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Magnesium in PDB 6wsi: Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis

Enzymatic activity of Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis

All present enzymatic activity of Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis:
4.1.3.1;

Protein crystallography data

The structure of Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6wsi was solved by I.V.Krieger, D.Mellott, 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) 71.05 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.17, 134.205, 161.036, 90, 90, 90
R / Rfree (%) 16.4 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis (pdb code 6wsi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis, PDB code: 6wsi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6wsi

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Magnesium binding site 1 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.0
occ:1.00
 OD2 A:ASP153 2.0 17.0 1.0
O A:HOH663 2.0 17.3 1.0
O1 A:GLV503 2.1 20.0 1.0
O3 A:GLV503 2.1 17.6 1.0
O A:HOH613 2.1 18.7 1.0
O A:HOH616 2.2 19.8 1.0
C1 A:GLV503 2.7 21.6 1.0
C2 A:GLV503 2.7 21.0 1.0
CG A:ASP153 3.1 17.6 1.0
OD1 A:ASP153 3.5 16.8 1.0
OD2 A:ASP108 4.0 18.8 1.0
O2 A:GLV503 4.0 21.2 1.0
N A:TRP93 4.0 15.8 1.0
NZ A:LYS189 4.0 20.0 1.0
N A:GLY92 4.1 14.7 1.0
CA A:GLY92 4.2 15.1 1.0
O08 A:U9S504 4.3 24.6 1.0
OD1 A:ASP108 4.3 17.7 1.0
CB A:ASP153 4.4 14.2 1.0
NH1 A:ARG228 4.4 21.6 1.0
CE A:LYS189 4.4 21.5 1.0
OE2 A:GLU155 4.5 20.4 1.0
CE1 A:HIS180 4.5 16.1 1.0
C A:GLY92 4.5 18.2 1.0
CG A:ASP108 4.6 17.4 1.0
OE1 A:GLU182 4.6 19.3 1.0
C05 A:U9S504 4.6 33.0 1.0
CG A:GLU155 4.7 21.1 1.0
OH A:TYR89 4.8 22.3 1.0
C06 A:U9S504 4.8 29.9 1.0
CD A:GLU155 4.9 22.5 1.0
CB A:TRP93 5.0 17.2 1.0
CA A:TRP93 5.0 15.1 1.0

Magnesium binding site 2 out of 8 in 6wsi

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Magnesium binding site 2 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:23.5
occ:1.00
 O A:ALA276 2.3 23.1 1.0
O A:ALA279 2.3 19.6 1.0
O2 A:GOL505 2.3 23.9 1.0
O A:HOH706 2.4 23.5 1.0
OE1 A:GLN308 2.4 22.8 1.0
O A:HOH850 2.7 27.8 1.0
CD A:GLN308 3.3 21.2 1.0
C2 A:GOL505 3.4 29.3 1.0
C A:ALA276 3.4 19.9 1.0
C A:ALA279 3.5 24.8 1.0
NE2 A:GLN308 3.6 19.9 1.0
C3 A:GOL505 3.9 31.8 1.0
O A:HOH639 4.0 22.3 1.0
CA A:ALA276 4.1 22.3 1.0
N A:ALA279 4.2 18.9 1.0
O A:ASP25 4.3 24.1 1.0
CA A:ALA279 4.4 21.9 1.0
N A:ASP280 4.4 18.3 1.0
O A:HOH650 4.4 23.5 1.0
O A:HOH847 4.5 31.4 1.0
N A:PRO277 4.5 23.7 1.0
CA A:ASP280 4.5 21.5 1.0
CB A:ALA276 4.6 21.7 1.0
CA A:PRO277 4.6 22.4 1.0
C1 A:GOL505 4.6 29.0 1.0
C A:PRO277 4.7 25.0 1.0
O3 A:GOL505 4.7 34.9 1.0
CG A:GLN308 4.7 20.6 1.0
C A:ASP280 4.8 19.2 1.0
O A:HOH607 4.8 35.3 1.0
O1 A:GOL505 4.8 24.0 1.0
O A:ASP280 4.9 20.9 1.0
N A:PHE278 4.9 21.3 1.0

Magnesium binding site 3 out of 8 in 6wsi

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Magnesium binding site 3 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:19.0
occ:1.00
 OD2 B:ASP153 2.1 17.5 1.0
O3 B:GLV503 2.1 18.9 1.0
O B:HOH629 2.1 18.0 1.0
O B:HOH612 2.1 17.1 1.0
O B:HOH619 2.1 17.8 1.0
O1 B:GLV503 2.2 20.1 1.0
C2 B:GLV503 2.9 19.0 1.0
C1 B:GLV503 2.9 20.9 1.0
CG B:ASP153 3.1 19.2 1.0
OD1 B:ASP153 3.4 16.9 1.0
NZ B:LYS189 4.0 22.6 1.0
OD2 B:ASP108 4.0 19.9 1.0
N B:TRP93 4.1 14.8 1.0
O2 B:GLV503 4.1 18.8 1.0
N B:GLY92 4.2 15.8 1.0
CA B:GLY92 4.2 15.9 1.0
OD1 B:ASP108 4.3 19.1 1.0
NH1 B:ARG228 4.3 21.7 1.0
O08 B:U9S504 4.3 21.1 1.0
CE B:LYS189 4.3 22.0 1.0
CB B:ASP153 4.4 17.4 1.0
OE2 B:GLU155 4.4 20.8 1.0
CE1 B:HIS180 4.5 16.2 1.0
C B:GLY92 4.5 18.2 1.0
CG B:GLU155 4.5 21.0 1.0
OE1 B:GLU182 4.6 18.9 1.0
CG B:ASP108 4.6 19.6 1.0
C05 B:U9S504 4.7 33.5 1.0
OH B:TYR89 4.8 19.9 1.0
CD B:GLU155 4.8 24.2 1.0
C06 B:U9S504 4.9 30.1 1.0

Magnesium binding site 4 out of 8 in 6wsi

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Magnesium binding site 4 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:21.9
occ:1.00
 O B:ALA276 2.3 22.5 1.0
O2 B:GOL506 2.3 24.5 1.0
OE1 B:GLN308 2.4 20.4 1.0
O B:ALA279 2.4 22.6 1.0
O B:HOH706 2.4 22.0 1.0
O B:HOH842 2.6 27.2 1.0
C2 B:GOL506 3.3 26.5 1.0
CD B:GLN308 3.3 23.1 1.0
C B:ALA276 3.4 18.2 1.0
C B:ALA279 3.6 21.6 1.0
NE2 B:GLN308 3.6 21.6 1.0
C3 B:GOL506 3.8 32.1 1.0
CA B:ALA276 4.1 19.8 1.0
O B:HOH671 4.2 20.2 1.0
N B:ALA279 4.2 23.8 1.0
O B:ASP25 4.3 23.3 1.0
N B:PRO277 4.4 21.7 1.0
O B:HOH687 4.4 26.7 1.0
O B:HOH850 4.4 30.5 1.0
CA B:ALA279 4.4 21.3 1.0
CB B:ALA276 4.5 22.0 1.0
N B:ASP280 4.5 18.0 1.0
CA B:PRO277 4.5 20.1 1.0
CA B:ASP280 4.6 19.1 1.0
C1 B:GOL506 4.6 28.2 1.0
C B:PRO277 4.6 22.0 1.0
CG B:GLN308 4.7 21.9 1.0
O3 B:GOL506 4.8 33.4 1.0
O1 B:GOL506 4.8 22.5 1.0
N B:PHE278 4.9 19.8 1.0
C B:ASP280 4.9 19.7 1.0
O B:ASP280 4.9 21.9 1.0
O B:HOH772 5.0 37.1 1.0
O B:PRO277 5.0 22.4 1.0

Magnesium binding site 5 out of 8 in 6wsi

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Magnesium binding site 5 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:18.1
occ:1.00
 O2 C:GLV503 2.0 18.4 1.0
OD2 C:ASP153 2.1 16.9 1.0
O C:HOH612 2.1 18.6 1.0
O1 C:GLV503 2.1 20.5 1.0
O C:HOH655 2.1 17.9 1.0
O C:HOH611 2.2 17.3 1.0
C2 C:GLV503 2.7 23.1 1.0
C1 C:GLV503 2.8 22.4 1.0
CG C:ASP153 3.1 16.5 1.0
OD1 C:ASP153 3.5 18.9 1.0
O3 C:GLV503 4.0 22.6 1.0
OD2 C:ASP108 4.0 19.5 1.0
NZ C:LYS189 4.0 20.1 1.0
N C:TRP93 4.0 13.7 1.0
N C:GLY92 4.1 15.2 1.0
OD1 C:ASP108 4.3 17.8 1.0
CA C:GLY92 4.3 16.4 1.0
O07 C:U9S504 4.3 22.1 1.0
CE C:LYS189 4.4 21.2 1.0
NH1 C:ARG228 4.4 21.7 1.0
CB C:ASP153 4.4 15.9 1.0
OE2 C:GLU155 4.4 19.4 1.0
CG C:GLU155 4.5 18.1 1.0
C C:GLY92 4.5 17.1 1.0
CE1 C:HIS180 4.5 17.5 1.0
CG C:ASP108 4.6 19.4 1.0
C05 C:U9S504 4.6 33.5 1.0
OE1 C:GLU182 4.6 18.9 1.0
CD C:GLU155 4.8 22.1 1.0
OH C:TYR89 4.8 19.9 1.0
C06 C:U9S504 4.8 29.3 1.0
CB C:TRP93 4.9 17.7 1.0
CA C:TRP93 5.0 16.5 1.0

Magnesium binding site 6 out of 8 in 6wsi

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Magnesium binding site 6 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:20.7
occ:1.00
 O C:ALA276 2.3 23.7 1.0
OE1 C:GLN308 2.3 21.5 1.0
O2 C:GOL505 2.3 22.4 1.0
O C:ALA279 2.3 20.5 1.0
O C:HOH710 2.4 24.2 1.0
O C:HOH858 2.7 30.4 1.0
CD C:GLN308 3.3 21.4 1.0
C2 C:GOL505 3.3 25.4 1.0
C C:ALA276 3.4 20.4 1.0
C C:ALA279 3.5 22.0 1.0
NE2 C:GLN308 3.6 21.8 1.0
C1 C:GOL505 3.8 33.3 1.0
CA C:ALA276 4.1 21.0 1.0
O C:HOH675 4.1 22.2 1.0
N C:ALA279 4.2 21.5 1.0
O C:HOH866 4.3 37.6 1.0
O C:ASP25 4.4 24.2 1.0
CA C:ALA279 4.4 21.2 1.0
N C:PRO277 4.4 22.2 1.0
O C:HOH742 4.5 28.9 1.0
N C:ASP280 4.5 19.3 1.0
CB C:ALA276 4.5 24.4 1.0
CA C:ASP280 4.5 20.4 1.0
O C:HOH764 4.6 35.8 1.0
CA C:PRO277 4.6 21.8 1.0
C3 C:GOL505 4.6 27.3 1.0
CG C:GLN308 4.7 25.3 1.0
C C:PRO277 4.7 23.0 1.0
O3 C:GOL505 4.8 22.0 1.0
C C:ASP280 4.8 23.9 1.0
O C:ASP280 4.8 19.9 1.0
N C:PHE278 4.9 18.7 1.0
O1 C:GOL505 5.0 31.9 1.0

Magnesium binding site 7 out of 8 in 6wsi

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Magnesium binding site 7 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:19.9
occ:1.00
 O D:ALA276 2.2 18.9 1.0
O D:ALA279 2.3 17.6 1.0
OE1 D:GLN308 2.4 20.3 1.0
O D:HOH673 2.4 22.3 1.0
O2 D:GOL505 2.5 23.1 1.0
O D:HOH846 2.7 28.6 1.0
CD D:GLN308 3.3 20.7 1.0
C D:ALA276 3.3 18.3 1.0
C2 D:GOL505 3.5 23.9 1.0
C D:ALA279 3.5 21.4 1.0
NE2 D:GLN308 3.6 18.9 1.0
C1 D:GOL505 3.9 29.8 1.0
CA D:ALA276 4.0 20.6 1.0
O D:HOH634 4.1 18.1 1.0
N D:ALA279 4.1 20.4 1.0
O D:ASP25 4.3 20.8 1.0
N D:PRO277 4.3 20.3 1.0
O D:HOH842 4.3 31.0 1.0
CA D:ALA279 4.4 20.7 1.0
N D:ASP280 4.4 17.8 1.0
CB D:ALA276 4.4 21.6 1.0
O D:HOH660 4.5 25.8 1.0
CA D:PRO277 4.5 19.8 1.0
CA D:ASP280 4.5 19.0 1.0
C D:PRO277 4.6 20.7 1.0
O D:HOH658 4.6 36.6 1.0
CG D:GLN308 4.7 18.5 1.0
C3 D:GOL505 4.7 25.3 1.0
N D:PHE278 4.8 19.3 1.0
O3 D:GOL505 4.8 21.2 1.0
C D:ASP280 4.9 23.7 1.0
O1 D:GOL505 4.9 33.2 1.0
CB D:ALA279 5.0 20.0 1.0
O D:ASP280 5.0 21.1 1.0

Magnesium binding site 8 out of 8 in 6wsi

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Magnesium binding site 8 out of 8 in the Intact Cis-2,3-Epoxysuccinic Acid Bound to 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 8 of Intact Cis-2,3-Epoxysuccinic Acid Bound to Isocitrate Lyase-1 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:18.7
occ:1.00
 OD2 D:ASP153 2.1 16.9 1.0
O D:HOH677 2.1 19.7 1.0
O D:HOH623 2.1 17.5 1.0
O2 D:GLV503 2.1 17.1 1.0
O D:HOH612 2.2 16.5 1.0
O1 D:GLV503 2.2 22.6 1.0
C2 D:GLV503 2.9 19.5 1.0
C1 D:GLV503 2.9 21.6 1.0
CG D:ASP153 3.1 17.1 1.0
OD1 D:ASP153 3.5 17.9 1.0
NZ D:LYS189 4.0 19.8 1.0
OD2 D:ASP108 4.0 18.9 1.0
N D:TRP93 4.1 14.8 1.0
O3 D:GLV503 4.1 19.3 1.0
N D:GLY92 4.1 16.2 1.0
CA D:GLY92 4.2 17.5 1.0
OD1 D:ASP108 4.3 18.3 1.0
O07 D:U9S504 4.3 24.3 1.0
NH1 D:ARG228 4.4 21.0 1.0
CB D:ASP153 4.4 13.5 1.0
OE2 D:GLU155 4.4 20.5 1.0
CE D:LYS189 4.5 23.1 1.0
CE1 D:HIS180 4.5 15.8 1.0
CG D:GLU155 4.5 19.5 1.0
C D:GLY92 4.5 16.8 1.0
CG D:ASP108 4.6 19.2 1.0
OE1 D:GLU182 4.6 19.4 1.0
C05 D:U9S504 4.8 32.1 1.0
CD D:GLU155 4.8 21.8 1.0
OH D:TYR89 4.8 20.0 1.0
C06 D:U9S504 4.9 29.1 1.0
CB D:TRP93 5.0 14.7 1.0

Reference:

T.V.Pham, D.M.Mellott, Z.Moghadamchargari, K.Chen, I.Krieger, A.Laganowsky, J.C.Sacchettini, T.D.Meek. Covalent Inactivation of Mycobacterium Tuberculosis Isocitrate Lyase By Cis -2,3-Epoxy-Succinic Acid. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 33688722
DOI: 10.1021/ACSCHEMBIO.0C00740
Page generated: Tue Oct 1 23:11:40 2024

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