Sodium in PDB 4l1f: Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation

The structure of Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation, PDB code: 4l1f was solved by A.M.Mowafy, N.P.Chowdhury, J.Demmer, V.Upadhyay, S.Kolzer, E.Jayamani, J.Kahnt, U.Demmer, U.Ermler, W.Buckel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.13 / 1.79
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.100, 141.400, 64.100, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.3

The binding sites of Sodium atom in the Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation (pdb code 4l1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation, PDB code: 4l1f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:31.4 occ:1.00 O A:GLY131 2.8 14.9 1.0 OG1 A:THR126 2.8 11.3 1.0 N4P A:COS402 2.9 23.6 1.0 C A:GLY131 3.6 12.4 1.0 C6P A:COS402 3.7 26.7 1.0 C5P A:COS402 3.8 26.3 1.0 C2P A:COS402 3.8 30.7 1.0 CD2 A:LEU125 3.8 13.4 1.0 CB A:THR126 3.9 10.5 1.0 C3P A:COS402 3.9 30.0 1.0 CA A:GLY131 4.0 13.1 1.0 CA A:THR126 4.0 10.6 1.0 CB A:ALA134 4.0 17.5 1.0 O A:ALA130 4.0 14.8 1.0 O4' A:FAD401 4.1 15.7 1.0 CG A:LEU125 4.1 13.0 1.0 N A:THR126 4.2 10.7 1.0 CG2 A:THR126 4.3 11.6 1.0 O2' A:FAD401 4.4 19.8 1.0 CA A:ALA134 4.6 18.5 1.0 CB A:LEU125 4.7 11.5 1.0 C A:ALA130 4.7 15.8 1.0 C A:LEU125 4.7 11.5 1.0 N A:GLY131 4.8 12.7 1.0 N A:THR132 4.8 10.9 1.0 O2 A:FAD401 4.9 14.4 1.0 C7P A:COS402 4.9 22.9 1.0 N1 A:FAD401 4.9 13.9 1.0 O5P A:COS402 5.0 22.0 1.0 C3' A:FAD401 5.0 13.6 1.0

Sodium binding site 2 out of 3 in the Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:31.9 occ:1.00 O A:TYR347 2.6 13.4 1.0 OE1 A:GLU350 2.8 16.3 1.0 N A:ARG351 3.3 9.5 1.0 CB A:ARG351 3.3 12.0 1.0 CA A:PRO348 3.5 15.8 1.0 CD A:GLU350 3.6 15.7 1.0 CG A:GLU350 3.6 12.6 1.0 C A:PRO348 3.6 13.4 1.0 O A:PRO348 3.6 14.5 1.0 C A:TYR347 3.7 14.3 1.0 O A:VAL345 3.8 18.4 1.0 CA A:ARG351 3.8 10.2 1.0 N A:PRO348 4.1 16.9 1.0 N A:GLU350 4.1 10.0 1.0 C A:GLU350 4.2 9.5 1.0 CA A:VAL345 4.2 17.4 1.0 C A:VAL345 4.3 18.4 1.0 N A:ALA349 4.3 12.5 1.0 O A:HOH503 4.3 11.3 1.0 CA A:GLU350 4.5 11.0 1.0 CB A:GLU350 4.6 11.8 1.0 CG A:ARG351 4.6 13.5 1.0 O A:THR344 4.6 12.7 1.0 OE2 A:GLU350 4.7 16.7 1.0 CD A:ARG351 4.8 15.7 1.0 C A:ALA349 4.8 9.4 1.0 CB A:PRO348 4.8 20.1 1.0 NE A:ARG351 4.8 17.3 1.0 CB A:VAL345 5.0 21.7 1.0 N A:TYR347 5.0 16.1 1.0 CA A:TYR347 5.0 16.1 1.0

Sodium binding site 3 out of 3 in the Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Electron Transferring Flavoprotein of Acidaminococcus Fermentans: Towards A Mechanism of Flavin-Based Electron Bifurcation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:42.8 occ:1.00 O B:HOH793 4.0 41.3 1.0 CB B:PHE3 4.0 20.4 1.0 O B:PHE3 4.0 22.7 1.0 OD1 B:ASN4 4.0 22.1 1.0 C B:PHE3 4.2 20.7 1.0 N B:ASN4 4.6 18.6 1.0 O B:HOH712 4.6 40.1 1.0 CG B:ASN4 4.7 21.0 1.0 CA B:PHE3 4.7 19.9 1.0 CA B:ASN4 4.8 18.8 1.0

N.P.Chowdhury, A.M.Mowafy, J.K.Demmer, V.Upadhyay, S.Koelzer, E.Jayamani, J.Kahnt, M.Hornung, U.Demmer, U.Ermler, W.Buckel. Studies on the Mechanism of Electron Bifurcation Catalyzed By Electron Transferring Flavoprotein (Etf) and Butyryl-Coa Dehydrogenase (Bcd) of Acidaminococcus Fermentans. J.Biol.Chem. V. 289 5145 2014.
ISSN: ISSN 0021-9258
PubMed: 24379410
DOI: 10.1074/JBC.M113.521013