Sodium in PDB 8qk0: Crystal Structure of Cytochrome Domain 3 From Pgca

The structure of Crystal Structure of Cytochrome Domain 3 From Pgca, PDB code: 8qk0 was solved by B.W.Nash, M.J.Edwards, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.28 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.564, 55.033, 37.456, 90, 99.3, 90
R / Rfree (%)	22.1 / 26.3

The structure of Crystal Structure of Cytochrome Domain 3 From Pgca also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Cytochrome Domain 3 From Pgca (pdb code 8qk0). 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 Domain 3 From Pgca, PDB code: 8qk0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Cytochrome Domain 3 From Pgca


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 Domain 3 From Pgca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:15.0 occ:1.00 O A:ALA16 2.2 21.1 1.0 O A:SER27 2.2 17.7 1.0 OD2 A:ASP25 2.4 16.4 1.0 O A:HIS19 2.4 12.1 1.0 OD1 A:ASP25 2.8 18.1 1.0 CG A:ASP25 2.9 19.9 1.0 C A:ALA16 3.2 18.4 1.0 C A:SER27 3.4 22.1 1.0 C A:HIS19 3.6 17.5 1.0 CA A:ALA16 3.7 16.6 1.0 CB A:ALA16 4.0 14.4 1.0 OG A:SER27 4.2 39.1 1.0 OH A:TYR11 4.2 14.3 1.0 N A:HIS19 4.3 13.9 1.0 N A:GLY28 4.3 24.5 1.0 CA A:GLY28 4.3 24.9 1.0 CB A:ASP25 4.4 16.6 1.0 CA A:SER27 4.4 22.8 1.0 N A:SER17 4.4 19.0 1.0 N A:SER27 4.4 25.4 1.0 N A:ARG20 4.5 12.7 1.0 C A:CYS18 4.5 16.2 1.0 CA A:ARG20 4.5 17.9 1.0 CA A:HIS19 4.6 14.6 1.0 C A:SER17 4.6 20.1 1.0 N A:CYS18 4.6 15.8 1.0 CB A:SER27 4.7 29.8 1.0 O A:CYS18 4.7 15.5 1.0 CA A:SER17 4.8 20.4 1.0 O A:SER17 4.9 20.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Cytochrome Domain 3 From Pgca


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 Domain 3 From Pgca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:17.6 occ:1.00 O A:HOH232 2.2 22.9 1.0 O A:ASP41 2.3 11.2 1.0 O A:PHE44 2.5 15.7 1.0 O A:HOH218 2.6 25.6 1.0 O A:HOH262 2.9 23.3 1.0 C A:ASP41 3.3 14.8 1.0 CA A:ASP41 3.6 14.8 1.0 C A:PHE44 3.7 16.9 1.0 CB A:ASP41 4.0 16.0 1.0 O A:HOH258 4.1 26.0 1.0 CA A:THR45 4.1 20.2 1.0 N A:THR45 4.4 17.9 1.0 OD1 A:ASP41 4.4 16.4 1.0 CG A:ASP41 4.5 15.4 1.0 N A:GLY42 4.5 16.3 1.0 OG1 A:THR45 4.5 16.0 1.0 CA A:PHE44 4.8 14.7 1.0 N A:PHE44 4.9 17.2 1.0 CB A:THR45 4.9 14.7 1.0 CA A:GLY42 5.0 15.4 1.0 N A:ASP41 5.0 14.0 1.0 O A:ILE40 5.0 15.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Cytochrome Domain 3 From Pgca


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 Domain 3 From Pgca within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:18.2 occ:1.00 O C:SER27 2.1 19.0 1.0 O C:HIS19 2.3 14.6 1.0 O C:ALA16 2.3 15.2 1.0 O C:HOH216 2.3 23.6 1.0 OD2 C:ASP25 2.3 17.5 1.0 OD1 C:ASP25 2.8 19.2 1.0 CG C:ASP25 2.9 20.3 1.0 C C:ALA16 3.3 16.9 1.0 C C:SER27 3.4 21.4 1.0 C C:HIS19 3.5 17.2 1.0 CA C:ALA16 3.8 18.3 1.0 OH C:TYR11 4.1 16.7 1.0 CB C:ALA16 4.2 12.5 1.0 CA C:GLY28 4.2 22.0 1.0 N C:GLY28 4.2 20.3 1.0 N C:HIS19 4.2 13.7 1.0 CB C:ASP25 4.3 18.6 1.0 CA C:SER27 4.4 24.1 1.0 N C:ARG20 4.4 12.6 1.0 CA C:HIS19 4.5 15.5 1.0 CA C:ARG20 4.5 17.4 1.0 N C:SER27 4.5 17.9 1.0 C C:CYS18 4.5 16.6 1.0 N C:SER17 4.5 20.5 1.0 C C:SER17 4.6 21.1 1.0 CB C:SER27 4.7 16.4 1.0 N C:CYS18 4.7 17.8 1.0 O C:SER17 4.7 21.6 1.0 O C:CYS18 4.8 16.4 1.0 CA C:SER17 4.9 20.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Cytochrome Domain 3 From Pgca


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 Domain 3 From Pgca within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:14.3 occ:1.00 O A:HOH246 1.9 16.8 1.0 O C:ASP41 2.3 11.6 1.0 O A:SER13 2.3 16.9 1.0 O C:PHE44 2.5 15.1 1.0 O C:HOH258 3.0 24.8 1.0 C C:ASP41 3.2 12.3 1.0 C A:SER13 3.3 19.6 1.0 CA A:SER13 3.5 15.4 1.0 CA C:ASP41 3.6 15.8 1.0 C C:PHE44 3.7 17.5 1.0 CB A:SER13 3.8 17.0 1.0 CB C:ASP41 3.8 15.8 1.0 O A:HOH254 3.9 23.2 1.0 CA C:THR45 4.3 19.4 1.0 N C:THR45 4.4 15.4 1.0 N C:GLY42 4.4 14.7 1.0 OD1 C:ASP41 4.5 15.8 1.0 CG C:ASP41 4.5 17.1 1.0 O A:HOH212 4.5 23.4 1.0 N A:ARG14 4.5 17.0 1.0 OG1 C:THR45 4.7 23.6 1.0 CA C:PHE44 4.8 15.8 1.0 N C:PHE44 4.8 19.6 1.0 CD1 C:LEU61 4.9 17.8 1.0 N A:SER13 4.9 15.8 1.0 CA C:GLY42 4.9 15.2 1.0 N C:ASP41 5.0 14.2 1.0 O A:ASP12 5.0 12.8 1.0 O C:ILE40 5.0 13.5 1.0 OG A:SER13 5.0 27.1 1.0

B.W.Nash, T.M.Fernandes, J.A.J.Burton, L.Morgado, J.H.Van Wonderen, D.A.Svistunenko, M.J.Edwards, C.A.Salgueiro, J.N.Butt, T.A.Clarke. Tethered Heme Domains in A Triheme Cytochrome Allow For Increased Electron Transport Distances. Protein Sci. V. 33 E5200 2024.
ISSN: ESSN 1469-896X
PubMed: 39470321
DOI: 10.1002/PRO.5200