Magnesium in PDB 7rbx: Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid

Enzymatic activity of Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid

All present enzymatic activity of Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid, PDB code: 7rbx was solved by Seattle Structural Genomics Center For Infectious Disease, T.E.Edwards, J.Abendroth, Seattle Structural Genomics Center Forinfectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.59 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.75, 136.27, 181.98, 90, 90, 90
R / Rfree (%) 14.3 / 16.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid (pdb code 7rbx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid, PDB code: 7rbx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7rbx

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Magnesium binding site 1 out of 4 in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic 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 Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:31.6
occ:1.00
 OD2 A:ASP147 2.1 22.1 1.0
O A:HOH668 2.2 27.8 1.0
O A:HOH633 2.2 26.7 1.0
O A:HOH613 2.3 30.9 1.0
O1 A:ITN502 2.4 30.7 1.0
CG A:ASP147 3.1 21.1 1.0
C1 A:ITN502 3.3 31.1 1.0
OD1 A:ASP147 3.4 20.0 1.0
O A:HOH630 3.5 26.5 1.0
O2 A:ITN502 3.7 30.2 1.0
OD2 A:ASP101 4.0 27.6 1.0
NZ A:LYS183 4.1 29.2 1.0
N A:TRP86 4.1 20.1 1.0
NH1 A:ARG222 4.1 24.2 1.0
N A:GLY85 4.2 20.3 1.0
CA A:GLY85 4.3 20.8 1.0
OD1 A:ASP101 4.3 27.5 1.0
CE A:LYS183 4.3 31.5 1.0
CB A:ASP147 4.4 19.6 1.0
CE1 A:HIS174 4.5 18.9 1.0
CG A:GLU149 4.5 25.9 1.0
C A:GLY85 4.5 21.6 1.0
C2 A:ITN502 4.6 30.0 1.0
CG A:ASP101 4.6 28.6 1.0
OE2 A:GLU149 4.7 32.1 1.0
OE1 A:GLU176 4.7 25.5 1.0
OH A:TYR82 4.8 23.4 1.0
CB A:TRP86 5.0 20.6 1.0

Magnesium binding site 2 out of 4 in 7rbx

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Magnesium binding site 2 out of 4 in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic 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 Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:32.5
occ:1.00
 OD2 B:ASP147 2.2 23.8 1.0
O B:HOH709 2.2 27.7 1.0
O B:HOH634 2.2 28.2 1.0
O B:HOH607 2.3 27.5 1.0
O2 B:ITN501 2.5 31.0 1.0
CG B:ASP147 3.2 24.8 1.0
C1 B:ITN501 3.4 34.1 1.0
OD1 B:ASP147 3.5 24.3 1.0
O B:HOH654 3.5 27.7 1.0
O1 B:ITN501 3.8 30.9 1.0
OD2 B:ASP101 3.9 26.7 1.0
NZ B:LYS183 4.0 28.1 1.0
N B:TRP86 4.0 21.6 1.0
N B:GLY85 4.1 22.0 1.0
NH1 B:ARG222 4.2 27.4 1.0
CA B:GLY85 4.2 22.8 1.0
OD1 B:ASP101 4.3 28.1 1.0
CE B:LYS183 4.3 29.8 1.0
C B:GLY85 4.5 22.8 1.0
CB B:ASP147 4.5 21.8 1.0
CG B:GLU149 4.5 25.4 1.0
CE1 B:HIS174 4.5 25.3 1.0
CG B:ASP101 4.5 27.8 1.0
OE2 B:GLU149 4.6 30.8 1.0
C2 B:ITN501 4.6 29.8 1.0
OE1 B:GLU176 4.8 26.0 1.0
OH B:TYR82 4.9 24.3 1.0
CD B:GLU149 5.0 30.5 1.0
CB B:TRP86 5.0 21.3 1.0
CA B:TRP86 5.0 21.8 1.0

Magnesium binding site 3 out of 4 in 7rbx

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Magnesium binding site 3 out of 4 in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic 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 Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:28.5
occ:1.00
 OD2 C:ASP147 2.2 21.7 1.0
O C:HOH689 2.2 27.0 1.0
O C:HOH690 2.2 23.6 1.0
O C:HOH615 2.4 27.8 1.0
O2 C:ITN502 2.5 28.3 1.0
CG C:ASP147 3.1 20.0 1.0
C1 C:ITN502 3.3 26.2 1.0
OD1 C:ASP147 3.5 20.6 1.0
O C:HOH611 3.5 24.5 1.0
O1 C:ITN502 3.6 27.7 1.0
OD2 C:ASP101 3.9 24.2 1.0
NZ C:LYS183 4.0 26.1 1.0
N C:TRP86 4.1 19.1 1.0
N C:GLY85 4.1 18.7 1.0
NH1 C:ARG222 4.2 24.6 1.0
CA C:GLY85 4.2 20.6 1.0
OD1 C:ASP101 4.2 25.2 1.0
CE C:LYS183 4.3 25.9 1.0
CG C:GLU149 4.4 22.8 1.0
C C:GLY85 4.5 24.0 1.0
CB C:ASP147 4.5 19.3 1.0
CG C:ASP101 4.5 26.7 1.0
CE1 C:HIS174 4.6 19.8 1.0
C2 C:ITN502 4.6 25.7 1.0
OE2 C:GLU149 4.6 29.9 1.0
OE1 C:GLU176 4.7 24.0 1.0
CD C:GLU149 4.9 25.0 1.0
OH C:TYR82 5.0 20.4 1.0
CB C:TRP86 5.0 19.1 1.0

Magnesium binding site 4 out of 4 in 7rbx

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Magnesium binding site 4 out of 4 in the Crystal Structure of Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic 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 Isocitrate Lyase and Phosphorylmutase:Isocitrate Lyase From Brucella Melitensis Biovar Abortus 2308 Bound to Itaconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:29.7
occ:1.00
 OD2 D:ASP147 2.2 22.6 1.0
O D:HOH621 2.2 27.0 1.0
O D:HOH647 2.2 28.3 1.0
O D:HOH605 2.3 28.1 1.0
O1 D:ITN502 2.3 30.5 1.0
CG D:ASP147 3.2 24.1 1.0
C1 D:ITN502 3.2 32.2 1.0
O D:HOH625 3.5 26.1 1.0
OD1 D:ASP147 3.5 23.0 1.0
O2 D:ITN502 3.6 28.4 1.0
OD2 D:ASP101 3.9 27.9 1.0
N D:TRP86 4.1 21.8 1.0
NZ D:LYS183 4.1 25.6 1.0
NH1 D:ARG222 4.1 27.2 1.0
N D:GLY85 4.1 23.1 1.0
OD1 D:ASP101 4.2 27.3 1.0
CA D:GLY85 4.3 22.9 1.0
CE D:LYS183 4.3 25.7 1.0
CG D:GLU149 4.4 26.4 1.0
C2 D:ITN502 4.5 26.9 1.0
C D:GLY85 4.5 21.1 1.0
CB D:ASP147 4.5 24.8 1.0
CG D:ASP101 4.5 26.5 1.0
OE2 D:GLU149 4.6 29.9 1.0
CE1 D:HIS174 4.6 20.8 1.0
OE1 D:GLU176 4.7 25.6 1.0
OH D:TYR82 4.9 24.3 1.0
CD D:GLU149 4.9 30.1 1.0
CB D:TRP86 5.0 23.4 1.0

Reference:

A.Demars, A.Vitali, A.Comein, E.Carlier, A.Azouz, S.Goriely, J.Smout, V.Flamand, M.Van Gysel, J.Wouters, J.Abendroth, T.E.Edwards, A.Machelart, E.Hoffmann, P.Brodin, X.De Bolle, E.Muraille. Aconitate Decarboxylase 1 Participates in the Control of Pulmonary Brucella Infection in Mice. Plos Pathog. V. 17 09887 2021.
ISSN: ESSN 1553-7374
PubMed: 34525130
DOI: 10.1371/JOURNAL.PPAT.1009887
Page generated: Fri Nov 5 15:33:51 2021

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