Sodium in PDB 6da7: Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222)

The structure of Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222), PDB code: 6da7 was solved by L.Han, J.D.Rudolf, C.-Y.Chang, M.D.Miller, J.Soman, G.N.Phillips Jr., B.Shen, Enzyme Discovery For Natural Product Biosynthesis (Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.77 / 1.83
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.352, 114.387, 194.351, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.3

The binding sites of Sodium atom in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222) (pdb code 6da7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222), PDB code: 6da7:

Sodium binding site 1 out of 1 in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222)


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 the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes with Apo Form at 1.83 A Resolution (I222) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:68.1 occ:1.00 OE2 A:GLU228 2.4 38.7 1.0 O A:HOH623 2.8 57.0 1.0 O3S A:EPE502 2.8 55.8 1.0 O A:HOH638 2.9 48.4 1.0 ND1 A:HIS187 3.1 50.1 1.0 ND2 A:ASN164 3.1 62.4 1.0 CD A:GLU228 3.3 47.0 1.0 CG A:ASN164 3.5 74.0 1.0 OE1 A:GLU228 3.6 35.5 1.0 O A:TRP165 3.6 39.0 1.0 O1S A:EPE502 3.7 50.6 1.0 CB A:ASN164 3.8 47.0 1.0 S A:EPE502 3.8 54.7 1.0 O A:HOH601 3.8 50.8 1.0 CB A:HIS187 3.8 46.4 1.0 O A:HOH613 3.8 54.6 1.0 CG A:HIS187 3.9 48.8 1.0 CE1 A:HIS187 4.1 48.8 1.0 OD1 A:ASN164 4.3 68.1 1.0 CB A:ALA166 4.4 32.4 1.0 C A:TRP165 4.4 38.5 1.0 N A:TRP165 4.5 36.6 1.0 CG A:GLU228 4.6 32.4 1.0 CA A:ASN164 4.6 42.3 1.0 O2S A:EPE502 4.6 56.7 1.0 O A:HOH621 4.8 47.9 1.0 C A:ASN164 4.9 42.1 1.0

T.Annaval, L.Han, J.D.Rudolf, G.Xie, D.Yang, C.Y.Chang, M.Ma, I.Crnovcic, M.D.Miller, J.Soman, W.Xu, G.N.Phillips Jr., B.Shen. Biochemical and Structural Characterization of Ttnd, A Prenylated Fmn-Dependent Decarboxylase From the Tautomycetin Biosynthetic Pathway. Acs Chem. Biol. V. 13 2728 2018.
ISSN: ESSN 1554-8937
PubMed: 30152678
DOI: 10.1021/ACSCHEMBIO.8B00673