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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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
Go back to
Magnesium Binding Sites List in 6edw
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: Mon Sep 30 23:53:39 2024
|