.0 CD A:LYS52 4.7 32.3 1.0 O A:LEU88 4.7 23.2 1.0 CD2 A:LEU53 4.8 25.2 1.0 N A:LEU53 4.8 24.1 1.0 CA A:LYS52 4.8 24.6 1.0 CG A:LYS52 4.9 29.4 1.0 O A:HOH552 4.9 37.0 1.0 C A:CYS87 5.0 18.4 1.0 CG A:PHE89 5.0 24.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of the Diheme C-Type Cytochrome DHC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:19.7 occ:1.00 OD2 B:ASP56 2.8 20.4 1.0 O B:HOH558 3.1 37.6 1.0 N B:PHE89 3.4 19.7 1.0 CB B:ARG86 3.7 21.4 1.0 CG B:ASP56 3.7 19.7 1.0 NE B:ARG86 3.8 33.1 1.0 OD1 B:ASP56 3.8 19.3 1.0 CB B:PHE89 3.9 20.8 1.0 CB B:LYS52 3.9 23.6 1.0 N B:LEU88 3.9 17.5 1.0 CA B:ARG86 3.9 19.8 1.0 C B:LEU88 4.0 19.7 1.0 C B:ARG86 4.0 20.1 1.0 CB B:LEU88 4.1 18.9 1.0 CA B:PHE89 4.1 19.8 1.0 O B:ARG86 4.1 20.4 1.0 CA B:LEU88 4.2 19.3 1.0 CG B:ARG86 4.2 24.0 1.0 NH2 B:ARG86 4.4 39.3 1.0 N B:CYS87 4.5 19.0 1.0 C B:LYS52 4.5 21.9 1.0 O B:LYS52 4.5 20.6 1.0 CD2 B:LEU53 4.5 25.9 1.0 CZ B:ARG86 4.6 37.4 1.0 CD B:ARG86 4.6 29.0 1.0 CD B:LYS52 4.7 31.2 1.0 N B:LEU53 4.8 21.8 1.0 O B:LEU88 4.8 21.3 1.0 C B:CYS87 4.9 18.5 1.0 CA B:LYS52 4.9 22.5 1.0 CG B:LYS52 4.9 26.2 1.0

D.Heitmann, O.Einsle. Structural and Biochemical Characterization of DHC2, A Novel Diheme Cytochrome C From Geobacter Sulfurreducens Biochemistry V. 44 12411 2005.
ISSN: ISSN 0006-2960
PubMed: 16156654
DOI: 10.1021/BI0509999