Sodium in PDB 3ic9: The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H.

The structure of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H., PDB code: 3ic9 was solved by K.Tan, E.Rakowski, S.Clancy, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.90 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.497, 246.353, 73.664, 90.00, 90.20, 90.00
R / Rfree (%)	18.6 / 23.3

The binding sites of Sodium atom in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. (pdb code 3ic9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H., PDB code: 3ic9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na491 b:36.7 occ:1.00 O A:THR314 2.4 28.6 1.0 O A:GLY309 2.5 25.3 1.0 OD1 A:ASN312 2.5 23.9 1.0 OD2 A:ASP324 2.5 23.1 1.0 O A:HOH633 2.7 26.1 1.0 CG A:ASN312 3.1 25.6 1.0 ND2 A:ASN312 3.2 25.5 1.0 C A:GLY309 3.3 25.8 1.0 CG A:ASP324 3.5 24.1 1.0 C A:THR314 3.5 28.9 1.0 CA A:GLY309 3.8 25.8 1.0 N A:GLY309 3.8 25.7 1.0 OD1 A:ASP324 3.9 23.8 1.0 O A:LEU315 4.0 27.3 1.0 N A:THR314 4.1 28.6 1.0 CA A:THR314 4.3 29.3 1.0 N A:ASP310 4.4 26.1 1.0 CB A:THR314 4.4 30.1 1.0 C A:LEU315 4.4 27.3 1.0 N A:LEU315 4.5 28.3 1.0 CB A:ASN312 4.5 25.6 1.0 CB A:ASP324 4.7 24.4 1.0 CB A:LEU315 4.8 27.4 1.0 CA A:ASP310 4.8 26.1 1.0 CA A:LEU315 4.8 27.6 1.0 C A:ALA308 4.8 25.9 1.0 N A:ASN312 4.9 25.8 1.0 C A:ASN312 5.0 26.3 1.0 CA A:ASN312 5.0 25.7 1.0

Sodium binding site 2 out of 4 in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na491 b:34.3 occ:1.00 OD1 B:ASN312 2.3 27.7 1.0 O B:THR314 2.3 29.7 1.0 O B:HOH821 2.4 33.8 1.0 O B:GLY309 2.5 25.8 1.0 OD2 B:ASP324 2.5 27.2 1.0 O B:HOH610 2.6 25.6 1.0 CG B:ASN312 3.0 27.2 1.0 ND2 B:ASN312 3.2 25.1 1.0 C B:GLY309 3.3 26.2 1.0 C B:THR314 3.4 28.4 1.0 CG B:ASP324 3.6 28.7 1.0 N B:GLY309 3.8 25.4 1.0 CA B:GLY309 3.9 25.8 1.0 N B:THR314 3.9 28.5 1.0 O B:LEU315 4.0 26.8 1.0 OD1 B:ASP324 4.0 27.9 1.0 CA B:THR314 4.1 28.6 1.0 CB B:THR314 4.3 28.7 1.0 N B:ASP310 4.3 26.7 1.0 C B:LEU315 4.4 27.2 1.0 CB B:ASN312 4.5 26.5 1.0 N B:LEU315 4.5 27.5 1.0 CB B:LEU315 4.5 27.3 1.0 CA B:LEU315 4.7 27.3 1.0 N B:ASN312 4.8 26.3 1.0 CB B:ASP324 4.8 28.1 1.0 CA B:ASP310 4.8 27.0 1.0 C B:ALA308 4.8 25.7 1.0 N B:ASN313 4.9 26.9 1.0 C B:ASN312 4.9 27.0 1.0 CA B:ASN312 4.9 26.7 1.0

Sodium binding site 3 out of 4 in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na491 b:33.6 occ:1.00 O C:HOH848 2.4 26.1 1.0 OD1 C:ASN312 2.4 25.2 1.0 O C:THR314 2.4 25.3 1.0 OD2 C:ASP324 2.5 25.0 1.0 O C:GLY309 2.8 26.3 1.0 CG C:ASN312 3.0 27.0 1.0 ND2 C:ASN312 3.1 26.3 1.0 C C:THR314 3.5 26.4 1.0 C C:GLY309 3.5 26.4 1.0 CG C:ASP324 3.6 25.5 1.0 N C:GLY309 3.9 26.0 1.0 CA C:GLY309 4.0 26.2 1.0 OD1 C:ASP324 4.0 28.0 1.0 N C:THR314 4.0 27.6 1.0 O C:LEU315 4.1 25.2 1.0 CA C:THR314 4.2 27.4 1.0 CB C:THR314 4.3 27.6 1.0 C C:LEU315 4.4 25.4 1.0 CB C:ASN312 4.5 26.0 1.0 N C:LEU315 4.5 25.8 1.0 N C:ASP310 4.5 26.4 1.0 CB C:LEU315 4.6 25.7 1.0 O C:HOH662 4.7 37.5 1.0 CA C:LEU315 4.7 25.7 1.0 CB C:ASP324 4.8 25.0 1.0 C C:ALA308 4.9 26.1 1.0 N C:ASN312 4.9 25.7 1.0 C C:ASN312 4.9 26.6 1.0 CA C:ASN312 5.0 26.5 1.0 CA C:ASP310 5.0 25.8 1.0 N C:ASN313 5.0 27.3 1.0

Sodium binding site 4 out of 4 in the The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na491 b:29.9 occ:1.00 O D:HOH925 2.3 34.7 1.0 O D:THR314 2.3 26.3 1.0 OD1 D:ASN312 2.4 23.6 1.0 O D:HOH697 2.4 30.6 1.0 OD2 D:ASP324 2.5 25.4 1.0 O D:GLY309 2.5 23.5 1.0 CG D:ASN312 3.1 25.5 1.0 ND2 D:ASN312 3.2 24.7 1.0 C D:GLY309 3.4 24.2 1.0 C D:THR314 3.4 27.2 1.0 CG D:ASP324 3.6 26.9 1.0 N D:GLY309 3.9 23.9 1.0 CA D:GLY309 3.9 23.4 1.0 O D:LEU315 3.9 26.5 1.0 OD1 D:ASP324 4.0 27.4 1.0 N D:THR314 4.1 27.4 1.0 O D:HOH677 4.2 43.6 1.0 CA D:THR314 4.2 28.1 1.0 C D:LEU315 4.3 26.2 1.0 N D:ASP310 4.3 25.0 1.0 CB D:THR314 4.4 28.5 1.0 N D:LEU315 4.4 27.4 1.0 CB D:ASN312 4.5 24.7 1.0 CB D:LEU315 4.5 26.5 1.0 CA D:LEU315 4.7 26.8 1.0 CA D:ASP310 4.7 25.3 1.0 CB D:ASP324 4.8 26.2 1.0 N D:ASN312 4.8 24.9 1.0 C D:ALA308 4.9 24.2 1.0 CA D:ASN312 4.9 25.2 1.0 N D:ASN313 4.9 26.4 1.0 C D:ASN312 4.9 25.4 1.0

K.Tan, E.Rakowski, S.Clancy, A.Joachimiak. The Structure of Dihydrolipoamide Dehydrogenase From Colwellia Psychrerythraea 34H. To Be Published.