Magnesium in PDB 3fsx: Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis
Enzymatic activity of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis
All present enzymatic activity of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis:
2.3.1.117;
Protein crystallography data
The structure of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis, PDB code: 3fsx
was solved by
L.Schuldt,
S.Weyand,
G.Kefala,
M.S.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.15
|
Space group
|
I 21 3 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
216.990,
216.990,
216.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.8 /
21.9
|
Other elements in 3fsx:
The structure of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis
(pdb code 3fsx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis, PDB code: 3fsx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 1 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg332
b:43.1
occ:1.00
|
OE2
|
B:GLU183
|
2.3
|
36.9
|
1.0
|
OE2
|
A:GLU183
|
2.4
|
41.0
|
1.0
|
OE2
|
C:GLU183
|
2.5
|
40.9
|
1.0
|
OE1
|
B:GLU183
|
2.7
|
38.1
|
1.0
|
OE1
|
A:GLU183
|
2.7
|
38.1
|
1.0
|
OE1
|
C:GLU183
|
2.8
|
41.5
|
1.0
|
CD
|
B:GLU183
|
2.9
|
36.9
|
1.0
|
CD
|
A:GLU183
|
2.9
|
32.0
|
1.0
|
CD
|
C:GLU183
|
3.0
|
38.3
|
1.0
|
NH1
|
B:ARG167
|
3.9
|
28.2
|
1.0
|
NH1
|
C:ARG167
|
4.0
|
26.4
|
1.0
|
NH2
|
A:ARG201
|
4.0
|
31.2
|
0.4
|
NH1
|
A:ARG167
|
4.0
|
33.9
|
1.0
|
NH2
|
B:ARG167
|
4.1
|
27.1
|
1.0
|
NH2
|
C:ARG167
|
4.1
|
33.1
|
1.0
|
NH2
|
A:ARG167
|
4.1
|
33.4
|
1.0
|
O
|
B:HOH483
|
4.1
|
32.0
|
1.0
|
CG
|
B:GLU183
|
4.3
|
35.9
|
1.0
|
CG
|
A:GLU183
|
4.4
|
31.4
|
1.0
|
CZ
|
C:ARG167
|
4.4
|
32.8
|
1.0
|
CZ
|
B:ARG167
|
4.4
|
35.7
|
1.0
|
CZ
|
A:ARG167
|
4.4
|
36.1
|
1.0
|
CG
|
C:GLU183
|
4.4
|
38.8
|
1.0
|
O
|
C:HOH503
|
4.5
|
26.3
|
1.0
|
CZ
|
A:ARG201
|
4.9
|
26.1
|
0.4
|
|
Magnesium binding site 2 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 2 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg333
b:46.7
occ:1.00
|
O
|
D:HOH541
|
2.2
|
30.2
|
1.0
|
O
|
A:HOH519
|
2.5
|
30.4
|
1.0
|
O
|
A:HOH512
|
2.6
|
34.9
|
1.0
|
OD1
|
A:ASP210
|
4.2
|
28.4
|
1.0
|
O
|
D:HOH527
|
4.3
|
32.3
|
1.0
|
OD2
|
A:ASP210
|
4.4
|
36.5
|
1.0
|
OD1
|
D:ASP210
|
4.4
|
28.4
|
1.0
|
O
|
A:PRO176
|
4.4
|
28.7
|
1.0
|
OD2
|
D:ASP210
|
4.5
|
32.9
|
1.0
|
N
|
A:ALA195
|
4.6
|
29.0
|
1.0
|
CG
|
A:ASP210
|
4.7
|
29.3
|
1.0
|
CB
|
A:ALA195
|
4.7
|
31.3
|
1.0
|
CG
|
D:ASP210
|
4.9
|
26.1
|
1.0
|
O
|
A:HOH542
|
5.0
|
34.8
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 3fsx
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Magnesium Binding Sites List in 3fsx
Magnesium binding site 3 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg332
b:53.6
occ:1.00
|
O
|
B:HOH547
|
2.3
|
28.3
|
1.0
|
O
|
B:HOH534
|
2.3
|
35.5
|
1.0
|
OD2
|
B:ASP253
|
4.0
|
30.8
|
1.0
|
OG
|
B:SER285
|
4.4
|
26.3
|
1.0
|
OD2
|
B:ASP252
|
4.4
|
34.3
|
1.0
|
CB
|
B:ASP252
|
4.5
|
24.4
|
1.0
|
CB
|
B:SER285
|
4.6
|
24.6
|
1.0
|
OD1
|
B:ASN286
|
4.6
|
33.0
|
1.0
|
ND2
|
B:ASN286
|
4.7
|
27.1
|
1.0
|
NH2
|
B:ARG237
|
4.7
|
48.4
|
1.0
|
CG
|
B:ASP252
|
4.9
|
28.2
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 3fsx
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Magnesium Binding Sites List in 3fsx
Magnesium binding site 4 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg332
b:27.1
occ:1.00
|
O
|
A:HOH401
|
2.1
|
34.9
|
1.0
|
OD2
|
C:ASP166
|
2.1
|
33.2
|
1.0
|
O
|
C:HOH401
|
2.1
|
27.2
|
1.0
|
OD2
|
B:ASP166
|
2.2
|
31.8
|
1.0
|
OD2
|
A:ASP166
|
2.2
|
31.5
|
1.0
|
O
|
B:HOH401
|
2.2
|
29.0
|
1.0
|
CG
|
C:ASP166
|
3.1
|
34.0
|
1.0
|
CG
|
B:ASP166
|
3.2
|
29.9
|
1.0
|
CG
|
A:ASP166
|
3.2
|
28.9
|
1.0
|
NA
|
A:NA334
|
3.4
|
40.3
|
1.0
|
OD1
|
C:ASP166
|
3.4
|
30.7
|
1.0
|
OD1
|
B:ASP166
|
3.5
|
36.2
|
1.0
|
OD1
|
A:ASP166
|
3.6
|
31.3
|
1.0
|
O
|
B:HOH471
|
3.8
|
24.4
|
1.0
|
O
|
C:HOH471
|
3.8
|
27.0
|
1.0
|
CB
|
C:ASP166
|
4.5
|
28.3
|
1.0
|
CB
|
B:ASP166
|
4.5
|
24.6
|
1.0
|
CB
|
A:ASP166
|
4.6
|
24.0
|
1.0
|
OD1
|
C:ASP164
|
4.7
|
33.2
|
1.0
|
OD1
|
B:ASP164
|
4.8
|
30.3
|
1.0
|
OD1
|
A:ASP164
|
4.8
|
32.0
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 5 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg332
b:21.8
occ:0.33
|
OD2
|
D:ASP166
|
2.0
|
31.5
|
1.0
|
O
|
D:HOH401
|
2.0
|
28.2
|
1.0
|
CG
|
D:ASP166
|
3.0
|
32.0
|
1.0
|
NA
|
D:NA334
|
3.1
|
48.3
|
0.3
|
OD1
|
D:ASP166
|
3.3
|
33.1
|
1.0
|
O
|
D:HOH471
|
3.8
|
22.4
|
1.0
|
CB
|
D:ASP166
|
4.4
|
27.6
|
1.0
|
OD1
|
D:ASP164
|
4.6
|
30.3
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 6 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg333
b:62.8
occ:0.33
|
OE2
|
D:GLU183
|
2.0
|
44.5
|
1.0
|
CD
|
D:GLU183
|
2.9
|
48.3
|
1.0
|
OE1
|
D:GLU183
|
3.0
|
40.5
|
1.0
|
O
|
D:HOH483
|
3.7
|
34.8
|
1.0
|
CG
|
D:GLU183
|
4.3
|
34.4
|
1.0
|
NH1
|
D:ARG201
|
4.7
|
34.4
|
1.0
|
O
|
D:HOH502
|
5.0
|
37.3
|
1.0
|
NH2
|
D:ARG167
|
5.0
|
37.1
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 7 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg331
b:54.2
occ:0.33
|
OD2
|
E:ASP166
|
2.4
|
41.7
|
1.0
|
CG
|
E:ASP166
|
3.4
|
36.0
|
1.0
|
OD1
|
E:ASP166
|
3.6
|
30.8
|
1.0
|
O
|
E:HOH411
|
3.8
|
38.8
|
1.0
|
NA
|
E:NA334
|
3.9
|
49.9
|
0.3
|
CB
|
E:ASP166
|
4.7
|
30.2
|
1.0
|
OD1
|
E:ASP164
|
4.9
|
25.8
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 8 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg332
b:55.7
occ:0.33
|
OE2
|
E:GLU183
|
2.0
|
39.3
|
1.0
|
CD
|
E:GLU183
|
3.1
|
36.6
|
1.0
|
OE1
|
E:GLU183
|
3.5
|
38.4
|
1.0
|
O
|
E:HOH412
|
3.9
|
47.6
|
1.0
|
CG
|
E:GLU183
|
4.3
|
29.4
|
1.0
|
NH1
|
E:ARG201
|
4.6
|
33.9
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 3fsx
Go back to
Magnesium Binding Sites List in 3fsx
Magnesium binding site 9 out
of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) 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 Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg333
b:44.6
occ:0.33
|
O
|
D:HOH511
|
2.5
|
32.2
|
1.0
|
O
|
E:SER295
|
3.0
|
26.9
|
1.0
|
C
|
E:SER295
|
3.8
|
25.5
|
1.0
|
CA
|
E:SER295
|
4.1
|
25.6
|
1.0
|
O
|
E:HOH419
|
4.4
|
32.1
|
1.0
|
CB
|
E:SER295
|
4.5
|
26.0
|
1.0
|
O
|
D:HOH512
|
4.6
|
33.2
|
1.0
|
O
|
D:SER295
|
5.0
|
24.5
|
1.0
|
|
Reference:
L.Schuldt,
S.Weyand,
G.Kefala,
M.S.Weiss.
The Three-Dimensional Structure of A Mycobacterial Dapd Provides Insights Into Dapd Diversity and Reveals Unexpected Particulars About the Enzymatic Mechanism. J.Mol.Biol. V. 389 863 2009.
ISSN: ISSN 0022-2836
PubMed: 19394346
DOI: 10.1016/J.JMB.2009.04.046
Page generated: Wed Aug 14 13:53:16 2024
|