Sodium in PDB 5v85: The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid)

The structure of The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid), PDB code: 5v85 was solved by M.G.Cuypers, M.Ericson, C.Subramanian, S.W.White, C.O.Rock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.89 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.899, 96.899, 159.921, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.8

The binding sites of Sodium atom in the The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid) (pdb code 5v85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid), PDB code: 5v85:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:66.2 occ:1.00 O A:HOH584 3.4 57.0 1.0 O A:HOH567 3.8 36.7 1.0 CD A:ARG87 4.0 70.8 1.0 OG A:SER84 4.1 24.9 1.0 CB A:SER84 4.6 24.8 1.0 CG A:ARG87 4.7 58.5 1.0 NE A:ARG87 5.0 83.4 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Protein of Degv Family COG1307 From Ruminococcus Gnavus Atcc 29149 (Alternative Refinement of Pdb 3JR7 with Vaccenic Acid) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:51.2 occ:1.00 N B:CYS77 3.5 24.8 1.0 O B:HOH444 3.7 45.3 1.0 CB B:CYS77 3.9 33.6 1.0 CA B:SER76 4.2 35.3 1.0 OG B:SER76 4.3 56.4 1.0 CA B:CYS77 4.3 32.6 1.0 C B:SER76 4.4 34.0 1.0 CD B:LYS188 4.6 53.6 1.0 O B:THR75 4.8 41.2 1.0 CB B:SER76 4.8 39.1 1.0 CE B:LYS188 5.0 65.3 1.0

M.G.Cuypers, M.Ericson, C.Subramanian, T.C.Broussard, D.J.Miller, S.W.White, C.O.Rock. The Crystal Structure of the Staphylococcus Aureus Fatty Acid Kinase (Fak) B1 Protein Loaded with Palmitic Acid to 1.83 Angstroem Resolution J.Biol.Chem. 2018.
ISSN: ESSN 1083-351X