Manganese in PDB 2ypp: 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules

All present enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules:
2.5.1.54;

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules, PDB code: 2ypp 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)	44.02 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.449, 203.449, 66.490, 90.00, 90.00, 120.00
R / Rfree (%)	13.923 / 16.375

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Manganese atom in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules (pdb code 2ypp). 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 in Complex with 3 Tyrosine Molecules, PDB code: 2ypp:
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 in Complex with 3 Tyrosine Molecules


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 in Complex with 3 Tyrosine Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn700 b:41.0 occ:0.70 OE2 A:GLU411 2.1 41.2 1.0 SG A:CYS87 2.6 34.1 1.0 OD2 A:ASP441 2.8 47.0 1.0 CD A:GLU411 2.8 35.8 1.0 OE1 A:GLU411 2.9 42.0 1.0 NE2 A:HIS369 3.0 46.2 1.0 CE1 A:HIS369 3.3 44.7 1.0 CB A:CYS87 3.7 28.2 1.0 CG A:ASP441 3.8 43.2 1.0 CB A:ASP441 4.0 41.4 1.0 CD2 A:HIS369 4.0 44.4 1.0 CA A:CYS87 4.2 26.1 1.0 NH2 A:ARG382 4.2 40.6 1.0 CG A:GLU411 4.3 32.0 1.0 ND1 A:HIS369 4.4 49.2 1.0 NH2 A:ARG126 4.4 19.7 1.0 O A:CYS87 4.8 26.9 1.0 CG A:HIS369 4.8 44.6 1.0 C A:CYS87 4.8 25.4 1.0 N A:ASP441 4.9 33.6 1.0 OD1 A:ASP441 4.9 43.2 1.0 NH1 A:ARG382 5.0 36.7 1.0

Manganese binding site 2 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with 3 Tyrosine Molecules


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 in Complex with 3 Tyrosine Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn700 b:46.3 occ:0.70 OE2 B:GLU411 2.1 46.5 1.0 SG B:CYS87 2.6 36.1 1.0 NE2 B:HIS369 2.6 36.0 1.0 OD2 B:ASP441 2.6 42.3 1.0 CD B:GLU411 2.7 35.1 1.0 OE1 B:GLU411 2.7 38.6 1.0 CE1 B:HIS369 3.3 33.7 1.0 CG B:ASP441 3.5 40.1 1.0 CB B:CYS87 3.6 26.3 1.0 CB B:ASP441 3.7 38.4 1.0 CD2 B:HIS369 3.8 34.2 1.0 CG B:GLU411 4.1 32.0 1.0 CA B:CYS87 4.1 23.7 1.0 NH2 B:ARG126 4.1 16.5 1.0 NH2 B:ARG382 4.5 48.8 1.0 ND1 B:HIS369 4.5 37.8 1.0 O B:CYS87 4.6 22.8 1.0 OD1 B:ASP441 4.6 38.9 1.0 C B:CYS87 4.7 23.2 1.0 CG B:HIS369 4.8 33.8 1.0 CZ B:ARG126 4.9 16.3 1.0 NH1 B:ARG382 5.0 41.8 1.0 N B:ASP441 5.0 34.9 1.0 CA B:ASP441 5.0 36.6 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