Sodium in PDB 6smo: Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide

The structure of Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide, PDB code: 6smo was solved by A.Braeuer, Q.Zhou, G.L.C.Grammbitter, M.Schmalhofer, M.Ruehl, V.R.I.Kaila, H.Bode, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	107.650, 107.650, 201.330, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.5

The binding sites of Sodium atom in the Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide (pdb code 6smo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide, PDB code: 6smo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:22.8 occ:1.00 OH D:TYR81 2.6 34.8 1.0 OD1 D:ASN171 2.9 34.7 1.0 O D:ILE112 3.0 33.3 1.0 O D:PHE152 3.6 37.3 1.0 CG D:ASN171 3.6 34.1 1.0 CZ D:TYR81 3.8 34.9 1.0 N D:ALA156 3.8 34.2 1.0 C D:ILE112 3.8 33.7 1.0 CB D:ALA156 4.0 33.0 1.0 CA D:SER153 4.0 38.8 1.0 CG2 D:ILE112 4.0 34.0 1.0 CB D:ASN171 4.1 33.8 1.0 CB D:ALA155 4.1 37.4 1.0 CB D:ILE112 4.1 33.9 1.0 N D:ALA155 4.3 38.1 1.0 CE1 D:TYR81 4.4 34.8 1.0 CA D:ALA156 4.5 33.3 1.0 O D:ALA113 4.5 33.3 1.0 C D:SER153 4.5 39.4 1.0 CG2 D:THR114 4.5 34.1 1.0 ND2 D:ASN171 4.5 34.3 1.0 CA D:ALA155 4.5 37.3 1.0 N D:SER154 4.5 39.4 1.0 CA D:ILE112 4.6 33.8 1.0 C D:PHE152 4.6 38.1 1.0 C D:ALA113 4.6 33.7 1.0 C D:ALA155 4.6 36.1 1.0 N D:ALA113 4.6 33.4 1.0 N D:SER153 4.8 38.6 1.0 CB D:SER153 4.8 39.0 1.0 CE2 D:TYR81 4.8 34.9 1.0 CA D:ASN171 4.8 33.3 1.0 CA D:ALA113 4.8 33.5 1.0 CB D:THR114 4.9 34.0 1.0

Sodium binding site 2 out of 2 in the Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Antde:Antf (Apo): Type II Pks Acyl-Carrier Protein in Complex with Its Ketosynthase Bound to the Hexaketide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:38.2 occ:1.00 O D:ILE343 2.3 34.7 1.0 O D:ALA340 2.5 37.2 1.0 O D:PHE341 3.3 39.5 1.0 C D:ILE343 3.4 34.8 1.0 N D:ILE343 3.6 36.7 1.0 C D:PHE341 3.6 38.8 1.0 N D:ASP392 3.6 38.9 1.0 C D:ALA340 3.7 37.5 1.0 CD1 D:ILE345 3.8 32.4 1.0 CA D:ILE343 3.9 35.8 1.0 CA D:PHE341 3.9 38.4 1.0 CB D:LEU391 3.9 40.0 1.0 O D:ASP392 4.0 38.0 1.0 CG1 D:ILE345 4.1 32.0 1.0 CB D:ILE343 4.1 35.9 1.0 CB D:ASP392 4.2 39.2 1.0 N D:PHE341 4.2 37.9 1.0 CD2 D:LEU391 4.2 40.7 1.0 C D:GLY342 4.3 37.9 1.0 N D:GLY342 4.3 38.8 1.0 CA D:ASP392 4.3 38.6 1.0 CA D:LEU391 4.4 39.9 1.0 CG D:LEU391 4.4 40.2 1.0 C D:LEU391 4.4 39.2 1.0 CD1 D:LEU391 4.5 39.8 1.0 N D:PRO344 4.6 34.0 1.0 C D:ASP392 4.6 37.6 1.0 CG2 D:ILE343 4.8 35.7 1.0 CA D:GLY342 4.9 38.6 1.0 CA D:ALA340 4.9 37.6 1.0 O D:GLY342 4.9 37.9 1.0 CA D:PRO344 5.0 33.5 1.0

A.Braeuer, Q.Zhou, G.L.C.Grammbitter, M.Schmalhofer, M.Ruehl, V.R.I.Kaila, H.Bode, M.Groll. Structural Snapshots of the Minimal Pks System Responsible For Octaketide Biosynthesis To Be Published.