Sodium in PDB 8dye: Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate

All present enzymatic activity of Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate:
1.3.5.1;

The structure of Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate, PDB code: 8dye was solved by P.Sharma, E.Maklashina, G.Cecchini, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.57 / 1.44
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	139.049, 69.299, 72.657, 90, 90, 90
R / Rfree (%)	15.5 / 17.3

The binding sites of Sodium atom in the Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate (pdb code 8dye). 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 of Human Sdha-SDHAF4 Assembly Intermediate, PDB code: 8dye:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate


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 Human Sdha-SDHAF4 Assembly Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na722 b:14.8 occ:1.00 O A:HOH992 2.3 16.5 1.0 O A:GLU440 2.4 12.8 1.0 O A:GLY411 2.4 15.2 1.0 O A:ASN409 2.5 15.7 1.0 O A:ALA442 2.5 16.0 1.0 O A:MET410 3.0 17.7 1.0 C A:MET410 3.3 16.3 1.0 C A:GLY411 3.3 14.2 1.0 C A:GLU440 3.4 12.2 1.0 HA A:GLU440 3.4 15.3 1.0 C A:ASN409 3.6 15.2 1.0 HA A:MET410 3.6 17.2 1.0 C A:ALA442 3.7 14.0 1.0 HA3 A:GLY412 3.7 16.7 1.0 O A:HOH993 3.7 17.9 1.0 HG3 A:GLU440 3.7 17.3 1.0 N A:GLY411 3.8 16.2 1.0 CA A:MET410 3.9 14.4 1.0 CA A:GLU440 3.9 12.7 1.0 HH A:TYR408 4.1 17.5 1.0 H A:ALA442 4.1 16.4 1.0 CA A:GLY411 4.1 16.3 1.0 N A:ALA442 4.1 13.7 1.0 HG2 A:GLU440 4.1 17.3 1.0 N A:MET410 4.2 15.5 1.0 HA A:CYS443 4.2 18.1 1.0 N A:GLY412 4.2 14.2 1.0 C A:ALA441 4.3 12.6 1.0 CG A:GLU440 4.3 14.4 1.0 HE2 A:TYR408 4.3 16.5 1.0 HB2 A:CYS443 4.3 17.8 1.0 H A:GLY411 4.3 19.5 1.0 O A:GLY439 4.4 13.0 1.0 HB3 A:ASN409 4.4 18.8 1.0 HB2 A:ASN409 4.4 18.8 1.0 CA A:GLY412 4.4 13.9 1.0 N A:ALA441 4.4 13.5 1.0 HA2 A:GLY411 4.4 19.5 1.0 CA A:ALA442 4.5 13.0 1.0 OH A:TYR408 4.5 14.6 1.0 HA A:ALA441 4.6 16.2 1.0 N A:CYS443 4.6 13.5 1.0 O A:HOH971 4.6 22.4 1.0 HD2 A:HIS447 4.6 18.1 1.0 CB A:ASN409 4.7 15.7 1.0 CA A:ALA441 4.7 13.5 1.0 O A:HOH1002 4.7 18.7 1.0 CE2 A:TYR408 4.7 13.7 1.0 CA A:ASN409 4.7 15.8 1.0 CA A:CYS443 4.8 15.1 1.0 CB A:GLU440 4.8 13.7 1.0 O A:ALA441 4.8 14.0 1.0 HA2 A:GLY412 4.8 16.7 1.0 CZ A:TYR408 4.9 13.1 1.0 HG A:CYS443 4.9 20.1 1.0 HA3 A:GLY411 4.9 19.5 1.0 H A:GLY412 5.0 17.0 1.0 CB A:CYS443 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Sdha-SDHAF4 Assembly Intermediate


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 Human Sdha-SDHAF4 Assembly Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na723 b:19.5 occ:1.00 H A:GLY73 2.1 15.2 1.0 H A:GLY70 2.3 16.0 1.0 O1P A:FAD701 2.6 13.5 1.0 O A:ALA255 2.8 12.6 1.0 HA3 A:GLY70 2.9 15.6 1.0 N A:GLY73 2.9 12.7 1.0 N A:GLY70 2.9 13.3 1.0 HB1 A:ALA255 2.9 17.1 1.0 HB3 A:ALA72 3.1 16.7 1.0 CA A:GLY70 3.2 13.0 1.0 H A:ALA72 3.2 14.9 1.0 HA3 A:GLY73 3.2 15.0 1.0 C A:GLY70 3.4 12.9 1.0 HB3 A:ALA255 3.4 17.1 1.0 CB A:ALA255 3.6 14.2 1.0 O A:GLY70 3.6 13.4 1.0 CA A:GLY73 3.6 12.5 1.0 N A:ALA72 3.7 12.4 1.0 HA3 A:GLY68 3.7 17.7 1.0 O5B A:FAD701 3.7 12.5 1.0 P A:FAD701 3.8 12.7 1.0 C A:ALA255 3.8 12.1 1.0 C A:ALA72 3.9 12.3 1.0 CB A:ALA72 3.9 13.9 1.0 N A:ALA69 4.0 14.1 1.0 C4B A:FAD701 4.0 13.7 1.0 C A:GLY68 4.0 15.0 1.0 C5B A:FAD701 4.0 14.7 1.0 O3P A:FAD701 4.0 12.7 1.0 N A:GLY71 4.0 13.1 1.0 CA A:ALA72 4.0 11.9 1.0 C A:ALA69 4.1 14.5 1.0 H A:ALA69 4.1 17.0 1.0 HA2 A:GLY70 4.1 15.6 1.0 H A:LEU74 4.2 14.8 1.0 HA2 A:GLY73 4.2 15.0 1.0 H A:GLY71 4.3 15.7 1.0 CA A:GLY68 4.3 14.8 1.0 CA A:ALA255 4.3 12.6 1.0 O A:GLY68 4.4 15.5 1.0 HB2 A:ALA255 4.4 17.1 1.0 O2P A:FAD701 4.4 13.3 1.0 HB2 A:ALA72 4.4 16.7 1.0 HA A:ALA69 4.4 17.7 1.0 CA A:ALA69 4.4 14.7 1.0 C A:GLY71 4.5 12.4 1.0 PA A:FAD701 4.5 13.3 1.0 HB1 A:ALA72 4.6 16.7 1.0 O A:HOH891 4.6 12.8 1.0 HA2 A:GLY68 4.6 17.7 1.0 HA A:ALA255 4.7 15.1 1.0 C A:GLY73 4.7 12.1 1.0 N A:LEU74 4.7 12.3 1.0 O4B A:FAD701 4.8 13.1 1.0 O2A A:FAD701 4.9 13.9 1.0 CA A:GLY71 4.9 13.4 1.0 N A:THR256 4.9 12.2 1.0 H A:GLY257 5.0 13.9 1.0 HA A:THR256 5.0 14.2 1.0 HA A:ALA72 5.0 14.3 1.0

P.Sharma, E.Maklashina, G.Cecchini, T.M.Iverson. Crystal Structure of Human Sdha-ADHAF4 Assembly Intermediate To Be Published.