Magnesium in PDB 7rb1: Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid

Enzymatic activity of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid

All present enzymatic activity of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid:
4.1.3.1;

Protein crystallography data

The structure of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid, PDB code: 7rb1 was solved by I.V.Krieger, D.Mellott, T.Meek, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.57 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.068, 140.301, 160.693, 90, 90, 90
R / Rfree (%) 17.1 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid (pdb code 7rb1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid, PDB code: 7rb1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7rb1

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Magnesium binding site 1 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.9
occ:1.00
 O A:HOH602 2.0 22.9 1.0
OD2 A:ASP153 2.0 22.8 1.0
O05 A:48J501 2.0 24.8 1.0
O A:HOH618 2.1 22.3 1.0
O01 A:48J501 2.1 23.1 0.9
O A:HOH601 2.2 27.9 1.0
C02 A:48J501 2.8 26.0 0.8
C04 A:48J501 2.9 27.4 0.9
CG A:ASP153 3.0 19.4 1.0
OD1 A:ASP153 3.4 24.4 1.0
OD2 A:ASP108 3.9 24.3 1.0
NZ A:LYS189 3.9 32.2 1.0
N A:TRP93 4.0 20.4 1.0
O03 A:48J501 4.0 26.3 0.8
O06 A:48J501 4.1 34.8 0.8
N A:GLY92 4.1 20.5 1.0
OD1 A:ASP108 4.2 24.1 1.0
CA A:GLY92 4.2 19.5 1.0
OE2 A:GLU182 4.3 28.3 0.1
NH1 A:ARG228 4.3 32.1 1.0
CE A:LYS189 4.3 34.5 1.0
CB A:ASP153 4.3 16.1 1.0
OE2 A:GLU155 4.4 30.7 1.0
CG A:GLU155 4.5 27.7 1.0
O3 A:54I504 4.5 37.9 0.7
CG A:ASP108 4.5 25.1 1.0
C A:GLY92 4.5 22.1 1.0
OE1 A:GLU182 4.5 28.9 0.9
CE1 A:HIS180 4.6 21.6 1.0
N1 A:54I504 4.6 38.0 0.9
CD A:GLU155 4.7 33.3 1.0
OH A:TYR89 4.9 23.2 1.0
CB A:TRP93 4.9 21.4 1.0
CA A:TRP93 4.9 21.2 1.0

Magnesium binding site 2 out of 8 in 7rb1

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Magnesium binding site 2 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:24.7
occ:1.00
 O A:ALA276 2.2 26.5 1.0
O A:ALA279 2.3 24.2 1.0
O A:HOH754 2.4 28.6 1.0
OE1 A:GLN308 2.4 25.9 1.0
O2 A:GOL505 2.5 27.3 1.0
O A:HOH782 2.6 34.3 1.0
C2 A:GOL505 3.3 30.4 1.0
C A:ALA276 3.3 27.5 1.0
CD A:GLN308 3.3 26.8 1.0
C A:ALA279 3.5 26.7 1.0
NE2 A:GLN308 3.6 25.4 1.0
C3 A:GOL505 3.8 36.0 1.0
CA A:ALA276 4.0 25.9 1.0
N A:ALA279 4.1 25.0 1.0
O A:HOH626 4.1 26.0 1.0
N A:PRO277 4.3 22.8 1.0
O A:ASP25 4.3 32.0 1.0
CA A:ALA279 4.4 25.4 1.0
CB A:ALA276 4.4 24.7 1.0
N A:ASP280 4.5 22.6 1.0
CA A:PRO277 4.5 24.9 1.0
O A:HOH691 4.5 30.9 1.0
CA A:ASP280 4.6 22.3 1.0
C A:PRO277 4.6 28.0 1.0
C1 A:GOL505 4.6 34.9 1.0
CG A:GLN308 4.7 24.1 1.0
O A:HOH697 4.8 42.2 1.0
N A:PHE278 4.8 23.7 1.0
C A:ASP280 4.9 25.8 1.0
O3 A:GOL505 4.9 40.8 1.0
O1 A:GOL505 4.9 26.0 1.0
O A:PRO277 4.9 29.2 1.0

Magnesium binding site 3 out of 8 in 7rb1

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Magnesium binding site 3 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:26.6
occ:1.00
 O01 B:48J501 2.0 26.1 0.9
OD2 B:ASP153 2.1 25.2 1.0
O B:HOH652 2.1 24.5 1.0
O B:HOH606 2.1 25.4 1.0
O B:HOH604 2.2 25.4 1.0
O05 B:48J501 2.2 30.7 0.9
C04 B:48J501 2.7 30.5 0.9
C02 B:48J501 2.8 29.7 0.8
CG B:ASP153 3.1 24.5 1.0
OD1 B:ASP153 3.4 25.1 1.0
NZ B:LYS189 3.6 38.1 1.0
OD2 B:ASP108 3.9 27.5 1.0
O03 B:48J501 4.0 29.4 1.0
O3 B:54I504 4.0 37.9 1.0
N B:TRP93 4.1 24.4 1.0
O06 B:48J501 4.1 34.8 0.5
OD1 B:ASP108 4.2 26.8 1.0
N B:GLY92 4.2 22.4 1.0
CA B:GLY92 4.3 23.1 1.0
OE2 B:GLU155 4.3 28.2 1.0
CG B:GLU155 4.3 26.6 1.0
CE B:LYS189 4.4 30.6 1.0
CB B:ASP153 4.4 24.4 1.0
CG B:ASP108 4.4 28.8 1.0
C3 B:54I504 4.5 39.3 0.6
CE1 B:HIS180 4.5 23.6 1.0
NH1 B:ARG228 4.5 37.0 1.0
C B:GLY92 4.5 21.8 1.0
N1 B:54I504 4.6 44.5 0.8
OE2 B:GLU182 4.6 33.8 1.0
CD B:GLU155 4.6 30.1 1.0
OH B:TYR89 4.8 28.1 1.0
CB B:TRP93 5.0 23.3 1.0

Magnesium binding site 4 out of 8 in 7rb1

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Magnesium binding site 4 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:31.2
occ:1.00
 NE2 B:GLN308 2.2 26.5 1.0
O B:ALA276 2.2 32.5 1.0
O2 B:GOL505 2.4 30.9 1.0
O B:ALA279 2.4 25.4 1.0
O B:HOH774 2.4 34.8 1.0
O B:HOH670 2.5 29.4 1.0
CD B:GLN308 3.2 28.0 1.0
C2 B:GOL505 3.3 36.0 1.0
C B:ALA276 3.4 29.2 1.0
OE1 B:GLN308 3.4 33.3 1.0
C B:ALA279 3.6 31.5 1.0
C1 B:GOL505 3.8 39.5 1.0
O B:HOH669 4.0 27.6 1.0
CA B:ALA276 4.1 29.0 1.0
N B:ALA279 4.2 27.0 1.0
O B:HOH733 4.4 36.2 1.0
O B:ASP25 4.4 32.1 1.0
N B:PRO277 4.4 30.4 1.0
CA B:ALA279 4.5 29.8 1.0
CA B:PRO277 4.5 29.9 1.0
N B:ASP280 4.5 23.2 1.0
CB B:ALA276 4.5 30.4 1.0
CA B:ASP280 4.6 24.3 1.0
CG B:GLN308 4.6 36.1 1.0
C B:PRO277 4.6 30.6 1.0
C3 B:GOL505 4.6 35.2 1.0
O1 B:GOL505 4.8 42.4 1.0
O3 B:GOL505 4.8 25.9 1.0
O B:HOH641 4.8 42.6 1.0
C B:ASP280 4.8 27.0 1.0
N B:PHE278 4.9 29.5 1.0
O B:ASP280 4.9 27.6 1.0
O B:PRO277 5.0 28.7 1.0

Magnesium binding site 5 out of 8 in 7rb1

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Magnesium binding site 5 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:26.4
occ:1.00
 O03 C:48J501 1.9 28.8 0.9
O06 C:48J501 2.0 29.9 0.9
O C:HOH602 2.0 28.4 1.0
OD2 C:ASP153 2.1 24.8 1.0
O C:HOH649 2.1 26.9 1.0
O C:HOH608 2.2 24.7 1.0
C02 C:48J501 2.7 28.1 0.8
C04 C:48J501 2.9 29.9 0.9
CG C:ASP153 3.1 22.6 1.0
NZ C:LYS189 3.5 45.7 1.0
OD1 C:ASP153 3.5 23.7 1.0
O01 C:48J501 3.9 26.6 0.9
O05 C:48J501 3.9 37.9 0.8
OD2 C:ASP108 3.9 31.2 1.0
N C:TRP93 4.1 25.9 1.0
OD1 C:ASP108 4.1 27.9 1.0
N C:GLY92 4.2 23.5 1.0
NH1 C:ARG228 4.3 36.7 1.0
CA C:GLY92 4.3 23.6 1.0
O3 C:54I504 4.3 42.6 0.9
CB C:ASP153 4.4 23.5 1.0
N1 C:54I504 4.4 43.3 0.8
OE2 C:GLU155 4.4 32.1 1.0
CG C:ASP108 4.5 27.3 1.0
C C:GLY92 4.5 22.6 1.0
CE1 C:HIS180 4.5 24.1 1.0
OE2 C:GLU182 4.6 34.1 1.0
CE C:LYS189 4.6 40.6 1.0
CG C:GLU155 4.7 31.8 1.0
CD C:GLU155 4.9 32.7 1.0
OH C:TYR89 4.9 25.3 1.0
CB C:TRP93 5.0 21.0 1.0

Magnesium binding site 6 out of 8 in 7rb1

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Magnesium binding site 6 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:26.9
occ:1.00
 O C:ALA276 2.2 30.6 1.0
O C:ALA279 2.3 28.6 1.0
O C:HOH624 2.4 30.8 1.0
OE1 C:GLN308 2.5 27.3 1.0
O2 C:GOL505 2.5 29.8 1.0
O C:HOH749 2.6 35.7 1.0
C C:ALA276 3.3 27.8 1.0
CD C:GLN308 3.4 28.2 1.0
C C:ALA279 3.5 30.3 1.0
NE2 C:GLN308 3.6 25.5 1.0
C2 C:GOL505 3.7 39.6 1.0
C1 C:GOL505 3.9 42.0 1.0
CA C:ALA276 4.0 29.3 1.0
N C:ALA279 4.1 26.2 1.0
O C:HOH648 4.2 30.5 1.0
O C:HOH735 4.2 36.4 1.0
O C:ASP25 4.2 31.7 1.0
N C:PRO277 4.3 29.2 1.0
CA C:ALA279 4.4 27.9 1.0
CA C:PRO277 4.4 29.3 1.0
N C:ASP280 4.5 26.5 1.0
CB C:ALA276 4.5 31.1 1.0
C C:PRO277 4.5 28.7 1.0
CA C:ASP280 4.6 28.7 1.0
N C:PHE278 4.7 26.2 1.0
CG C:GLN308 4.8 28.3 1.0
O1 C:GOL505 4.8 46.1 1.0
O3 C:GOL505 4.8 26.7 1.0
C3 C:GOL505 4.9 35.9 1.0
C C:ASP280 4.9 28.8 1.0
O C:PRO277 4.9 29.8 1.0

Magnesium binding site 7 out of 8 in 7rb1

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Magnesium binding site 7 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:28.0
occ:1.00
 OD2 D:ASP153 2.0 25.9 1.0
O D:HOH628 2.0 29.4 1.0
O3 D:GLV501 2.1 27.5 1.0
O D:HOH608 2.1 29.7 1.0
O1 D:GLV501 2.2 31.6 1.0
O D:HOH612 2.2 26.1 1.0
C2 D:GLV501 2.8 33.0 1.0
C1 D:GLV501 2.9 37.1 1.0
CG D:ASP153 3.1 27.3 1.0
OD1 D:ASP153 3.5 24.2 1.0
NZ D:LYS189 3.6 42.9 1.0
OD2 D:ASP108 3.9 30.9 1.0
N D:TRP93 4.0 26.1 1.0
O2 D:GLV501 4.0 35.8 1.0
N D:GLY92 4.1 24.3 1.0
OD1 D:ASP108 4.2 29.9 1.0
CA D:GLY92 4.2 21.4 1.0
CB D:ASP153 4.4 23.6 1.0
NH1 D:ARG228 4.4 37.6 1.0
OE1 D:GLU155 4.4 33.7 1.0
C D:GLY92 4.5 23.7 1.0
OE1 D:GLU182 4.5 39.1 1.0
CG D:ASP108 4.5 29.1 1.0
CE D:LYS189 4.5 36.4 1.0
CG D:GLU155 4.6 29.9 1.0
CE1 D:HIS180 4.6 23.9 1.0
N1 D:54I504 4.7 52.7 0.8
CD D:GLU155 4.8 35.0 1.0
O3 D:54I504 4.8 53.6 0.9
OH D:TYR89 4.9 25.9 1.0
CB D:TRP93 5.0 27.5 1.0
CA D:TRP93 5.0 24.1 1.0

Magnesium binding site 8 out of 8 in 7rb1

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Magnesium binding site 8 out of 8 in the Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Isocitrate Lyase-1 From Mycobacterium Tuberculosis Covalently Modified By 5-Descarboxy-5-Nitro-D-Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:29.8
occ:1.00
 O2 D:GOL505 2.1 33.1 1.0
O D:ALA276 2.3 28.1 1.0
O D:HOH692 2.3 31.8 1.0
O D:ALA279 2.4 29.4 1.0
OE1 D:GLN308 2.4 29.5 1.0
O D:HOH754 2.6 33.5 1.0
C2 D:GOL505 3.3 34.7 1.0
C D:ALA276 3.4 27.5 1.0
CD D:GLN308 3.4 30.1 1.0
C D:ALA279 3.5 29.0 1.0
NE2 D:GLN308 3.7 27.2 1.0
CA D:ALA276 4.0 27.8 1.0
C3 D:GOL505 4.0 40.2 1.0
O D:HOH630 4.1 27.3 1.0
N D:ALA279 4.1 26.0 1.0
O D:ASP25 4.3 31.1 1.0
C1 D:GOL505 4.3 36.6 1.0
N D:PRO277 4.3 27.2 1.0
CB D:ALA276 4.4 29.5 1.0
CA D:ALA279 4.4 29.2 1.0
N D:ASP280 4.4 25.0 1.0
CA D:PRO277 4.5 26.4 1.0
O D:HOH712 4.5 34.2 1.0
CA D:ASP280 4.5 25.5 1.0
O3 D:GOL505 4.6 41.1 1.0
C D:PRO277 4.6 30.0 1.0
O D:HOH657 4.7 45.1 1.0
CG D:GLN308 4.8 31.8 1.0
N D:PHE278 4.8 28.6 1.0
C D:ASP280 4.9 27.7 1.0

Reference:

D.M.Mellott, D.Torres, I.V.Krieger, S.A.Cameron, Z.Moghadamchargari, A.Laganowsky, J.C.Sacchettini, T.D.Meek, L.D.Harris. Mechanism-Based Inactivation of Mycobacterium Tuberculosis Isocitrate Lyase 1 By (2 R ,3 S )-2-Hydroxy-3-(Nitromethyl)Succinic Acid. J.Am.Chem.Soc. V. 143 17666 2021.
ISSN: ESSN 1520-5126
PubMed: 34664502
DOI: 10.1021/JACS.1C07970
Page generated: Fri Dec 17 10:52:36 2021

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