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Magnesium in PDB 9hra: Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid

Enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid

All present enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid, PDB code: 9hra was solved by W.Stuart, M.Isupov, N.J.Harmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.59 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.199, 101.203, 115.683, 90, 91.15, 90
R / Rfree (%) 20.8 / 25.7

Other elements in 9hra:

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid also contains other interesting chemical elements:

Chlorine (Cl) 23 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid (pdb code 9hra). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid, PDB code: 9hra:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9hra

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:38.8
occ:1.00
OD2 A:ASP81 2.0 41.7 1.0
O A:HOH418 2.0 28.7 1.0
O A:HOH405 2.0 46.0 1.0
O A:HOH404 2.0 39.8 1.0
O A:PYR302 2.3 40.9 1.0
O3 A:PYR302 2.5 47.0 1.0
CG A:ASP81 3.0 38.4 1.0
C A:PYR302 3.1 50.8 1.0
CA A:PYR302 3.2 54.3 1.0
OD1 A:ASP81 3.4 36.5 1.0
OD1 A:ASP83 3.6 70.5 1.0
OD2 A:ASP54 4.1 52.7 1.0
N A:GLY44 4.1 41.7 1.0
CA A:GLY43 4.1 43.4 1.0
N A:GLY43 4.2 36.4 1.0
OXT A:PYR302 4.3 41.1 1.0
CB A:ASP81 4.3 29.4 1.0
O4 A:SIN301 4.3 85.1 1.0
OD1 A:ASP54 4.4 56.7 1.0
CE1 A:HIS108 4.4 28.0 1.0
OE1 A:GLU110 4.5 60.6 1.0
C A:GLY43 4.5 37.9 1.0
CB A:PYR302 4.6 59.8 1.0
NH2 A:ARG152 4.6 53.2 1.0
OH A:TYR40 4.6 26.4 1.0
CG A:ASP54 4.6 43.2 1.0
O1 A:EDO305 4.7 55.3 1.0
CG A:ASP83 4.7 66.9 1.0
NE2 A:HIS108 5.0 30.4 1.0

Magnesium binding site 2 out of 8 in 9hra

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:29.7
occ:1.00
OD2 B:ASP81 2.0 46.8 1.0
O B:HOH417 2.0 26.6 1.0
O B:HOH403 2.0 25.8 1.0
O B:HOH408 2.0 26.8 1.0
OXT B:PYR302 2.3 43.7 1.0
O3 B:PYR302 2.5 26.8 1.0
CG B:ASP81 3.1 43.9 1.0
C B:PYR302 3.1 44.0 1.0
CA B:PYR302 3.2 39.6 1.0
OD1 B:ASP83 3.5 64.0 1.0
OD1 B:ASP81 3.5 37.4 1.0
OD2 B:ASP54 3.8 28.3 1.0
N B:GLY44 3.8 29.1 1.0
CA B:GLY43 3.9 29.9 1.0
N B:GLY43 4.0 26.5 1.0
OD1 B:ASP54 4.1 50.9 1.0
O2 B:EDO305 4.2 58.5 1.0
C B:GLY43 4.3 35.6 1.0
O3 B:SIN301 4.3 40.5 1.0
O B:PYR302 4.3 38.8 1.0
CG B:ASP54 4.4 33.9 1.0
CB B:ASP81 4.4 41.8 1.0
CB B:PYR302 4.6 31.4 1.0
CE1 B:HIS108 4.7 27.1 1.0
NH2 B:ARG152 4.7 45.9 1.0
CG B:ASP83 4.7 58.0 1.0
OH B:TYR40 4.7 23.4 1.0
OE1 B:GLU110 4.7 50.0 1.0
CA B:GLY44 4.8 35.5 1.0

Magnesium binding site 3 out of 8 in 9hra

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:62.0
occ:1.00
OD2 D:ASP81 2.0 47.5 1.0
O D:HOH404 2.0 50.7 1.0
O D:HOH402 2.0 32.7 1.0
O D:HOH410 2.0 45.1 1.0
O3 D:PYR302 2.5 69.7 1.0
O D:PYR302 2.6 52.6 1.0
CG D:ASP81 3.0 51.1 1.0
CA D:PYR302 3.3 59.3 1.0
C D:PYR302 3.4 62.4 1.0
OD1 D:ASP81 3.5 60.3 1.0
OD1 D:ASP83 3.5 84.1 1.0
N D:GLY44 3.9 36.2 1.0
OD2 D:ASP54 3.9 45.6 1.0
CA D:GLY43 4.0 44.5 1.0
N D:GLY43 4.1 39.0 1.0
OD1 D:ASP54 4.2 43.3 1.0
CB D:ASP81 4.3 47.4 1.0
C D:GLY43 4.4 33.3 1.0
CG D:ASP54 4.5 57.2 1.0
O D:HOH423 4.5 32.7 1.0
OXT D:PYR302 4.5 58.7 1.0
CE1 D:HIS108 4.6 36.4 1.0
OH D:TYR40 4.6 48.1 1.0
OE1 D:GLU110 4.7 54.1 1.0
NH2 D:ARG152 4.7 63.9 1.0
CB D:PYR302 4.7 42.7 1.0
CG D:ASP83 4.7 50.8 1.0
O4 D:SIN301 4.8 78.9 1.0
O3 D:SIN301 4.8 74.5 1.0
CA D:GLY44 4.9 37.8 1.0

Magnesium binding site 4 out of 8 in 9hra

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg308

b:45.1
occ:1.00
OD2 F:ASP81 2.0 48.7 1.0
O F:HOH401 2.0 39.5 1.0
O F:HOH407 2.0 50.0 1.0
O F:HOH405 2.0 35.4 1.0
OXT F:PYR303 2.3 36.2 1.0
O3 F:PYR303 2.5 44.3 1.0
CG F:ASP81 3.0 54.2 1.0
C F:PYR303 3.1 48.2 1.0
CA F:PYR303 3.2 54.4 1.0
OD1 F:ASP83 3.3 54.9 1.0
OD1 F:ASP81 3.4 55.0 1.0
OD2 F:ASP54 4.1 43.0 1.0
N F:GLY44 4.1 45.3 1.0
CA F:GLY43 4.1 48.9 1.0
N F:GLY43 4.2 40.0 1.0
OD1 F:ASP54 4.3 56.4 1.0
O F:PYR303 4.3 47.8 1.0
CB F:ASP81 4.3 40.5 1.0
CE1 F:HIS108 4.4 40.0 1.0
OE1 F:GLU110 4.5 58.9 1.0
NH2 F:ARG152 4.5 66.5 1.0
O3 F:SIN302 4.5 64.7 1.0
C F:GLY43 4.5 37.8 1.0
CG F:ASP83 4.6 55.9 1.0
CG F:ASP54 4.6 41.5 1.0
CB F:PYR303 4.7 38.5 1.0
OH F:TYR40 4.7 42.3 1.0

Magnesium binding site 5 out of 8 in 9hra

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg308

b:51.0
occ:1.00
OD2 G:ASP81 2.0 42.3 1.0
O G:HOH411 2.0 54.9 1.0
O G:HOH405 2.0 33.9 1.0
O G:HOH407 2.0 28.8 1.0
OXT G:PYR302 2.3 46.1 1.0
O3 G:PYR302 2.5 58.8 1.0
CG G:ASP81 3.0 30.7 1.0
C G:PYR302 3.1 47.5 1.0
CA G:PYR302 3.2 53.7 1.0
OD1 G:ASP81 3.4 29.9 1.0
OD1 G:ASP83 3.5 43.6 1.0
OD2 G:ASP54 4.0 37.5 1.0
O1 G:EDO305 4.1 40.4 1.0
N G:GLY44 4.1 34.9 1.0
CA G:GLY43 4.1 33.4 1.0
N G:GLY43 4.2 27.4 1.0
O G:PYR302 4.3 44.8 1.0
CB G:ASP81 4.3 25.1 1.0
OD1 G:ASP54 4.4 34.7 1.0
O3 G:SIN301 4.4 40.0 1.0
CE1 G:HIS108 4.5 36.2 1.0
C G:GLY43 4.5 39.1 1.0
NH2 G:ARG152 4.5 38.5 1.0
OE1 G:GLU110 4.5 40.4 1.0
CB G:PYR302 4.6 49.4 1.0
OH G:TYR40 4.6 39.8 1.0
CG G:ASP54 4.6 34.2 1.0
CG G:ASP83 4.7 48.5 1.0
C1 G:EDO305 4.8 47.2 1.0

Magnesium binding site 6 out of 8 in 9hra

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg306

b:36.7
occ:1.00
OD2 I:ASP81 2.0 44.1 1.0
O I:HOH428 2.0 47.8 1.0
O I:HOH408 2.0 43.2 1.0
O I:HOH412 2.0 44.6 1.0
O I:PYR302 2.3 34.3 1.0
O3 I:PYR302 2.5 35.8 1.0
CG I:ASP81 3.1 37.4 1.0
C I:PYR302 3.1 43.7 1.0
CA I:PYR302 3.2 47.6 1.0
OD1 I:ASP81 3.5 42.9 1.0
OD1 I:ASP83 3.5 67.6 1.0
N I:GLY44 3.9 28.7 1.0
O1 I:EDO304 3.9 58.3 1.0
CA I:GLY43 3.9 34.4 1.0
OD2 I:ASP54 4.0 34.5 1.0
N I:GLY43 4.0 38.3 1.0
OD1 I:ASP54 4.2 66.5 1.0
OXT I:PYR302 4.3 30.2 1.0
C I:GLY43 4.3 30.4 1.0
O3 I:SIN301 4.3 81.7 1.0
CB I:ASP81 4.3 32.7 1.0
C1 I:EDO304 4.4 42.4 1.0
CG I:ASP54 4.5 43.7 1.0
CB I:PYR302 4.6 36.6 1.0
CE1 I:HIS108 4.6 30.9 1.0
OH I:TYR40 4.7 54.6 1.0
CG I:ASP83 4.7 72.8 1.0
NH2 I:ARG152 4.7 85.0 1.0
OE1 I:GLU110 4.7 84.4 1.0
CA I:GLY44 4.9 28.6 1.0

Magnesium binding site 7 out of 8 in 9hra

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg307

b:29.4
occ:1.00
OD2 J:ASP81 2.0 31.7 1.0
O J:HOH416 2.0 29.1 1.0
O J:HOH423 2.0 24.5 1.0
O J:HOH429 2.0 36.0 1.0
O3 J:PYR302 2.5 31.2 1.0
OXT J:PYR302 2.5 34.1 1.0
CG J:ASP81 3.0 34.2 1.0
CA J:PYR302 3.2 37.6 1.0
C J:PYR302 3.3 42.6 1.0
OD1 J:ASP81 3.4 38.7 1.0
OD1 J:ASP83 3.6 54.3 1.0
CE1 J:HIS108 4.2 27.5 1.0
OD2 J:ASP54 4.3 35.2 1.0
N J:GLY44 4.3 30.2 1.0
CB J:ASP81 4.3 24.0 1.0
CA J:GLY43 4.3 46.9 1.0
NH2 J:ARG152 4.3 51.6 1.0
OE1 J:GLU110 4.3 54.5 1.0
N J:GLY43 4.3 38.7 1.0
O1 J:EDO306 4.3 85.2 1.0
O J:PYR302 4.5 38.9 1.0
OH J:TYR40 4.5 25.3 1.0
OD1 J:ASP54 4.6 44.2 1.0
CB J:PYR302 4.7 34.5 1.0
C J:GLY43 4.7 44.5 1.0
CG J:ASP83 4.8 55.0 1.0
O4 J:SIN301 4.8 64.7 1.0
NE2 J:HIS108 4.8 26.9 1.0
CG J:ASP54 4.8 45.6 1.0

Magnesium binding site 8 out of 8 in 9hra

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg307

b:41.9
occ:1.00
OD2 L:ASP81 2.0 38.6 1.0
O L:HOH404 2.0 26.0 1.0
O L:HOH406 2.0 42.0 1.0
O L:HOH422 2.0 38.2 1.0
OXT L:PYR302 2.3 36.5 1.0
O3 L:PYR302 2.5 38.9 1.0
CG L:ASP81 3.0 39.9 1.0
C L:PYR302 3.1 39.2 1.0
CA L:PYR302 3.2 37.7 1.0
OD1 L:ASP81 3.3 37.1 1.0
OD1 L:ASP83 3.4 51.3 1.0
CA L:GLY43 4.1 34.4 1.0
N L:GLY44 4.2 32.1 1.0
OD2 L:ASP54 4.2 50.2 1.0
N L:GLY43 4.2 38.3 1.0
O1 L:EDO305 4.2 58.2 1.0
CB L:ASP81 4.3 36.2 1.0
O L:PYR302 4.3 40.1 1.0
OD1 L:ASP54 4.4 50.5 1.0
CE1 L:HIS108 4.4 30.7 1.0
OE1 L:GLU110 4.5 53.3 1.0
NH2 L:ARG152 4.5 48.3 1.0
O3 L:SIN301 4.5 55.1 1.0
C L:GLY43 4.6 44.6 1.0
CG L:ASP83 4.6 53.2 1.0
OH L:TYR40 4.7 25.4 1.0
CB L:PYR302 4.7 29.9 1.0
CG L:ASP54 4.7 46.0 1.0
NE2 L:HIS108 5.0 27.5 1.0

Reference:

W.S.Stuart, C.H.Jenkins, P.M.Ireland, M.N.Isupov, I.H.Norville, N.J.Harmer. Structure and Catalytic Mechanism of Methylisocitrate Lyase, A Potential Drug Target Against Coxiella Burnetii. J.Biol.Chem. V. 301 08517 2025.
ISSN: ESSN 1083-351X
PubMed: 40250561
DOI: 10.1016/J.JBC.2025.108517
Page generated: Sat Aug 23 06:02:47 2025

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