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Magnesium in PDB 4nq1: Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site

Enzymatic activity of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site

All present enzymatic activity of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site:
4.2.1.52;

Protein crystallography data

The structure of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site, PDB code: 4nq1 was solved by T.Siddiqui, J.J.Paxman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.27 / 1.65
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.310, 89.310, 290.180, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 18.7

Other elements in 4nq1:

The structure of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site (pdb code 4nq1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site, PDB code: 4nq1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4nq1

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Magnesium binding site 1 out of 5 in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:30.0
occ:0.50
 O A:HOH826 2.0 14.4 0.5
O A:HOH838 2.1 30.0 0.5
O A:HOH825 2.1 13.4 0.5
O A:HOH631 2.1 10.9 0.5
O A:HOH628 2.2 8.1 0.5
O A:HOH827 2.2 14.4 0.5
O A:SER179 3.7 14.6 0.5
O A:SER179 3.9 15.2 0.5
O A:SER154 4.0 13.8 1.0
O A:ILE156 4.3 13.1 1.0
O A:ALA151 4.4 13.4 1.0
CA A:SER154 4.5 11.5 1.0
C A:SER154 4.7 11.1 1.0
OG A:SER179 4.7 15.6 0.5
C A:SER179 4.8 14.6 0.5
C A:SER179 4.8 14.7 0.5
CB A:SER154 4.9 11.5 1.0

Magnesium binding site 2 out of 5 in 4nq1

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Magnesium binding site 2 out of 5 in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:14.2
occ:0.50
 O A:HOH828 2.0 23.6 0.5
O A:HOH829 2.1 18.5 0.5
O A:HOH840 2.2 30.0 0.5
O A:HOH839 2.2 30.0 0.5
O A:HOH831 2.2 13.0 0.5
O A:HOH830 2.2 14.8 0.5
O A:ALA96 4.1 14.0 1.0
O A:HOH798 4.2 33.7 1.0
O A:HOH710 4.2 35.4 1.0
O A:HOH416 4.3 14.9 1.0
O A:MET92 4.5 14.1 0.5
O A:MET92 4.5 14.8 0.5
CA A:GLY95 4.7 14.1 1.0
O A:GLY95 4.7 15.0 1.0
C A:GLY95 4.7 15.0 1.0

Magnesium binding site 3 out of 5 in 4nq1

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Magnesium binding site 3 out of 5 in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:7.0
occ:0.50
 O B:HOH859 2.0 14.4 0.5
O B:HOH860 2.0 14.1 0.5
O B:HOH862 2.1 17.6 0.5
O B:HOH858 2.1 16.9 0.5
O B:HOH619 2.1 5.9 0.5
O B:HOH861 2.2 13.5 0.5
O B:SER179 3.8 14.6 0.5
O B:SER179 3.8 13.3 0.5
O B:HOH451 3.9 16.4 1.0
O B:SER154 4.0 13.1 1.0
O B:HOH425 4.0 14.1 1.0
O B:ALA151 4.3 14.1 1.0
O B:ILE156 4.3 12.6 1.0
CA B:SER154 4.5 12.0 1.0
C B:SER154 4.7 11.4 1.0
C B:SER179 4.8 14.5 0.5
OG B:SER179 4.9 19.3 0.5
C B:SER179 4.9 13.1 0.5
CB B:SER154 4.9 10.8 1.0

Magnesium binding site 4 out of 5 in 4nq1

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Magnesium binding site 4 out of 5 in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:14.9
occ:0.50
 O B:HOH873 2.0 30.0 0.5
O B:HOH666 2.1 10.6 0.5
O B:HOH875 2.2 30.0 0.5
O B:HOH874 2.2 30.0 0.5
O B:HOH863 2.2 14.8 0.5
O B:HOH877 2.2 30.0 0.5
O B:ALA96 4.1 12.6 1.0
O B:HOH853 4.2 34.1 1.0
O B:HOH544 4.3 26.3 1.0
O B:HOH440 4.4 17.0 1.0
O B:MET92 4.5 12.0 0.5
O B:MET92 4.6 13.4 0.5
CA B:GLY95 4.6 15.5 1.0
O B:GLY95 4.6 15.0 1.0
C B:GLY95 4.6 14.6 1.0

Magnesium binding site 5 out of 5 in 4nq1

Go back to Magnesium Binding Sites List in 4nq1
Magnesium binding site 5 out of 5 in the Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Legionella Pneumophila Dihydrodipicolinate Synthase with First Substrate Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:27.3
occ:1.00
 O B:HOH665 2.0 22.7 0.8
O B:HOH536 2.1 20.3 0.8
O B:HOH620 2.1 11.5 0.5
O B:HOH474 2.1 17.6 0.8
O B:HOH664 2.1 19.2 0.6
O A:HOH547 2.2 21.1 0.8
OE1 B:GLU274 3.8 26.6 1.0
OE2 B:GLU274 3.9 32.9 1.0
O A:HOH648 3.9 36.5 1.0
O B:GLU271 4.1 12.8 0.5
OE2 B:GLU271 4.1 27.1 0.5
O B:GLU271 4.2 12.6 0.5
CD B:GLU274 4.2 25.3 1.0
OE1 A:GLU112 4.3 12.2 0.6
OE2 A:GLU112 4.3 14.6 0.6
O B:HOH595 4.3 28.8 1.0
O B:LEU272 4.5 14.3 1.0
CB B:GLU271 4.6 13.6 0.5
CD B:GLU271 4.6 19.0 0.5
CG B:GLU271 4.7 18.2 0.5
CD A:GLU112 4.8 14.0 0.6
C B:GLU271 4.9 13.4 0.5
O B:HOH656 4.9 29.6 0.5
O B:HOH554 4.9 25.0 1.0
C B:GLU271 4.9 13.2 0.5
CA B:SER273 5.0 15.9 1.0

Reference:

T.Siddiqui, J.J.Paxman, C.Dogovski, S.Panjikar, M.A.Perugini. Legionella Pneumophila Dhdps: the First Case of Non-Lysine Inhibition in A Gram-Negative Pathogen To Be Published.
Page generated: Mon Dec 14 19:15:20 2020

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