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Manganese in PDB 3pfp: Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor

Enzymatic activity of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor

All present enzymatic activity of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor:
2.5.1.54;

Protein crystallography data

The structure of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor, PDB code: 3pfp was solved by S.Reichau, W.Jiao, S.R.Walker, R.D.Hutton, E.J.Parker, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.90 / 2.35
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 203.579, 203.579, 66.490, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19.6

Other elements in 3pfp:

The structure of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor (pdb code 3pfp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor, PDB code: 3pfp:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3pfp

Go back to Manganese Binding Sites List in 3pfp
Manganese binding site 1 out of 2 in the Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn700

b:2.0
occ:0.80
 OE1 A:GLU411 2.0 13.7 1.0
O8 A:036716 2.0 12.5 0.4
OD1 A:ASP441 2.1 17.8 1.0
NE2 A:HIS369 2.1 12.8 1.0
O8 A:035463 2.3 10.5 0.4
SG A:CYS87 2.4 17.2 1.0
OE2 A:GLU411 2.5 16.9 1.0
CD A:GLU411 2.6 15.3 1.0
CG A:ASP441 3.0 20.1 1.0
C1 A:036716 3.0 15.1 0.4
CD2 A:HIS369 3.1 15.6 1.0
CE1 A:HIS369 3.2 15.9 1.0
C1 A:035463 3.3 12.2 0.4
CB A:ASP441 3.3 19.1 1.0
CB A:CYS87 3.5 15.8 1.0
O9 A:036716 3.8 14.4 0.4
C2 A:036716 3.9 13.8 0.4
C3 A:035463 4.0 12.5 0.4
C4 A:036716 4.0 15.3 0.4
OD2 A:ASP441 4.1 20.8 1.0
CG A:GLU411 4.1 12.6 1.0
O9 A:035463 4.1 10.4 0.4
CA A:CYS87 4.1 15.1 1.0
NZ A:LYS133 4.1 23.4 1.0
NH2 A:ARG126 4.2 15.9 1.0
NH2 A:ARG382 4.2 17.9 1.0
C2 A:035463 4.2 10.9 0.4
ND1 A:HIS369 4.3 13.3 1.0
CG A:HIS369 4.3 16.2 1.0
C4 A:035463 4.3 14.5 0.4
C3 A:036716 4.5 14.6 0.4
CA A:ASP441 4.7 18.9 1.0
N A:ASP441 4.8 18.4 1.0
O10 A:035463 4.8 7.5 0.4
NH1 A:ARG382 4.8 14.8 1.0
O A:CYS87 4.8 15.2 1.0
CE A:LYS133 4.8 23.1 1.0
CZ A:ARG126 4.8 15.1 1.0
C A:CYS87 4.8 15.1 1.0
NH1 A:ARG126 4.9 16.4 1.0
CZ A:ARG382 5.0 17.9 1.0

Manganese binding site 2 out of 2 in 3pfp

Go back to Manganese Binding Sites List in 3pfp
Manganese binding site 2 out of 2 in the Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase From Mycobacterium Tuberculosis in Complex with An Active Site Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:2.0
occ:0.80
 OD2 B:ASP441 2.0 16.1 1.0
O8 B:035771 2.0 9.4 0.4
OE1 B:GLU411 2.0 13.3 1.0
NE2 B:HIS369 2.1 10.9 1.0
O8 B:036463 2.2 4.9 0.4
SG B:CYS87 2.4 13.8 1.0
OE2 B:GLU411 2.6 13.4 1.0
CD B:GLU411 2.6 13.9 1.0
CG B:ASP441 3.0 18.1 1.0
CE1 B:HIS369 3.1 11.2 1.0
C1 B:035771 3.1 13.5 0.4
CD2 B:HIS369 3.1 12.9 1.0
C1 B:036463 3.2 7.6 0.4
CB B:ASP441 3.4 16.4 1.0
CB B:CYS87 3.5 13.7 1.0
O9 B:035771 3.8 13.1 0.4
C2 B:036463 3.9 5.6 0.4
C3 B:035771 3.9 13.3 0.4
O9 B:036463 4.0 7.6 0.4
C2 B:035771 4.0 12.5 0.4
C4 B:035771 4.1 15.1 0.4
OD1 B:ASP441 4.1 16.6 1.0
CG B:GLU411 4.1 12.0 1.0
CA B:CYS87 4.1 13.2 1.0
NZ B:LYS133 4.2 16.7 1.0
ND1 B:HIS369 4.2 10.4 1.0
NH2 B:ARG382 4.2 16.5 1.0
NH2 B:ARG126 4.2 13.5 1.0
C4 B:036463 4.2 6.0 0.4
CG B:HIS369 4.2 13.4 1.0
O10 B:035771 4.6 10.2 0.4
C3 B:036463 4.7 4.6 0.4
CA B:ASP441 4.7 16.2 1.0
CE B:LYS133 4.7 16.6 1.0
CZ B:ARG126 4.8 13.1 1.0
N B:ASP441 4.8 16.5 1.0
NH1 B:ARG126 4.8 11.8 1.0
C6 B:035771 4.8 15.9 0.4
O B:CYS87 4.9 13.2 1.0
C B:CYS87 4.9 13.3 1.0
NH1 B:ARG382 4.9 13.9 1.0
O B:HOH711 4.9 22.0 1.0
C5 B:036463 4.9 6.2 0.4

Reference:

S.Reichau, W.Jiao, S.R.Walker, R.D.Hutton, E.N.Baker, E.J.Parker. Potent Inhibitors of A Shikimate Pathway Enzyme From Mycobacterium Tuberculosis: Combining Mechanism- and Modeling-Based Design J.Biol.Chem. V. 286 16197 2011.
ISSN: ISSN 0021-9258
PubMed: 21454647
DOI: 10.1074/JBC.M110.211649
Page generated: Sat Oct 5 17:29:40 2024

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