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Magnesium in PDB 6edw: Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form, PDB code: 6edw was solved by G.Bashiri, R.Bhusal, I.Leung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.32 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.824, 136.078, 138.924, 90.00, 99.59, 90.00
R / Rfree (%) 16.8 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form (pdb code 6edw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form, PDB code: 6edw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6edw

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Magnesium binding site 1 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:21.0
occ:1.00
 O A:ALA450 2.2 18.0 1.0
O A:HOH1452 2.3 23.9 1.0
OE1 A:GLN482 2.3 18.6 1.0
O A:ALA453 2.3 18.0 1.0
O A:HOH1477 2.4 26.6 1.0
C A:ALA450 3.3 17.2 1.0
CD A:GLN482 3.3 17.6 1.0
C A:ALA453 3.6 19.9 1.0
NE2 A:GLN482 3.6 18.8 1.0
O A:HOH1469 3.9 49.8 1.0
CD1 A:ILE37 3.9 20.9 1.0
CA A:ALA450 4.0 19.8 1.0
N A:ALA453 4.3 18.8 1.0
N A:PRO451 4.3 16.4 1.0
CB A:ALA450 4.4 18.8 1.0
CA A:PRO451 4.4 17.3 1.0
CA A:ALA453 4.5 16.1 1.0
O A:HOH1488 4.5 41.7 1.0
N A:ASP454 4.5 19.1 1.0
CA A:ASP454 4.6 18.8 1.0
O A:HOH1213 4.7 18.3 1.0
CG A:GLN482 4.7 18.0 1.0
C A:PRO451 4.7 16.3 1.0
C A:ASP454 4.8 18.0 1.0
N A:PHE452 4.9 17.2 1.0
O A:HOH1154 4.9 18.5 1.0
O A:ASP454 4.9 19.5 1.0

Magnesium binding site 2 out of 7 in 6edw

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Magnesium binding site 2 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:30.0
occ:1.00
 OD1 A:ASP179 2.2 21.0 1.0
O A:HOH984 2.3 36.5 1.0
O A:HOH945 2.4 24.5 1.0
OD2 A:ASP177 2.7 20.0 1.0
O A:HOH1126 3.2 40.4 1.0
CG A:ASP177 3.4 16.4 1.0
NZ A:LYS213 3.4 61.2 1.0
CG A:ASP179 3.5 27.7 1.0
OD1 A:ASP177 3.5 14.8 1.0
OD1 A:ASP123 3.6 29.6 1.0
CA A:GLY107 3.8 21.3 1.0
O A:HOH1160 4.0 40.0 1.0
O A:HOH901 4.1 29.6 1.0
N A:GLY107 4.1 17.6 1.0
OH A:TYR127 4.2 17.6 1.0
OD2 A:ASP179 4.3 22.5 1.0
CG A:ASP123 4.4 25.6 1.0
CB A:ASP179 4.4 16.5 1.0
OD2 A:ASP123 4.4 30.2 1.0
C A:GLY107 4.4 17.4 1.0
CA A:ASP179 4.5 16.0 1.0
N A:TRP108 4.6 15.9 1.0
OE1 A:GLU206 4.7 29.8 1.0
CE A:LYS213 4.7 52.2 1.0
CB A:ASP177 4.7 15.5 1.0
CB A:ALA125 4.9 17.7 1.0
O A:HOH1304 4.9 41.3 1.0
OE2 A:GLU206 4.9 31.5 1.0
N A:ASP179 5.0 13.8 1.0

Magnesium binding site 3 out of 7 in 6edw

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Magnesium binding site 3 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:20.3
occ:1.00
 O B:ALA450 2.2 18.4 1.0
NE2 B:GLN482 2.2 13.5 1.0
O B:HOH1560 2.3 28.2 1.0
O B:ALA453 2.3 17.1 1.0
O B:HOH1595 2.4 27.0 1.0
CD B:GLN482 3.3 18.9 1.0
C B:ALA450 3.3 16.8 1.0
C B:ALA453 3.5 16.5 1.0
OE1 B:GLN482 3.5 22.4 1.0
O B:HOH1629 3.8 45.3 1.0
CA B:ALA450 4.0 19.2 1.0
CD1 B:ILE37 4.0 21.6 1.0
N B:ALA453 4.3 17.2 1.0
N B:PRO451 4.3 16.1 1.0
O B:HOH1532 4.3 39.9 1.0
CB B:ALA450 4.3 18.4 1.0
CA B:ALA453 4.4 18.4 1.0
N B:ASP454 4.5 15.6 1.0
CA B:PRO451 4.5 18.6 1.0
CA B:ASP454 4.5 15.4 1.0
CG B:GLN482 4.6 21.1 1.0
O B:HOH1203 4.7 21.0 1.0
C B:ASP454 4.8 16.5 1.0
C B:PRO451 4.8 18.8 1.0
O B:HOH1283 4.8 17.6 1.0
O B:ASP454 4.9 18.1 1.0
N B:PHE452 4.9 16.3 1.0
O B:HOH938 5.0 27.8 1.0

Magnesium binding site 4 out of 7 in 6edw

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Magnesium binding site 4 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:21.3
occ:1.00
 O C:ALA450 2.2 15.9 1.0
O C:HOH1454 2.3 25.4 1.0
NE2 C:GLN482 2.3 13.8 1.0
O C:ALA453 2.3 16.7 1.0
O C:HOH1460 2.3 22.5 1.0
C C:ALA450 3.3 16.4 1.0
CD C:GLN482 3.3 18.9 1.0
C C:ALA453 3.6 19.5 1.0
OE1 C:GLN482 3.6 22.7 1.0
CD1 C:ILE37 4.0 18.6 1.0
CA C:ALA450 4.0 19.9 1.0
O C:HOH1512 4.1 43.7 1.0
O C:HOH1455 4.2 37.5 1.0
N C:ALA453 4.3 16.6 1.0
N C:PRO451 4.3 16.4 1.0
CB C:ALA450 4.4 21.2 1.0
CA C:PRO451 4.5 16.6 1.0
CA C:ALA453 4.5 17.4 1.0
N C:ASP454 4.5 15.2 1.0
CA C:ASP454 4.6 18.1 1.0
O C:HOH1170 4.6 18.5 1.0
CG C:GLN482 4.7 18.4 1.0
C C:PRO451 4.8 14.4 1.0
C C:ASP454 4.8 16.3 1.0
O C:HOH1147 4.9 16.9 1.0
N C:PHE452 4.9 16.9 1.0
O C:ASP454 4.9 17.6 1.0

Magnesium binding site 5 out of 7 in 6edw

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Magnesium binding site 5 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:30.0
occ:1.00
 OD1 C:ASP179 2.2 19.5 1.0
O C:HOH920 2.3 27.8 1.0
O C:HOH1217 2.4 45.9 1.0
OD2 C:ASP177 2.6 25.0 1.0
O C:HOH993 3.3 43.4 1.0
CG C:ASP177 3.3 18.0 1.0
OD1 C:ASP177 3.4 14.0 1.0
NZ C:LYS213 3.4 61.9 1.0
CG C:ASP179 3.4 25.0 1.0
OD1 C:ASP123 3.7 27.6 1.0
O C:HOH1029 3.9 49.3 1.0
CA C:GLY107 4.0 16.5 1.0
N C:GLY107 4.2 16.8 1.0
O C:HOH942 4.3 28.7 1.0
OD2 C:ASP179 4.3 24.3 1.0
CB C:ASP179 4.3 19.5 1.0
CA C:ASP179 4.3 14.8 1.0
OH C:TYR127 4.3 14.6 1.0
OE1 C:GLU206 4.5 28.0 1.0
OD2 C:ASP123 4.5 31.0 1.0
CG C:ASP123 4.5 26.6 1.0
C C:GLY107 4.6 17.6 1.0
CE C:LYS213 4.7 68.5 1.0
CB C:ASP177 4.7 15.8 1.0
O C:HOH1027 4.7 33.9 1.0
N C:TRP108 4.8 16.2 1.0
OE2 C:GLU206 4.8 38.1 1.0
N C:ASP179 4.8 13.2 1.0
CB C:ALA125 4.9 21.3 1.0
CD C:GLU206 5.0 29.5 1.0

Magnesium binding site 6 out of 7 in 6edw

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Magnesium binding site 6 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:23.3
occ:1.00
 O D:ALA450 2.3 20.4 1.0
NE2 D:GLN482 2.3 14.1 1.0
O D:HOH1510 2.3 21.9 1.0
O D:ALA453 2.3 18.2 1.0
O D:HOH1524 2.4 28.8 1.0
CD D:GLN482 3.3 17.5 1.0
C D:ALA450 3.4 16.0 1.0
C D:ALA453 3.5 20.5 1.0
OE1 D:GLN482 3.5 22.7 1.0
O D:HOH1576 3.8 42.4 1.0
CD1 D:ILE37 4.0 22.6 1.0
CA D:ALA450 4.1 18.4 1.0
O D:HOH1511 4.2 42.8 1.0
N D:ALA453 4.3 17.8 1.0
N D:PRO451 4.3 17.6 1.0
CB D:ALA450 4.4 21.4 1.0
N D:ASP454 4.4 15.3 1.0
CA D:ALA453 4.5 20.4 1.0
CA D:PRO451 4.5 20.7 1.0
CA D:ASP454 4.5 15.8 1.0
O D:HOH1227 4.6 21.0 1.0
CG D:GLN482 4.6 16.7 1.0
C D:ASP454 4.8 17.7 1.0
C D:PRO451 4.8 17.4 1.0
O D:ASP454 4.9 15.5 1.0
O D:HOH1241 4.9 17.6 1.0
N D:PHE452 4.9 18.3 1.0
O D:HOH950 5.0 32.6 1.0

Magnesium binding site 7 out of 7 in 6edw

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Magnesium binding site 7 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis ICL2 in the Apo Form


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 Mycobacterium Tuberculosis ICL2 in the Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:30.0
occ:1.00
 OD1 D:ASP179 2.2 20.9 1.0
O D:HOH922 2.3 41.7 1.0
O D:HOH934 2.5 29.6 1.0
OD2 D:ASP177 2.7 21.0 1.0
O D:HOH1177 3.2 41.9 1.0
CG D:ASP177 3.4 17.5 1.0
NZ D:LYS213 3.4 55.0 1.0
OD1 D:ASP123 3.5 31.1 1.0
CG D:ASP179 3.5 18.2 1.0
OD1 D:ASP177 3.5 16.9 1.0
CA D:GLY107 3.7 16.6 1.0
O D:HOH983 3.9 44.6 1.0
O D:HOH908 4.0 26.5 1.0
O D:HOH1456 4.0 44.8 1.0
N D:GLY107 4.0 16.3 1.0
OH D:TYR127 4.2 17.5 1.0
OD2 D:ASP179 4.3 18.4 1.0
CG D:ASP123 4.3 25.2 1.0
C D:GLY107 4.3 15.2 1.0
OD2 D:ASP123 4.3 33.0 1.0
CB D:ASP179 4.4 15.2 1.0
N D:TRP108 4.5 15.0 1.0
CA D:ASP179 4.5 14.5 1.0
OE1 D:GLU206 4.7 26.9 1.0
CB D:ASP177 4.8 18.0 1.0
CB D:ALA125 4.8 20.2 1.0
CE D:LYS213 4.9 60.5 1.0
O D:HOH1200 4.9 32.6 1.0
OE2 D:GLU206 5.0 33.3 1.0

Reference:

R.P.Bhusal, W.Jiao, B.X.C.Kwai, J.Reynisson, A.J.Collins, J.Sperry, G.Bashiri, I.K.H.Leung. Acetyl-Coa-Mediated Activation of Mycobacterium Tuberculosis Isocitrate Lyase 2. Nat Commun V. 10 4639 2019.
ISSN: ESSN 2041-1723
PubMed: 31604954
DOI: 10.1038/S41467-019-12614-7
Page generated: Wed Aug 13 05:40:00 2025

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