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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2ypp:

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

Manganese Binding Sites:

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 2ypp

Go back to Manganese Binding Sites List in 2ypp
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 2ypp

Go back to Manganese Binding Sites List in 2ypp
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

Reference:

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
Page generated: Tue Dec 15 04:06:56 2020

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