Atomistry » Manganese » PDB 5dcd-5ekd » 5e40
Atomistry »
  Manganese »
    PDB 5dcd-5ekd »
      5e40 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy