Manganese in PDB 2ypo: 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Phenylalanine Bound in Only One Site

All present enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Phenylalanine Bound in Only One Site:
2.5.1.54;

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Phenylalanine Bound in Only One Site, PDB code: 2ypo 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)	44.16 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	203.969, 203.969, 66.600, 90.00, 90.00, 120.00
R / Rfree (%)	13.829 / 15.93

The binding sites of Manganese atom in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Phenylalanine Bound in Only One Site (pdb code 2ypo). 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 Phenylalanine Bound in Only One Site, PDB code: 2ypo:
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 Phenylalanine Bound in Only One Site


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 Phenylalanine Bound in Only One Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn700 b:25.4 occ:1.00 O A:HOH2051 2.2 31.8 1.0 OE2 A:GLU411 2.2 25.3 1.0 OD2 A:ASP441 2.3 27.7 1.0 SG A:CYS87 2.4 22.4 1.0 OE1 A:GLU411 2.6 22.5 1.0 NE2 A:HIS369 2.7 30.4 1.0 CD A:GLU411 2.7 24.6 1.0 CG A:ASP441 3.1 29.0 1.0 CB A:CYS87 3.4 18.3 1.0 CE1 A:HIS369 3.4 27.9 1.0 CB A:ASP441 3.5 27.7 1.0 CD2 A:HIS369 3.6 28.9 1.0 CA A:CYS87 4.1 17.0 1.0 NH2 A:ARG382 4.2 25.3 1.0 O A:HOH2163 4.2 34.1 1.0 CG A:GLU411 4.2 22.6 1.0 OD1 A:ASP441 4.2 27.2 1.0 NH2 A:ARG126 4.2 23.0 1.0 O A:HOH2018 4.3 25.6 1.0 O A:HOH2076 4.4 27.8 1.0 ND1 A:HIS369 4.5 27.9 1.0 CG A:HIS369 4.7 24.8 1.0 CA A:ASP441 4.7 25.0 1.0 N A:ASP441 4.7 21.4 1.0 C A:CYS87 4.7 17.8 1.0 O A:CYS87 4.7 20.1 1.0 CZ A:ARG126 4.9 21.8 1.0 NH1 A:ARG382 4.9 24.7 1.0

Manganese binding site 2 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with Phenylalanine Bound in Only One Site


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 Phenylalanine Bound in Only One Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn700 b:25.3 occ:1.00 OE2 B:GLU411 2.2 23.8 1.0 OD2 B:ASP441 2.3 26.2 1.0 SG B:CYS87 2.5 22.6 1.0 OE1 B:GLU411 2.6 20.7 1.0 NE2 B:HIS369 2.6 22.9 1.0 CD B:GLU411 2.7 24.2 1.0 CG B:ASP441 3.2 27.9 1.0 CD2 B:HIS369 3.5 23.5 1.0 CE1 B:HIS369 3.5 23.1 1.0 CB B:ASP441 3.5 25.6 1.0 CB B:CYS87 3.5 18.4 1.0 O B:HOH2103 4.2 34.0 1.0 CA B:CYS87 4.2 18.1 1.0 CG B:GLU411 4.2 19.4 1.0 NH2 B:ARG382 4.2 25.5 1.0 NH2 B:ARG126 4.2 19.3 1.0 OD1 B:ASP441 4.2 26.1 1.0 O B:HOH2097 4.3 25.7 1.0 ND1 B:HIS369 4.6 23.5 1.0 CG B:HIS369 4.6 19.9 1.0 CA B:ASP441 4.7 25.4 1.0 N B:ASP441 4.8 21.9 1.0 C B:CYS87 4.8 17.2 1.0 NH1 B:ARG382 4.8 24.5 1.0 O B:CYS87 4.8 19.8 1.0 CZ B:ARG126 4.8 18.1 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