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Magnesium in PDB 6vb9: Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis

Enzymatic activity of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis

All present enzymatic activity of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis:
4.1.3.1;

Protein crystallography data

The structure of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6vb9 was solved by I.V.Krieger, T.V.Pham, T.D.Meek, J.C.Sacchettini, Tb Structural Genomicsconsortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.065, 129.065, 167.825, 90, 90, 90
R / Rfree (%) 17.9 / 22.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis (pdb code 6vb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6vb9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6vb9

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Magnesium binding site 1 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.4
occ:1.00
 OD2 A:ASP153 2.0 16.6 1.0
O5 A:OXD503 2.0 17.9 0.5
O5 A:OXD503 2.0 17.9 0.5
O A:HOH643 2.0 19.3 1.0
O6 A:OXD503 2.1 20.4 0.5
O6 A:OXD503 2.1 20.4 0.5
O A:HOH606 2.2 18.1 1.0
O A:HOH622 2.2 14.6 1.0
C2 A:OXD503 2.9 18.9 0.5
C2 A:OXD503 2.9 18.9 0.5
C1 A:OXD503 3.0 20.3 0.5
C1 A:OXD503 3.0 20.3 0.5
CG A:ASP153 3.0 16.1 1.0
OD1 A:ASP153 3.4 18.4 1.0
OD2 A:ASP108 3.9 15.3 1.0
NZ A:LYS189 4.0 15.7 1.0
O3 A:OXD503 4.0 21.0 0.7
N A:TRP93 4.1 13.9 1.0
O4 A:OXD503 4.1 19.0 0.5
O4 A:OXD503 4.1 19.0 0.5
NH1 A:ARG228 4.1 21.4 1.0
O01 A:QVA191 4.2 19.3 1.0
OD1 A:ASP108 4.3 18.3 1.0
N A:GLY92 4.3 17.8 1.0
CB A:ASP153 4.3 18.0 1.0
CA A:GLY92 4.3 18.9 1.0
CE A:LYS189 4.4 19.8 1.0
CE1 A:HIS180 4.4 19.0 1.0
CG A:GLU155 4.4 22.8 1.0
OE1 A:GLU155 4.4 19.5 1.0
OE1 A:GLU182 4.5 18.2 1.0
CG A:ASP108 4.5 17.6 1.0
C A:GLY92 4.5 17.3 1.0
C02 A:QVA191 4.8 24.0 1.0
CD A:GLU155 4.8 16.4 1.0
OH A:TYR89 4.8 24.3 1.0

Magnesium binding site 2 out of 7 in 6vb9

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Magnesium binding site 2 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.1
occ:1.00
 O A:ALA276 2.2 29.6 1.0
O A:HOH765 2.2 30.8 1.0
OE1 A:GLN308 2.3 27.8 1.0
O A:HOH818 2.5 34.8 1.0
O A:ALA279 2.5 25.9 1.0
O A:HOH827 2.7 25.5 1.0
CD A:GLN308 3.3 27.2 1.0
C A:ALA276 3.3 28.0 1.0
NE2 A:GLN308 3.7 26.7 1.0
C A:ALA279 3.7 28.4 1.0
CA A:ALA276 4.0 30.1 1.0
O A:HOH702 4.1 28.6 1.0
O A:ASP25 4.2 35.4 1.0
N A:ALA279 4.3 22.7 1.0
N A:PRO277 4.3 29.7 1.0
CB A:ALA276 4.4 28.3 1.0
CA A:PRO277 4.5 30.0 1.0
O A:HOH679 4.5 29.7 1.0
CA A:ALA279 4.6 26.9 1.0
CG A:GLN308 4.6 28.7 1.0
N A:ASP280 4.7 24.9 1.0
C A:PRO277 4.7 31.8 1.0
O A:HOH767 4.7 31.6 1.0
CA A:ASP280 4.7 21.7 1.0
N A:PHE278 4.9 30.7 1.0

Magnesium binding site 3 out of 7 in 6vb9

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Magnesium binding site 3 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:19.5
occ:1.00
 O6 B:OXD503 2.0 22.4 1.0
OD2 B:ASP153 2.1 19.0 1.0
O B:HOH645 2.1 17.3 1.0
O B:HOH619 2.2 15.8 1.0
O5 B:OXD503 2.2 23.6 1.0
O B:HOH602 2.2 16.5 1.0
C1 B:OXD503 2.9 26.2 1.0
C2 B:OXD503 3.0 22.0 1.0
CG B:ASP153 3.1 17.3 1.0
OD1 B:ASP153 3.5 18.0 1.0
OD2 B:ASP108 3.9 18.4 1.0
O4 B:OXD503 4.0 24.9 0.6
NZ B:LYS189 4.0 18.5 1.0
N B:TRP93 4.0 16.6 1.0
O01 B:QVA191 4.1 22.8 1.0
O3 B:OXD503 4.2 23.1 1.0
N B:GLY92 4.2 17.4 1.0
NH1 B:ARG228 4.2 25.4 1.0
CA B:GLY92 4.2 20.8 1.0
OD1 B:ASP108 4.2 16.1 1.0
CG B:GLU155 4.3 21.6 1.0
CE B:LYS189 4.3 17.0 1.0
OE2 B:GLU155 4.3 20.4 1.0
CB B:ASP153 4.4 16.4 1.0
CG B:ASP108 4.5 17.1 1.0
C B:GLY92 4.5 18.5 1.0
CE1 B:HIS180 4.6 21.0 1.0
OE1 B:GLU182 4.6 24.4 1.0
CD B:GLU155 4.7 20.0 1.0
C02 B:QVA191 4.7 24.5 1.0
OH B:TYR89 4.9 23.5 1.0
CB B:TRP93 4.9 19.2 1.0
CA B:TRP93 5.0 18.6 1.0

Magnesium binding site 4 out of 7 in 6vb9

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Magnesium binding site 4 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:21.5
occ:1.00
 OD2 C:ASP153 2.0 21.2 1.0
O C:HOH628 2.0 17.4 1.0
O5 C:OXD504 2.1 23.2 0.5
O5 C:OXD504 2.1 23.2 0.5
O C:HOH640 2.1 18.0 1.0
O C:HOH614 2.2 16.9 1.0
O4 C:OXD504 2.2 21.4 0.5
O4 C:OXD504 2.2 21.4 0.5
C1 C:OXD504 2.8 22.6 0.5
C1 C:OXD504 2.8 22.6 0.5
C2 C:OXD504 2.8 24.1 0.5
C2 C:OXD504 2.8 24.2 0.5
CG C:ASP153 3.1 20.8 1.0
OD1 C:ASP153 3.4 18.5 1.0
NZ C:LYS189 3.9 18.2 1.0
OD2 C:ASP108 3.9 21.1 1.0
N C:TRP93 4.0 18.0 1.0
O6 C:OXD504 4.0 23.7 0.5
O6 C:OXD504 4.0 23.8 0.5
O3 C:OXD504 4.1 23.4 0.5
N C:GLY92 4.1 18.1 1.0
OD1 C:ASP108 4.2 18.2 1.0
CE C:LYS189 4.2 17.6 1.0
CA C:GLY92 4.2 15.7 1.0
CG C:GLU155 4.2 19.9 1.0
O03 C:QVA191 4.3 22.1 1.0
OE2 C:GLU155 4.3 20.2 1.0
CB C:ASP153 4.3 19.5 1.0
NH1 C:ARG228 4.4 24.0 1.0
C C:GLY92 4.5 20.8 1.0
CG C:ASP108 4.5 20.5 1.0
CE1 C:HIS180 4.5 18.0 1.0
OE1 C:GLU182 4.6 16.1 1.0
CD C:GLU155 4.6 19.8 1.0
OH C:TYR89 4.9 23.9 1.0
C02 C:QVA191 4.9 26.2 1.0
CA C:TRP93 4.9 19.1 1.0
CB C:TRP93 5.0 22.8 1.0

Magnesium binding site 5 out of 7 in 6vb9

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Magnesium binding site 5 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:29.3
occ:1.00
 O C:ALA276 2.3 26.6 1.0
O C:ALA279 2.4 22.9 1.0
O C:HOH636 2.4 27.6 1.0
OE1 C:GLN308 2.4 25.0 1.0
O C:HOH814 2.6 26.9 1.0
O C:HOH800 2.6 26.1 1.0
CD C:GLN308 3.4 27.6 1.0
C C:ALA276 3.4 21.5 1.0
C C:ALA279 3.5 26.5 1.0
NE2 C:GLN308 3.7 26.4 1.0
O C:HOH778 3.9 26.9 1.0
CA C:ALA276 4.1 23.0 1.0
N C:ALA279 4.2 26.1 1.0
O C:ASP25 4.2 28.5 1.0
CA C:ALA279 4.4 24.2 1.0
N C:PRO277 4.4 20.7 1.0
N C:ASP280 4.5 18.8 1.0
O C:HOH716 4.5 34.4 1.0
O C:HOH764 4.5 37.8 1.0
CB C:ALA276 4.5 26.2 1.0
CA C:PRO277 4.5 24.9 1.0
O C:HOH766 4.6 27.3 1.0
CA C:ASP280 4.6 25.3 1.0
C C:PRO277 4.6 26.4 1.0
CG C:GLN308 4.8 30.0 1.0
C C:ASP280 4.9 28.2 1.0
O C:ASP280 4.9 26.7 1.0
N C:PHE278 4.9 21.2 1.0
CB C:ALA279 4.9 26.3 1.0
O C:PRO277 4.9 24.6 1.0

Magnesium binding site 6 out of 7 in 6vb9

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Magnesium binding site 6 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:30.8
occ:1.00
 O D:HOH730 2.3 24.7 1.0
O D:ALA276 2.4 24.2 1.0
OE1 D:GLN308 2.4 26.2 1.0
O D:HOH738 2.4 26.7 1.0
O D:ALA279 2.5 25.0 1.0
O D:HOH796 2.5 28.1 1.0
CD D:GLN308 3.3 28.9 1.0
C D:ALA276 3.5 22.0 1.0
NE2 D:GLN308 3.6 24.7 1.0
C D:ALA279 3.6 29.4 1.0
O D:HOH696 4.1 26.9 1.0
O D:ASP25 4.1 33.1 1.0
CA D:ALA276 4.2 26.4 1.0
N D:ALA279 4.2 26.0 1.0
O D:HOH646 4.3 33.5 1.0
N D:PRO277 4.4 25.2 1.0
CA D:ALA279 4.5 27.8 1.0
CA D:PRO277 4.5 24.7 1.0
CB D:ALA276 4.6 28.7 1.0
O D:HOH720 4.6 27.1 1.0
N D:ASP280 4.6 25.2 1.0
C D:PRO277 4.7 26.4 1.0
CA D:ASP280 4.7 24.4 1.0
CG D:GLN308 4.7 27.2 1.0
CB D:ALA279 4.9 29.4 1.0
N D:PHE278 4.9 23.0 1.0
C D:ASP280 5.0 23.8 1.0

Magnesium binding site 7 out of 7 in 6vb9

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Magnesium binding site 7 out of 7 in the Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Covalent Adduct of Cis-2,3-Epoxysuccinic Acid with Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:24.7
occ:1.00
 OD2 D:ASP153 2.0 24.5 1.0
O4 D:OXD503 2.0 23.5 0.5
O4 D:OXD503 2.0 23.5 0.5
O D:HOH605 2.1 18.2 1.0
O D:HOH620 2.1 20.9 1.0
O5 D:OXD503 2.1 23.8 0.5
O5 D:OXD503 2.1 23.8 0.5
O D:HOH633 2.3 27.2 1.0
C2 D:OXD503 2.8 23.1 0.5
C2 D:OXD503 2.8 23.1 0.5
C1 D:OXD503 3.0 23.5 0.5
C1 D:OXD503 3.0 23.5 0.5
CG D:ASP153 3.1 21.6 1.0
OD1 D:ASP153 3.6 19.5 1.0
O3 D:OXD503 3.8 25.0 0.5
N D:TRP93 3.8 19.9 1.0
OD2 D:ASP108 3.9 21.9 1.0
N D:GLY92 4.0 19.3 1.0
O6 D:OXD503 4.0 23.2 0.5
O6 D:OXD503 4.0 23.2 0.5
NZ D:LYS189 4.1 20.2 1.0
CA D:GLY92 4.1 18.9 1.0
OD1 D:ASP108 4.1 22.5 1.0
CG D:GLU155 4.2 23.0 1.0
CB D:ASP153 4.3 17.1 1.0
C D:GLY92 4.3 22.8 1.0
NH1 D:ARG228 4.3 25.4 1.0
O01 D:QVA191 4.3 26.0 1.0
OE2 D:GLU155 4.3 23.4 1.0
CE D:LYS189 4.4 22.7 1.0
CG D:ASP108 4.5 25.8 1.0
CE1 D:HIS180 4.6 19.9 1.0
CD D:GLU155 4.6 19.2 1.0
CA D:TRP93 4.8 18.9 1.0
CB D:TRP93 4.8 21.3 1.0
OE1 D:GLU182 4.8 23.9 1.0
OH D:TYR89 4.9 23.9 1.0

Reference:

T.V.Pham, K.Chen, I.K.Krieger, J.C.Sacchettini, T.Emde, T.D.Meek. Covalent Inactivation of Mycobacterium Tuberculosis Isocitrate Lyase By Cis-2,3-Epoxy-Succinate To Be Published.
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