Sodium in PDB 5ups: Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand

The structure of Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand, PDB code: 5ups was solved by J.Osipiuk, C.Hatzos-Skintges, M.Endres, G.Babnigg, J.D.Rudolf, C.-Y.Chang, M.Ma, B.Shen, G.N.Phillips Jr., A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), Enzyme Discovery For Natural Productbiosynthesis (Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.669, 162.669, 114.135, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 18.8

The binding sites of Sodium atom in the Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand (pdb code 5ups). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand, PDB code: 5ups:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:41.3 occ:1.00 O A:VAL433 2.3 34.9 1.0 O A:HOH914 2.4 45.1 1.0 O A:HIS430 2.4 38.5 1.0 O A:GLU428 2.4 34.7 1.0 O A:HOH1081 2.4 57.8 1.0 O A:HOH1083 2.5 46.1 1.0 C A:HIS430 3.4 38.5 1.0 C A:VAL433 3.4 34.3 1.0 C A:GLU428 3.5 33.9 1.0 N A:VAL433 4.0 33.4 1.0 CA A:PRO431 4.1 39.3 1.0 CA A:VAL433 4.1 35.5 1.0 N A:PRO431 4.2 39.2 1.0 C A:GLN429 4.2 37.2 1.0 CA A:GLU428 4.2 33.5 1.0 N A:HIS430 4.2 35.2 1.0 C A:PRO431 4.2 37.8 1.0 O A:PRO431 4.2 38.8 1.0 CB A:VAL433 4.3 35.8 1.0 O A:GLN429 4.4 36.3 1.0 CA A:HIS430 4.4 36.9 1.0 N A:ARG434 4.5 36.5 1.0 N A:GLN429 4.5 34.1 1.0 OE2 A:GLU457 4.5 47.9 1.0 CA A:GLN429 4.7 39.3 1.0 CB A:GLU428 4.8 34.2 1.0 CA A:ARG434 4.8 37.3 1.0 N A:ALA432 4.9 35.7 1.0 CG1 A:VAL433 5.0 36.1 1.0

Sodium binding site 2 out of 2 in the Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Acyl-Coa Synthetase PTMA2 From Streptomyces Platensis in Complex with SBNP663 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:43.5 occ:1.00 O B:VAL433 2.3 38.5 1.0 O B:HOH998 2.3 52.5 1.0 O B:HIS430 2.3 43.4 1.0 O B:GLU428 2.4 39.6 1.0 O B:HOH742 2.5 43.3 1.0 O B:HOH971 2.5 45.6 1.0 C B:HIS430 3.4 42.2 1.0 C B:VAL433 3.4 39.2 1.0 C B:GLU428 3.5 38.2 1.0 N B:VAL433 3.9 42.1 1.0 C B:GLN429 4.0 40.7 1.0 N B:HIS430 4.0 39.5 1.0 O B:PRO431 4.0 46.3 1.0 CA B:VAL433 4.0 39.1 1.0 CA B:PRO431 4.1 44.2 1.0 C B:PRO431 4.1 41.8 1.0 N B:PRO431 4.2 42.6 1.0 CB B:VAL433 4.2 39.8 1.0 CA B:GLU428 4.3 38.3 1.0 O B:GLN429 4.3 43.8 1.0 CA B:HIS430 4.4 41.9 1.0 N B:GLN429 4.4 37.2 1.0 CA B:GLN429 4.4 41.0 1.0 N B:ARG434 4.5 41.4 1.0 OE2 B:GLU457 4.7 50.1 1.0 CA B:ARG434 4.8 41.6 1.0 N B:ALA432 4.9 40.9 1.0 CB B:GLU428 4.9 38.4 1.0 C B:ALA432 5.0 40.1 1.0 CG1 B:VAL433 5.0 40.3 1.0

N.Wang, J.D.Rudolf, L.B.Dong, J.Osipiuk, C.Hatzos-Skintges, M.Endres, C.Y.Chang, G.Babnigg, A.Joachimiak, G.N.Phillips, B.Shen. Natural Separation of the Acyl-Coa Ligase Reaction Results in A Non-Adenylating Enzyme. Nat. Chem. Biol. V. 14 730 2018.
ISSN: ESSN 1552-4469
PubMed: 29867143
DOI: 10.1038/S41589-018-0061-0