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Magnesium in PDB 6xpp: Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase

Enzymatic activity of Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase

All present enzymatic activity of Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase, PDB code: 6xpp was solved by B.X.C.Kwai, G.Bashiri, I.K.H.Leung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.314, 133.171, 159.318, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase (pdb code 6xpp). 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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase, PDB code: 6xpp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6xpp

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Magnesium binding site 1 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.6
occ:1.00
 OD2 A:ASP153 2.1 18.2 1.0
O A:HOH660 2.2 22.5 1.0
O A:HOH625 2.2 21.6 1.0
O A:HOH604 2.3 25.1 1.0
O1 A:ITN501 2.4 30.3 1.0
CG A:ASP153 3.1 16.0 1.0
C1 A:ITN501 3.4 27.8 1.0
OD1 A:ASP153 3.4 16.3 1.0
O A:HOH733 3.4 26.8 1.0
O2 A:ITN501 3.7 26.8 1.0
OD2 A:ASP108 3.9 21.4 1.0
NZ A:LYS189 4.1 31.4 1.0
N A:TRP93 4.1 15.5 1.0
NH1 A:ARG228 4.1 21.7 1.0
N A:GLY92 4.2 14.3 1.0
OD1 A:ASP108 4.3 21.0 1.0
CA A:GLY92 4.3 14.5 1.0
CE1 A:HIS180 4.4 15.4 1.0
CE A:LYS189 4.4 28.5 1.0
CB A:ASP153 4.4 15.6 1.0
CG A:ASP108 4.5 21.5 1.0
OE2 A:GLU155 4.5 22.8 1.0
C A:GLY92 4.6 14.2 1.0
C2 A:ITN501 4.7 30.4 1.0
OE1 A:GLU182 4.7 19.4 1.0
CG A:GLU155 4.7 20.8 1.0
OH A:TYR89 4.8 17.8 1.0
CB A:TRP93 4.9 14.9 1.0
CD A:GLU155 5.0 26.9 1.0

Magnesium binding site 2 out of 8 in 6xpp

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Magnesium binding site 2 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:20.7
occ:1.00
 O A:ALA276 2.3 20.3 1.0
OE1 A:GLN308 2.3 20.0 1.0
O A:ALA279 2.3 19.3 1.0
O A:HOH962 2.4 21.8 1.0
O A:HOH763 2.4 22.1 1.0
O A:HOH938 2.5 28.8 1.0
CD A:GLN308 3.3 17.2 1.0
C A:ALA276 3.4 18.6 1.0
C A:ALA279 3.5 19.7 1.0
NE2 A:GLN308 3.5 17.8 1.0
CA A:ALA276 4.1 18.1 1.0
O A:HOH805 4.1 20.3 1.0
N A:ALA279 4.1 18.5 1.0
O A:ASP25 4.2 26.1 1.0
O A:HOH804 4.3 35.4 1.0
CA A:ALA279 4.3 19.2 1.0
N A:PRO277 4.4 18.9 1.0
N A:ASP280 4.5 19.0 1.0
CB A:ALA276 4.5 20.6 1.0
CA A:PRO277 4.5 21.7 1.0
C A:PRO277 4.6 20.7 1.0
CG A:GLN308 4.6 19.2 1.0
O A:HOH697 4.6 28.8 1.0
CA A:ASP280 4.7 19.0 1.0
O A:HOH679 4.7 22.3 1.0
O A:HOH937 4.7 37.5 1.0
CB A:ALA279 4.8 20.6 1.0
CB A:ASP25 4.8 30.4 1.0
N A:PHE278 4.8 18.3 1.0
O A:PRO277 5.0 22.7 1.0
C A:ASP280 5.0 17.7 1.0

Magnesium binding site 3 out of 8 in 6xpp

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Magnesium binding site 3 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:26.1
occ:1.00
 OD2 B:ASP153 2.1 17.1 1.0
O B:HOH637 2.2 22.4 1.0
O B:HOH643 2.2 22.4 1.0
O B:HOH615 2.2 23.3 1.0
O2 B:ITN501 2.4 27.5 1.0
CG B:ASP153 3.0 15.3 1.0
C1 B:ITN501 3.3 25.6 1.0
OD1 B:ASP153 3.3 16.4 1.0
O B:HOH665 3.5 24.3 1.0
O1 B:ITN501 3.7 24.4 1.0
OD2 B:ASP108 3.9 22.0 1.0
NZ B:LYS189 4.0 28.6 1.0
N B:TRP93 4.1 14.8 1.0
NH1 B:ARG228 4.2 22.6 1.0
N B:GLY92 4.2 15.1 1.0
OD1 B:ASP108 4.3 21.8 1.0
CA B:GLY92 4.3 15.9 1.0
CE B:LYS189 4.4 27.0 1.0
CE1 B:HIS180 4.4 16.2 1.0
CB B:ASP153 4.4 14.6 1.0
OE2 B:GLU155 4.5 23.2 1.0
CG B:ASP108 4.5 21.3 1.0
C B:GLY92 4.6 14.4 1.0
C2 B:ITN501 4.6 24.4 1.0
CG B:GLU155 4.7 21.9 1.0
OE1 B:GLU182 4.7 23.5 1.0
OH B:TYR89 4.8 15.8 1.0
CD B:GLU155 4.9 26.8 1.0
CB B:TRP93 5.0 14.9 1.0

Magnesium binding site 4 out of 8 in 6xpp

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Magnesium binding site 4 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:20.1
occ:1.00
 O B:ALA276 2.3 20.1 1.0
O B:ALA279 2.3 19.8 1.0
OE1 B:GLN308 2.3 20.2 1.0
O B:HOH938 2.4 19.8 1.0
O B:HOH728 2.4 20.6 1.0
O B:HOH930 2.5 26.1 1.0
CD B:GLN308 3.3 19.9 1.0
C B:ALA276 3.4 18.5 1.0
C B:ALA279 3.5 19.9 1.0
NE2 B:GLN308 3.5 19.2 1.0
CA B:ALA276 4.0 18.1 1.0
O B:HOH737 4.0 20.0 1.0
N B:ALA279 4.1 18.7 1.0
O B:ASP25 4.2 24.8 1.0
CA B:ALA279 4.3 19.6 1.0
O B:HOH761 4.3 37.9 1.0
N B:PRO277 4.3 19.2 1.0
N B:ASP280 4.4 19.2 1.0
CB B:ALA276 4.5 18.8 1.0
CA B:PRO277 4.5 20.4 1.0
C B:PRO277 4.6 18.6 1.0
CG B:GLN308 4.7 20.9 1.0
CA B:ASP280 4.7 17.6 1.0
O B:HOH700 4.7 25.4 1.0
CB B:ALA279 4.7 21.5 1.0
O B:HOH705 4.7 19.7 1.0
CB B:ASP25 4.7 33.7 1.0
N B:PHE278 4.8 18.4 1.0
C B:ASP280 5.0 17.2 1.0
O B:PRO277 5.0 20.2 1.0

Magnesium binding site 5 out of 8 in 6xpp

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Magnesium binding site 5 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:24.4
occ:1.00
 OD2 C:ASP153 2.2 17.8 1.0
O C:HOH614 2.2 22.9 1.0
O C:HOH654 2.2 23.6 1.0
O C:HOH608 2.3 20.9 1.0
O1 C:ITN501 2.3 26.2 1.0
CG C:ASP153 3.1 16.7 1.0
C1 C:ITN501 3.3 27.6 1.0
OD1 C:ASP153 3.4 15.4 1.0
O C:HOH691 3.6 22.2 1.0
O2 C:ITN501 3.7 23.6 1.0
OD2 C:ASP108 3.9 20.4 1.0
NZ C:LYS189 4.0 27.5 1.0
N C:TRP93 4.1 14.9 1.0
NH1 C:ARG228 4.2 21.4 1.0
OD1 C:ASP108 4.2 19.2 1.0
N C:GLY92 4.3 14.8 1.0
CE C:LYS189 4.3 24.4 1.0
CA C:GLY92 4.3 16.0 1.0
CE1 C:HIS180 4.5 15.1 1.0
OE2 C:GLU155 4.5 28.4 1.0
CG C:ASP108 4.5 18.5 1.0
CB C:ASP153 4.5 15.3 1.0
C2 C:ITN501 4.6 24.1 1.0
C C:GLY92 4.6 15.9 1.0
CG C:GLU155 4.6 19.7 1.0
OE1 C:GLU182 4.7 22.9 1.0
CD C:GLU155 4.9 24.1 1.0
OH C:TYR89 4.9 17.1 1.0
CB C:TRP93 4.9 14.7 1.0

Magnesium binding site 6 out of 8 in 6xpp

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Magnesium binding site 6 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:18.2
occ:1.00
 O C:ALA276 2.2 18.2 1.0
OE1 C:GLN308 2.3 18.2 1.0
O C:ALA279 2.4 16.9 1.0
O C:HOH755 2.4 19.4 1.0
O C:HOH954 2.4 17.2 1.0
O C:HOH940 2.5 26.3 1.0
CD C:GLN308 3.3 16.6 1.0
C C:ALA276 3.3 18.4 1.0
C C:ALA279 3.5 19.7 1.0
NE2 C:GLN308 3.6 15.9 1.0
CA C:ALA276 4.0 19.2 1.0
O C:HOH936 4.0 34.8 1.0
N C:ALA279 4.1 16.4 1.0
O C:HOH810 4.1 18.2 1.0
O C:ASP25 4.2 21.9 1.0
CA C:ALA279 4.3 17.5 1.0
N C:PRO277 4.3 17.9 1.0
CB C:ALA276 4.4 18.6 1.0
O C:HOH874 4.5 32.8 1.0
N C:ASP280 4.5 17.0 1.0
CA C:PRO277 4.5 17.6 1.0
C C:PRO277 4.6 18.2 1.0
CG C:GLN308 4.6 17.4 1.0
CA C:ASP280 4.7 17.0 1.0
O C:HOH756 4.7 23.5 1.0
CB C:ALA279 4.7 18.9 1.0
O C:HOH675 4.7 17.8 1.0
CB C:ASP25 4.8 30.6 1.0
N C:PHE278 4.8 16.5 1.0
O C:PRO277 5.0 18.8 1.0

Magnesium binding site 7 out of 8 in 6xpp

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Magnesium binding site 7 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:22.8
occ:1.00
 OD2 D:ASP153 2.1 17.9 1.0
O D:HOH609 2.3 22.0 1.0
O D:HOH634 2.3 20.9 1.0
O D:HOH631 2.3 20.5 1.0
O2 D:ITN501 2.4 24.9 1.0
CG D:ASP153 3.1 15.5 1.0
C1 D:ITN501 3.3 21.4 1.0
OD1 D:ASP153 3.4 16.3 1.0
O D:HOH621 3.5 20.6 1.0
O1 D:ITN501 3.7 21.6 1.0
OD2 D:ASP108 4.0 18.5 1.0
NZ D:LYS189 4.1 26.0 1.0
N D:TRP93 4.1 14.2 1.0
NH1 D:ARG228 4.2 19.0 1.0
N D:GLY92 4.2 14.0 1.0
CA D:GLY92 4.3 14.1 1.0
OD1 D:ASP108 4.3 19.1 1.0
CE D:LYS189 4.4 24.5 1.0
CE1 D:HIS180 4.4 15.0 1.0
CB D:ASP153 4.4 15.3 1.0
C D:GLY92 4.5 17.1 1.0
CG D:ASP108 4.5 18.6 1.0
OE2 D:GLU155 4.5 25.4 1.0
C2 D:ITN501 4.6 20.9 1.0
CG D:GLU155 4.7 19.9 1.0
OE1 D:GLU182 4.8 19.7 1.0
OH D:TYR89 4.8 17.7 1.0
CB D:TRP93 4.9 16.6 1.0
CD D:GLU155 4.9 22.6 1.0
CA D:TRP93 5.0 15.3 1.0

Magnesium binding site 8 out of 8 in 6xpp

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Magnesium binding site 8 out of 8 in the Crystal Structure of Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase


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 Itaconate Modified Mycobaterium Tuberculosis Isocitrate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:21.5
occ:1.00
 O D:ALA276 2.2 19.8 1.0
O D:ALA279 2.3 20.6 1.0
OE1 D:GLN308 2.4 21.6 1.0
O D:HOH748 2.4 24.4 1.0
O D:HOH912 2.4 28.9 1.0
O D:HOH929 2.5 21.8 1.0
CD D:GLN308 3.3 21.3 1.0
C D:ALA276 3.3 18.6 1.0
C D:ALA279 3.5 20.8 1.0
NE2 D:GLN308 3.6 20.4 1.0
O D:HOH809 4.0 20.5 1.0
CA D:ALA276 4.0 19.3 1.0
N D:ALA279 4.1 19.1 1.0
O D:ASP25 4.2 25.8 1.0
CA D:ALA279 4.3 19.7 1.0
O D:HOH808 4.3 35.2 1.0
N D:PRO277 4.3 22.7 1.0
N D:ASP280 4.5 17.8 1.0
CB D:ALA276 4.5 21.4 1.0
CA D:PRO277 4.5 21.9 1.0
O D:HOH897 4.5 39.9 1.0
C D:PRO277 4.6 21.1 1.0
O D:HOH659 4.7 30.7 1.0
CA D:ASP280 4.7 19.9 1.0
CG D:GLN308 4.7 22.7 1.0
CB D:ALA279 4.7 21.6 1.0
O D:HOH655 4.8 23.3 1.0
N D:PHE278 4.8 20.4 1.0
CB D:ASP25 4.8 36.9 1.0
O D:PRO277 5.0 22.6 1.0

Reference:

B.X.C.Kwai, G.Bashiri, I.K.H.Leung, J.Sperry. Itaconate Is A Covalent Inhibitor of the Mycobacterium Tuberculosis Isocitrate Lyase Rsc Med Chem 2020.
ISSN: ESSN 2632-8682
DOI: 10.1039/D0MD00301H
Page generated: Tue Oct 1 23:37:15 2024

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