Sodium in PDB 4eie: Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002

The structure of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002, PDB code: 4eie was solved by S.Krzywda, W.Bialek, P.Zatwarnicki, M.Jaskolski, A.Szczepaniak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.03
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.130, 56.130, 49.640, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.3

The structure of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 (pdb code 4eie). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002, PDB code: 4eie:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:23.5 occ:0.50 H2 A:HOH297 2.3 27.2 0.0 H2 A:HOH306 2.6 24.9 0.0 O A:HOH306 2.7 25.2 0.5 O A:HOH297 3.0 27.3 0.8 H1 A:HOH306 3.4 24.9 0.0 H1 A:HOH297 3.4 27.2 0.0 OD2 A:ASP63 3.8 19.8 0.4 HZ2 A:LYS64 4.1 18.2 0.0 OD1 A:ASP63 4.2 17.6 0.4 O A:HOH225 4.3 17.4 1.0 HZ3 A:LYS64 4.3 18.2 0.0 CG A:ASP63 4.5 15.8 0.4 HE2 A:LYS64 4.5 17.9 0.5 H2 A:HOH281 4.6 28.2 0.0 NZ A:LYS64 4.6 18.2 0.5 H1 A:HOH311 4.8 23.7 0.0 O A:HOH261 4.8 13.8 0.6 HB2 A:ASP63 4.8 12.7 0.6 H1 A:HOH225 4.9 17.2 0.0 H2 A:HOH225 5.0 17.2 0.0 H2 A:HOH261 5.0 13.7 0.0

Sodium binding site 2 out of 4 in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:22.4 occ:0.65 H1 A:HOH226 1.8 20.5 0.0 OE1 A:GLN8 2.4 22.4 0.8 OE1 A:GLU11 2.4 17.9 0.8 O A:HOH226 2.5 20.6 1.0 H2 A:HOH226 2.6 20.5 0.0 CD A:GLN8 3.3 20.4 0.8 HE22 A:GLN8 3.3 25.8 0.0 HB2 A:GLU11 3.5 13.1 1.0 CD A:GLU11 3.6 15.9 0.8 HA A:GLN8 3.6 13.2 1.0 NE2 A:GLN8 3.6 25.2 0.8 HB3 A:GLU11 3.8 13.0 1.0 CB A:GLU11 4.0 13.8 1.0 HB3 A:GLN8 4.3 14.2 1.0 CG A:GLU11 4.4 15.1 1.0 HE21 A:GLN8 4.5 25.8 0.0 OE2 A:GLU11 4.5 19.8 0.8 CA A:GLN8 4.5 13.4 1.0 CG A:GLN8 4.5 17.1 1.0 O A:GLN8 4.6 12.3 1.0 CB A:GLN8 4.6 15.1 1.0 HG2 A:GLU11 4.9 14.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:16.8 occ:0.65 H1 A:HOH290 2.1 24.3 0.0 O A:HOH240 2.4 24.4 1.0 O A:VAL25 2.4 12.8 1.0 O A:HOH290 2.5 24.3 1.0 H2 A:HOH240 2.7 24.6 0.0 H1 A:HOH240 3.1 24.6 0.0 H2 A:HOH290 3.2 24.3 0.0 C A:VAL25 3.4 10.5 1.0 H1 A:HOH302 3.6 26.5 0.0 HA A:ARG26 3.8 11.8 1.0 H A:ARG27 3.9 13.6 1.0 HA A:VAL25 4.0 9.6 1.0 O A:ILE24 4.2 9.7 1.0 CA A:VAL25 4.3 9.6 1.0 N A:ARG26 4.3 11.3 1.0 O A:HOH302 4.5 26.2 0.5 CA A:ARG26 4.5 11.9 1.0 HB2 A:ARG27 4.6 15.0 0.8 N A:ARG27 4.6 14.1 1.0 O A:HOH289 4.7 19.8 1.0 H2 A:HOH289 4.8 19.7 0.0 C A:ILE24 4.9 8.8 1.0 N A:VAL25 5.0 9.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Cytochrome C6C From Synechococcus Sp. Pcc 7002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:17.1 occ:0.65 H1 A:HOH236 1.9 20.4 0.0 H1 A:HOH281 2.2 28.2 0.0 O A:ASP63 2.4 14.5 1.0 O A:HOH281 2.5 28.4 0.8 O A:HOH241 2.6 28.6 1.0 H2 A:HOH236 2.6 20.4 0.0 O A:HOH236 2.6 20.2 1.0 H2 A:HOH241 2.9 28.5 0.0 H2 A:HOH281 3.1 28.2 0.0 HB3 A:ASP63 3.3 12.7 0.6 H1 A:HOH241 3.4 28.5 0.0 HB2 A:ASP63 3.5 12.3 0.4 C A:ASP63 3.6 12.2 1.0 O A:HOH276 3.8 18.6 0.5 H2 A:HOH276 3.9 19.4 0.0 HA A:LYS64 4.1 12.7 1.0 CB A:ASP63 4.2 13.3 0.6 CB A:ASP63 4.2 12.9 0.4 H1 A:HOH266 4.2 25.6 0.0 CA A:ASP63 4.3 11.3 1.0 HA A:ASP63 4.3 11.8 1.0 CG A:ASP63 4.5 15.8 0.4 HB2 A:ASP63 4.5 12.7 0.6 N A:LYS64 4.6 11.8 1.0 OD2 A:ASP63 4.6 19.8 0.4 H1 A:HOH276 4.7 19.4 0.0 CA A:LYS64 4.8 12.8 1.0

W.Bialek, S.Krzywda, P.Zatwarnicki, M.Jaskolski, A.Szczepaniak. Cytochrome C6 and C6C From Synechococcus Sp. Pcc 7002 - Structure and Function. To Be Published.