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Manganese in PDB 5e40: 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site

Enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site

All present enzymatic activity of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site:
2.5.1.54;

Protein crystallography data

The structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site, PDB code: 5e40 was solved by S.Reichau, W.Jiao, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 2.05
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 205.451, 205.451, 66.803, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 20.7

Manganese Binding Sites:

The binding sites of Manganese atom in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site (pdb code 5e40). 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 From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site, PDB code: 5e40:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5e40

Go back to Manganese Binding Sites List in 5e40
Manganese binding site 1 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding 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 From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:34.5
occ:1.00
 O A:HOH724 2.0 34.9 1.0
OE2 A:GLU411 2.1 23.5 1.0
OD2 A:ASP441 2.3 26.1 1.0
NE2 A:HIS369 2.4 25.9 1.0
SG A:CYS87 2.5 23.2 1.0
OE1 A:GLU411 2.6 23.4 1.0
CD A:GLU411 2.7 23.1 1.0
CG A:ASP441 3.2 25.6 1.0
CE1 A:HIS369 3.3 25.8 1.0
CD2 A:HIS369 3.3 26.1 1.0
CB A:CYS87 3.5 22.7 1.0
CB A:ASP441 3.5 25.5 1.0
CA A:CYS87 4.1 22.4 1.0
NH1 A:ARG382 4.2 27.0 1.0
O A:HOH614 4.2 46.3 1.0
O A:HOH766 4.2 34.4 1.0
CG A:GLU411 4.2 22.8 1.0
O A:HOH696 4.2 38.1 1.0
NH2 A:ARG126 4.2 23.6 1.0
O A:HOH824 4.3 29.4 1.0
OD1 A:ASP441 4.4 25.5 1.0
ND1 A:HIS369 4.4 26.0 1.0
CG A:HIS369 4.5 26.3 1.0
O A:CYS87 4.7 23.0 1.0
C A:CYS87 4.7 22.6 1.0
CA A:ASP441 4.7 25.4 1.0
N A:ASP441 4.8 25.7 1.0
CZ A:ARG126 4.9 23.2 1.0
NH2 A:ARG382 4.9 26.6 1.0

Manganese binding site 2 out of 2 in 5e40

Go back to Manganese Binding Sites List in 5e40
Manganese binding site 2 out of 2 in the 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding 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 From Mycobacterium Tuberculosis with D-Tyrosine Bound in the Phenylalanine Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn506

b:34.7
occ:1.00
 O B:HOH760 2.0 34.8 1.0
OE2 B:GLU411 2.1 22.6 1.0
OD2 B:ASP441 2.3 27.5 1.0
NE2 B:HIS369 2.3 26.6 1.0
SG B:CYS87 2.6 23.6 1.0
OE1 B:GLU411 2.6 22.9 1.0
CD B:GLU411 2.7 22.7 1.0
CG B:ASP441 3.2 27.3 1.0
CE1 B:HIS369 3.2 26.6 1.0
CD2 B:HIS369 3.4 26.5 1.0
CB B:ASP441 3.5 26.8 1.0
CB B:CYS87 3.5 23.1 1.0
NH2 B:ARG382 4.0 27.2 1.0
O B:HOH611 4.0 45.7 1.0
O B:HOH715 4.2 42.5 1.0
CA B:CYS87 4.2 22.6 1.0
O B:HOH809 4.2 32.6 1.0
CG B:GLU411 4.2 22.2 1.0
O B:HOH868 4.3 34.2 1.0
OD1 B:ASP441 4.3 28.0 1.0
NH2 B:ARG126 4.3 21.9 1.0
ND1 B:HIS369 4.4 26.3 1.0
CG B:HIS369 4.5 26.3 1.0
CA B:ASP441 4.7 26.2 1.0
N B:ASP441 4.8 26.7 1.0
NH1 B:ARG382 4.8 26.9 1.0
O B:CYS87 4.8 22.2 1.0
C B:CYS87 4.8 22.5 1.0
CZ B:ARG382 4.9 27.3 1.0

Reference:

S.Reichau, N.J.Blackmore, W.Jiao, E.J.Parker. Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium Tuberculosis Using -Amino Acids. Plos One V. 11 52723 2016.
ISSN: ESSN 1932-6203
PubMed: 27128682
DOI: 10.1371/JOURNAL.PONE.0152723
Page generated: Sat Oct 5 23:58:35 2024

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