Magnesium in PDB 6ovt: Crystal Structure of Ilvd From Mycobacterium Tuberculosis
Enzymatic activity of Crystal Structure of Ilvd From Mycobacterium Tuberculosis
All present enzymatic activity of Crystal Structure of Ilvd From Mycobacterium Tuberculosis:
4.2.1.9;
Protein crystallography data
The structure of Crystal Structure of Ilvd From Mycobacterium Tuberculosis, PDB code: 6ovt
was solved by
S.C.Almo,
T.L.Grove,
J.B.Bonanno,
E.N.Baker,
G.Bashiri,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
80.55 /
1.88
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.406,
88.406,
483.307,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16 /
20.1
|
Other elements in 6ovt:
The structure of Crystal Structure of Ilvd From Mycobacterium Tuberculosis also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis
(pdb code 6ovt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
Crystal Structure of Ilvd From Mycobacterium Tuberculosis, PDB code: 6ovt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 1 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:23.2
occ:1.00
|
OQ2
|
A:KCX139
|
1.9
|
23.4
|
1.0
|
O
|
A:HOH707
|
2.0
|
17.8
|
1.0
|
OD2
|
A:ASP138
|
2.1
|
24.1
|
1.0
|
OD2
|
A:ASP96
|
2.1
|
20.7
|
1.0
|
OE2
|
A:GLU465
|
2.2
|
19.6
|
1.0
|
O
|
A:HOH737
|
2.2
|
23.4
|
1.0
|
CX
|
A:KCX139
|
2.9
|
22.6
|
1.0
|
CG
|
A:ASP138
|
3.1
|
24.8
|
1.0
|
CD
|
A:GLU465
|
3.1
|
22.3
|
1.0
|
CG
|
A:ASP96
|
3.2
|
19.6
|
1.0
|
OE1
|
A:GLU465
|
3.4
|
23.4
|
1.0
|
NZ
|
A:KCX139
|
3.4
|
22.3
|
1.0
|
CB
|
A:ASP138
|
3.6
|
23.4
|
1.0
|
CB
|
A:ASP96
|
3.6
|
21.5
|
1.0
|
OG1
|
A:THR219
|
3.8
|
23.4
|
1.0
|
O
|
A:HOH1005
|
3.8
|
23.4
|
1.0
|
ND2
|
A:ASN292
|
3.8
|
20.4
|
1.0
|
OQ1
|
A:KCX139
|
4.0
|
23.0
|
1.0
|
O
|
A:HOH861
|
4.1
|
27.8
|
1.0
|
OD1
|
A:ASP138
|
4.1
|
22.6
|
1.0
|
CB
|
A:THR219
|
4.1
|
21.0
|
1.0
|
OD1
|
A:ASP96
|
4.3
|
22.6
|
1.0
|
NH1
|
A:ARG489
|
4.5
|
23.5
|
1.0
|
CG
|
A:GLU465
|
4.5
|
20.0
|
1.0
|
OG
|
A:SER491
|
4.5
|
27.8
|
1.0
|
CA
|
A:SER491
|
4.6
|
24.2
|
1.0
|
CG2
|
A:THR219
|
4.7
|
20.7
|
1.0
|
N
|
A:GLY492
|
4.8
|
25.0
|
1.0
|
CE
|
A:KCX139
|
4.8
|
21.0
|
1.0
|
CB
|
A:SER491
|
4.9
|
24.7
|
1.0
|
CE
|
A:MET105
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 2 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:50.5
occ:1.00
|
O
|
A:HOH936
|
1.9
|
56.8
|
1.0
|
O
|
A:HOH932
|
1.9
|
69.2
|
1.0
|
O
|
A:HOH775
|
2.1
|
47.5
|
1.0
|
O
|
A:HOH1014
|
2.2
|
43.5
|
1.0
|
O
|
A:HOH965
|
2.2
|
30.2
|
1.0
|
OD1
|
A:ASP69
|
2.2
|
30.8
|
1.0
|
CG
|
A:ASP69
|
3.4
|
30.9
|
1.0
|
O
|
A:ASP69
|
3.9
|
22.3
|
1.0
|
O
|
A:HOH1052
|
3.9
|
38.8
|
1.0
|
OE1
|
A:GLU88
|
4.1
|
26.3
|
1.0
|
O
|
C:HOH947
|
4.1
|
30.0
|
1.0
|
OD2
|
A:ASP69
|
4.1
|
36.9
|
1.0
|
OE2
|
A:GLU88
|
4.2
|
23.6
|
1.0
|
O
|
A:HOH1030
|
4.3
|
28.9
|
1.0
|
CA
|
A:ASP69
|
4.4
|
22.0
|
1.0
|
C
|
A:ASP69
|
4.4
|
19.0
|
1.0
|
OD1
|
A:ASN73
|
4.4
|
31.1
|
0.5
|
O
|
C:HOH965
|
4.4
|
55.3
|
1.0
|
CB
|
A:ASP69
|
4.5
|
25.9
|
1.0
|
CD
|
A:GLU88
|
4.6
|
23.4
|
1.0
|
O
|
A:HOH776
|
4.8
|
40.2
|
1.0
|
O
|
C:HOH869
|
4.9
|
59.7
|
1.0
|
CG
|
A:ASN73
|
5.0
|
24.5
|
0.5
|
|
Magnesium binding site 3 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 3 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:42.6
occ:1.00
|
O
|
A:HOH1072
|
2.0
|
45.4
|
1.0
|
O
|
A:HOH1082
|
2.0
|
37.3
|
1.0
|
O
|
A:HOH841
|
2.0
|
43.8
|
1.0
|
O
|
A:HOH824
|
2.0
|
38.9
|
1.0
|
O
|
A:HOH1058
|
2.2
|
47.3
|
1.0
|
O
|
A:HOH713
|
2.2
|
28.5
|
1.0
|
O
|
A:HOH843
|
4.1
|
41.0
|
1.0
|
OD2
|
A:ASP270
|
4.2
|
23.7
|
1.0
|
OD1
|
A:ASP270
|
4.2
|
25.6
|
1.0
|
OG1
|
A:THR267
|
4.3
|
27.2
|
1.0
|
O
|
A:GLY265
|
4.4
|
28.2
|
1.0
|
CG
|
A:ASP270
|
4.6
|
24.9
|
1.0
|
CG2
|
A:THR267
|
4.7
|
24.3
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 4 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:36.5
occ:1.00
|
OQ1
|
B:KCX139
|
2.0
|
33.3
|
1.0
|
OD2
|
B:ASP96
|
2.1
|
29.4
|
1.0
|
OD2
|
B:ASP138
|
2.1
|
29.1
|
1.0
|
OE2
|
B:GLU465
|
2.2
|
32.7
|
1.0
|
O
|
B:HOH810
|
2.3
|
36.9
|
1.0
|
O
|
B:HOH905
|
2.3
|
32.3
|
1.0
|
CX
|
B:KCX139
|
3.0
|
35.4
|
1.0
|
CG
|
B:ASP96
|
3.1
|
30.6
|
1.0
|
CG
|
B:ASP138
|
3.1
|
34.0
|
1.0
|
CD
|
B:GLU465
|
3.2
|
39.9
|
1.0
|
OE1
|
B:GLU465
|
3.4
|
35.8
|
1.0
|
NZ
|
B:KCX139
|
3.4
|
34.5
|
1.0
|
CB
|
B:ASP96
|
3.5
|
30.0
|
1.0
|
CB
|
B:ASP138
|
3.6
|
30.4
|
1.0
|
OG1
|
B:THR219
|
3.8
|
39.6
|
1.0
|
O
|
B:HOH769
|
4.1
|
27.6
|
1.0
|
OQ2
|
B:KCX139
|
4.2
|
32.4
|
1.0
|
OD1
|
B:ASP138
|
4.2
|
30.9
|
1.0
|
OD1
|
B:ASP96
|
4.3
|
29.4
|
1.0
|
ND2
|
B:ASN292
|
4.4
|
35.7
|
1.0
|
CB
|
B:THR219
|
4.4
|
34.2
|
1.0
|
CG
|
B:GLU465
|
4.6
|
38.4
|
1.0
|
O
|
B:HOH946
|
4.6
|
47.6
|
1.0
|
O
|
B:HOH859
|
4.6
|
35.2
|
1.0
|
CA
|
B:ASP96
|
4.9
|
29.6
|
1.0
|
CE
|
B:KCX139
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 5 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:50.4
occ:1.00
|
O
|
B:HOH898
|
1.7
|
53.2
|
1.0
|
O
|
B:HOH759
|
2.0
|
48.6
|
1.0
|
O
|
B:HOH819
|
2.2
|
31.8
|
1.0
|
O
|
B:HOH921
|
2.2
|
48.9
|
1.0
|
OD1
|
B:ASP69
|
2.3
|
37.6
|
1.0
|
O
|
B:HOH755
|
2.4
|
51.5
|
1.0
|
CG
|
B:ASP69
|
3.5
|
32.8
|
1.0
|
O
|
B:ASP69
|
4.0
|
23.0
|
1.0
|
OD2
|
B:ASP69
|
4.0
|
41.0
|
1.0
|
O
|
D:HOH972
|
4.1
|
31.9
|
1.0
|
OE1
|
B:GLU88
|
4.2
|
29.4
|
1.0
|
OE2
|
B:GLU88
|
4.2
|
26.2
|
1.0
|
C
|
B:ASP69
|
4.6
|
23.1
|
1.0
|
CB
|
B:ASP69
|
4.7
|
27.2
|
1.0
|
CD
|
B:GLU88
|
4.7
|
25.9
|
1.0
|
CA
|
B:ASP69
|
4.7
|
23.8
|
1.0
|
O
|
B:HOH703
|
4.7
|
40.5
|
1.0
|
CB
|
B:ASN73
|
4.9
|
29.5
|
1.0
|
O
|
B:HOH926
|
4.9
|
35.4
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 6 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:48.4
occ:1.00
|
O
|
B:HOH842
|
2.0
|
47.4
|
1.0
|
O
|
B:HOH945
|
2.0
|
54.2
|
1.0
|
O
|
B:HOH846
|
2.0
|
44.3
|
1.0
|
O
|
B:HOH715
|
2.0
|
42.4
|
1.0
|
O
|
B:HOH956
|
2.0
|
50.9
|
1.0
|
O
|
B:HOH947
|
2.1
|
54.8
|
1.0
|
OD2
|
B:ASP270
|
4.0
|
37.4
|
1.0
|
OD1
|
B:ASP270
|
4.2
|
36.4
|
1.0
|
OG1
|
B:THR267
|
4.3
|
31.3
|
1.0
|
O
|
B:GLY265
|
4.3
|
35.6
|
1.0
|
O
|
B:HOH780
|
4.4
|
50.2
|
1.0
|
CG
|
B:ASP270
|
4.6
|
37.6
|
1.0
|
CG2
|
B:THR267
|
4.6
|
34.7
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 7 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:32.3
occ:1.00
|
OQ2
|
C:KCX139
|
2.0
|
27.9
|
1.0
|
OD2
|
C:ASP138
|
2.1
|
34.6
|
1.0
|
O
|
C:HOH926
|
2.1
|
30.1
|
1.0
|
O
|
C:HOH829
|
2.2
|
34.2
|
1.0
|
OD2
|
C:ASP96
|
2.3
|
28.9
|
1.0
|
OE2
|
C:GLU465
|
2.3
|
39.4
|
1.0
|
CX
|
C:KCX139
|
3.1
|
32.1
|
1.0
|
CG
|
C:ASP138
|
3.2
|
33.8
|
1.0
|
CG
|
C:ASP96
|
3.2
|
29.5
|
1.0
|
CD
|
C:GLU465
|
3.3
|
40.2
|
1.0
|
NZ
|
C:KCX139
|
3.4
|
30.7
|
1.0
|
CB
|
C:ASP96
|
3.5
|
25.9
|
1.0
|
OE1
|
C:GLU465
|
3.5
|
38.1
|
1.0
|
CB
|
C:ASP138
|
3.6
|
29.9
|
1.0
|
OG1
|
C:THR219
|
3.7
|
29.4
|
1.0
|
O
|
C:HOH977
|
4.0
|
46.0
|
1.0
|
O
|
C:HOH919
|
4.1
|
42.3
|
1.0
|
OQ1
|
C:KCX139
|
4.1
|
28.9
|
1.0
|
O
|
C:HOH803
|
4.2
|
26.5
|
1.0
|
ND2
|
C:ASN292
|
4.2
|
27.7
|
1.0
|
O
|
C:HOH840
|
4.3
|
29.2
|
1.0
|
OD1
|
C:ASP138
|
4.3
|
35.3
|
1.0
|
CB
|
C:THR219
|
4.4
|
26.6
|
1.0
|
OD1
|
C:ASP96
|
4.4
|
28.9
|
1.0
|
CG
|
C:GLU465
|
4.7
|
41.3
|
1.0
|
CE
|
C:KCX139
|
4.9
|
24.6
|
1.0
|
CA
|
C:ASP96
|
4.9
|
26.6
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 8 out
of 12 in the Crystal Structure of Ilvd 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 Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg604
b:41.6
occ:1.00
|
O
|
C:HOH874
|
2.0
|
51.7
|
1.0
|
O
|
C:HOH961
|
2.0
|
49.0
|
1.0
|
O
|
C:HOH869
|
2.1
|
59.7
|
1.0
|
O
|
C:HOH847
|
2.1
|
29.1
|
1.0
|
O
|
C:HOH851
|
2.2
|
44.6
|
1.0
|
OD1
|
C:ASP69
|
2.3
|
34.5
|
1.0
|
CG
|
C:ASP69
|
3.5
|
32.9
|
1.0
|
O
|
C:ASP69
|
4.0
|
20.6
|
1.0
|
OD2
|
C:ASP69
|
4.1
|
38.0
|
1.0
|
OE1
|
C:GLU88
|
4.1
|
27.9
|
1.0
|
O
|
A:HOH1030
|
4.1
|
28.9
|
1.0
|
OE2
|
C:GLU88
|
4.2
|
28.3
|
1.0
|
O
|
C:HOH701
|
4.5
|
48.0
|
1.0
|
CD
|
C:GLU88
|
4.6
|
27.1
|
1.0
|
C
|
C:ASP69
|
4.6
|
21.9
|
1.0
|
CB
|
C:ASP69
|
4.7
|
25.0
|
1.0
|
CA
|
C:ASP69
|
4.7
|
22.5
|
1.0
|
O
|
C:HOH721
|
4.9
|
42.1
|
1.0
|
O
|
C:HOH947
|
4.9
|
30.0
|
1.0
|
O
|
A:HOH932
|
4.9
|
69.2
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 9 out
of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg605
b:39.2
occ:1.00
|
O
|
C:HOH993
|
2.0
|
38.8
|
1.0
|
O
|
C:HOH986
|
2.0
|
44.5
|
1.0
|
O
|
C:HOH886
|
2.0
|
34.8
|
1.0
|
O
|
C:HOH723
|
2.1
|
35.8
|
1.0
|
O
|
C:HOH802
|
2.1
|
39.4
|
1.0
|
O
|
C:HOH1005
|
2.2
|
40.5
|
1.0
|
O
|
C:HOH933
|
4.1
|
40.6
|
1.0
|
OD2
|
C:ASP270
|
4.1
|
25.1
|
1.0
|
OD1
|
C:ASP270
|
4.2
|
27.2
|
1.0
|
O
|
C:GLY265
|
4.3
|
26.1
|
1.0
|
OG1
|
C:THR267
|
4.4
|
23.4
|
1.0
|
O
|
C:HOH728
|
4.5
|
35.8
|
1.0
|
CG
|
C:ASP270
|
4.6
|
25.9
|
1.0
|
O
|
C:HOH1006
|
4.7
|
60.5
|
1.0
|
CG2
|
C:THR267
|
4.7
|
22.9
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 6ovt
Go back to
Magnesium Binding Sites List in 6ovt
Magnesium binding site 10 out
of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:40.0
occ:1.00
|
OE2
|
D:GLU465
|
1.9
|
33.0
|
0.6
|
OQ1
|
D:KCX139
|
2.0
|
34.4
|
1.0
|
O
|
D:HOH905
|
2.0
|
33.6
|
1.0
|
OD2
|
D:ASP138
|
2.2
|
37.3
|
1.0
|
O
|
D:HOH906
|
2.3
|
38.2
|
1.0
|
OD2
|
D:ASP96
|
2.3
|
31.8
|
1.0
|
CD
|
D:GLU465
|
2.9
|
39.5
|
0.6
|
OE1
|
D:GLU465
|
3.0
|
41.5
|
0.4
|
CX
|
D:KCX139
|
3.1
|
33.5
|
1.0
|
OE1
|
D:GLU465
|
3.2
|
40.3
|
0.6
|
CG
|
D:ASP96
|
3.4
|
28.8
|
1.0
|
CG
|
D:ASP138
|
3.4
|
35.9
|
1.0
|
NZ
|
D:KCX139
|
3.4
|
35.8
|
1.0
|
CB
|
D:ASP96
|
3.7
|
29.5
|
1.0
|
OG1
|
D:THR219
|
3.9
|
30.5
|
1.0
|
CB
|
D:ASP138
|
3.9
|
31.2
|
1.0
|
O
|
D:HOH799
|
3.9
|
29.9
|
1.0
|
OQ2
|
D:KCX139
|
4.1
|
34.3
|
1.0
|
ND2
|
D:ASN292
|
4.2
|
32.0
|
1.0
|
CD
|
D:GLU465
|
4.2
|
38.7
|
0.4
|
CG
|
D:GLU465
|
4.3
|
38.0
|
0.6
|
OD1
|
D:ASP138
|
4.4
|
32.5
|
1.0
|
OD1
|
D:ASP96
|
4.5
|
31.6
|
1.0
|
CB
|
D:THR219
|
4.5
|
28.6
|
1.0
|
O
|
D:HOH1009
|
4.6
|
46.6
|
1.0
|
O
|
D:HOH922
|
4.7
|
30.1
|
1.0
|
OE2
|
D:GLU465
|
4.8
|
42.0
|
0.4
|
CE
|
D:KCX139
|
4.8
|
30.8
|
1.0
|
NH1
|
D:ARG489
|
4.9
|
31.8
|
1.0
|
|
Reference:
G.Bashiri,
T.L.Grove,
S.S.Hegde,
T.Lagautriere,
G.J.Gerfen,
S.C.Almo,
C.J.Squire,
J.S.Blanchard,
E.N.Baker.
The Active Site of Themycobacterium Tuberculosisbranched-Chain Amino Acid Biosynthesis Enzyme Dihydroxyacid Dehydratase Contains A 2FE-2S Cluster. J.Biol.Chem. V. 294 13158 2019.
ISSN: ESSN 1083-351X
PubMed: 31315931
DOI: 10.1074/JBC.RA119.009498
Page generated: Tue Oct 1 13:42:02 2024
|