Manganese in PDB 2ypq: 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound

All present enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound:
2.5.1.54;

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound, PDB code: 2ypq was solved by N.J.Blackmore, S.Reichau, W.Jiao, R.D.Hutton, E.N.Baker, G.B.Jameson, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	175.67 / 2.76
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.777, 202.777, 66.747, 90.00, 90.00, 120.00
R / Rfree (%)	17.73 / 24.888

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound (pdb code 2ypq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound, PDB code: 2ypq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1463 b:48.5 occ:1.00 OE2 A:GLU411 1.6 35.5 1.0 NE2 A:HIS369 2.1 57.7 1.0 OD2 A:ASP441 2.2 57.2 1.0 SG A:CYS87 2.5 43.1 1.0 CD A:GLU411 2.7 41.1 1.0 CE1 A:HIS369 2.9 67.1 1.0 CG A:ASP441 3.2 49.6 1.0 CD2 A:HIS369 3.2 72.2 1.0 OE1 A:GLU411 3.3 68.8 1.0 CB A:ASP441 3.6 46.3 1.0 CB A:CYS87 3.8 41.1 1.0 CG A:GLU411 4.0 38.3 1.0 NH2 A:ARG126 4.1 32.9 1.0 ND1 A:HIS369 4.1 58.6 1.0 OD1 A:ASP441 4.2 38.2 1.0 CA A:CYS87 4.3 39.7 1.0 CG A:HIS369 4.3 62.9 1.0 NH2 A:ARG382 4.3 65.8 1.0 O A:CYS87 4.6 37.9 1.0 CZ A:ARG126 4.7 47.8 1.0 NH1 A:ARG126 4.7 57.9 1.0 NH1 A:ARG382 4.8 61.7 1.0 C A:CYS87 4.8 25.6 1.0 O1 A:PO41466 4.8 40.0 1.0 CA A:ASP441 5.0 39.0 1.0

Manganese binding site 2 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Tryptophan and Tyrosine Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1463 b:29.6 occ:0.50 OD2 B:ASP441 2.3 14.3 1.0 OE2 B:GLU411 2.4 21.2 1.0 SG B:CYS87 2.5 29.6 1.0 NE2 B:HIS369 2.6 38.8 1.0 CE1 B:HIS369 3.3 49.7 1.0 CG B:ASP441 3.4 43.3 1.0 CD B:GLU411 3.6 36.1 1.0 CD2 B:HIS369 3.6 37.9 1.0 NH2 B:ARG126 3.7 38.1 1.0 CB B:CYS87 4.0 41.7 1.0 CB B:ASP441 4.1 43.4 1.0 OE1 B:GLU411 4.2 42.0 1.0 OD1 B:ASP441 4.3 23.9 1.0 O B:CYS87 4.3 40.2 1.0 CA B:CYS87 4.5 30.8 1.0 ND1 B:HIS369 4.5 50.2 1.0 CZ B:ARG126 4.6 42.3 1.0 CG B:HIS369 4.7 37.0 1.0 CG B:GLU411 4.7 37.6 1.0 NH1 B:ARG126 4.8 46.2 1.0 C B:CYS87 4.8 38.6 1.0 O2 B:PO41467 5.0 59.2 1.0 SG B:CYS440 5.0 64.3 1.0

N.J.Blackmore, S.Reichau, W.Jiao, R.D.Hutton, E.N.Baker, G.B.Jameson, E.J.Parker. Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis. J.Mol.Biol. V. 425 1582 2013.
ISSN: ISSN 0022-2836
PubMed: 23274137
DOI: 10.1016/J.JMB.2012.12.019