Magnesium in PDB 6da6: Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121)

The structure of Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121), PDB code: 6da6 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)	26.13 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.215, 137.117, 284.074, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121) (pdb code 6da6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121), PDB code: 6da6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:57.0 occ:1.00 O A:HOH625 2.0 62.0 1.0 O A:HOH601 2.1 48.5 1.0 O A:HOH664 2.1 58.6 1.0 O A:HOH666 2.1 54.7 1.0 O A:HOH662 2.1 52.3 1.0 OE2 A:GLU228 2.4 48.3 1.0 CD A:GLU228 3.5 56.2 1.0 O A:MET220 3.7 39.5 1.0 ND2 A:ASN164 3.9 56.6 1.0 O A:ALA218 4.1 38.5 1.0 CG A:GLU228 4.2 36.4 1.0 O A:TRP165 4.3 46.4 1.0 O A:HOH608 4.4 57.9 1.0 OE1 A:GLU228 4.5 39.6 1.0 ND1 A:HIS187 4.6 90.6 1.0 C A:MET220 4.8 40.0 1.0 NH1 A:ARG386 4.8 99.8 1.0 NE2 A:GLN186 4.9 0.8 1.0 C A:ALA218 4.9 38.8 1.0 O A:VAL217 4.9 42.9 1.0 N A:LEU222 5.0 41.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:59.7 occ:1.00 O B:HOH633 2.0 61.2 1.0 O B:HOH655 2.1 67.3 1.0 O B:HOH650 2.1 63.3 1.0 O B:HOH659 2.1 62.2 1.0 O B:HOH601 2.1 48.1 1.0 OE2 B:GLU228 2.4 56.5 1.0 CD B:GLU228 3.4 54.3 1.0 O B:MET220 3.7 44.1 1.0 ND2 B:ASN164 3.7 39.2 1.0 CG B:GLU228 4.0 36.4 1.0 O B:HOH626 4.1 45.0 1.0 O B:ALA218 4.2 40.2 1.0 O B:TRP165 4.3 45.0 1.0 OE1 B:GLU228 4.5 47.0 1.0 ND1 B:HIS187 4.6 73.2 1.0 NH1 B:ARG386 4.8 89.7 1.0 C B:MET220 4.8 40.0 1.0 NE2 B:GLN186 4.8 0.2 1.0 CG B:ASN164 4.9 48.0 1.0 N B:LEU222 4.9 39.6 1.0 C B:ALA218 5.0 39.3 1.0 O B:VAL217 5.0 41.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Ttnd Decarboxylase From the Tautomycetin Biosynthesis Pathway of Streptomyces Griseochromogenes, Apo Form at 2.6 A Resolution (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:73.1 occ:1.00 OE2 D:GLU228 2.3 0.2 1.0 CD D:GLU228 3.1 0.6 1.0 O D:MET220 3.6 50.2 1.0 O D:ALA218 3.7 58.8 1.0 CG D:GLU228 3.8 86.0 1.0 OD1 D:ASN164 3.8 0.7 1.0 OE1 D:GLU228 3.8 73.8 1.0 O D:TRP165 3.9 0.2 1.0 C D:ALA218 4.5 57.7 1.0 O D:VAL217 4.5 58.1 1.0 C D:MET220 4.8 47.8 1.0 CA D:ALA218 4.9 52.6 1.0 C D:TRP165 4.9 0.1 1.0 CG D:ASN164 4.9 0.6 1.0 CA D:ALA166 5.0 0.2 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