Manganese in PDB 7rue: Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
Enzymatic activity of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
All present enzymatic activity of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone:
2.5.1.54;
Protein crystallography data
The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue
was solved by
M.Heimhalt,
P.Mukherjee,
R.Grainger,
R.Szabla,
C.Brown,
R.Turner,
M.S.Junop,
P.J.Berti,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.21 /
2.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
210.281,
53.2,
150.79,
90,
116.01,
90
|
R / Rfree (%)
|
20.1 /
26.3
|
Other elements in 7rue:
The structure of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
(pdb code 7rue). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone, PDB code: 7rue:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7rue
Go back to
Manganese Binding Sites List in 7rue
Manganese binding site 1 out
of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:53.5
occ:1.00
|
OD2
|
A:ASP326
|
2.0
|
46.9
|
1.0
|
OE1
|
A:GLU302
|
2.0
|
50.4
|
1.0
|
NE2
|
A:HIS268
|
2.8
|
49.4
|
1.0
|
O03
|
A:7QH401
|
2.8
|
46.0
|
0.9
|
SG
|
A:CYS61
|
2.8
|
44.0
|
1.0
|
CD
|
A:GLU302
|
3.0
|
53.4
|
1.0
|
CG
|
A:ASP326
|
3.1
|
52.4
|
1.0
|
OE2
|
A:GLU302
|
3.3
|
50.1
|
1.0
|
CD2
|
A:HIS268
|
3.3
|
53.2
|
1.0
|
CB
|
A:CYS61
|
3.6
|
49.3
|
1.0
|
CB
|
A:ASP326
|
3.7
|
51.1
|
1.0
|
C04
|
A:7QH401
|
3.8
|
48.9
|
0.9
|
NZ
|
A:LYS97
|
3.9
|
45.4
|
1.0
|
CE1
|
A:HIS268
|
3.9
|
52.4
|
1.0
|
NH2
|
A:ARG92
|
4.0
|
44.6
|
1.0
|
OD1
|
A:ASP326
|
4.1
|
51.4
|
1.0
|
N01
|
A:7QH401
|
4.1
|
55.4
|
0.9
|
N02
|
A:7QH401
|
4.2
|
58.3
|
0.9
|
CG
|
A:GLU302
|
4.4
|
44.3
|
1.0
|
CA
|
A:CYS61
|
4.4
|
49.8
|
1.0
|
CG
|
A:HIS268
|
4.6
|
56.0
|
1.0
|
O
|
A:CYS61
|
4.8
|
48.8
|
1.0
|
CE
|
A:LYS97
|
4.8
|
50.7
|
1.0
|
ND1
|
A:HIS268
|
4.8
|
54.5
|
1.0
|
N03
|
A:7QH401
|
4.9
|
44.3
|
0.9
|
C
|
A:CYS61
|
4.9
|
46.6
|
1.0
|
CZ
|
A:ARG92
|
5.0
|
49.5
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7rue
Go back to
Manganese Binding Sites List in 7rue
Manganese binding site 2 out
of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn402
b:26.7
occ:1.00
|
OD2
|
B:ASP326
|
2.1
|
32.1
|
1.0
|
OE1
|
B:GLU302
|
2.1
|
32.7
|
1.0
|
O03
|
B:7QH401
|
2.3
|
29.5
|
0.8
|
NE2
|
B:HIS268
|
2.5
|
25.2
|
1.0
|
SG
|
B:CYS61
|
2.5
|
28.1
|
1.0
|
CG
|
B:ASP326
|
3.0
|
27.8
|
1.0
|
CD
|
B:GLU302
|
3.1
|
30.1
|
1.0
|
CD2
|
B:HIS268
|
3.3
|
25.7
|
1.0
|
OE2
|
B:GLU302
|
3.3
|
25.5
|
1.0
|
C04
|
B:7QH401
|
3.3
|
28.4
|
0.8
|
CE1
|
B:HIS268
|
3.5
|
27.6
|
1.0
|
CB
|
B:ASP326
|
3.6
|
27.5
|
1.0
|
CB
|
B:CYS61
|
3.8
|
29.0
|
1.0
|
OD1
|
B:ASP326
|
4.0
|
35.3
|
1.0
|
NZ
|
B:LYS97
|
4.0
|
24.3
|
1.0
|
NH1
|
B:ARG92
|
4.1
|
26.2
|
1.0
|
N01
|
B:7QH401
|
4.2
|
34.9
|
0.8
|
N03
|
B:7QH401
|
4.2
|
23.3
|
0.8
|
N02
|
B:7QH401
|
4.2
|
31.5
|
0.8
|
CA
|
B:CYS61
|
4.4
|
23.7
|
1.0
|
CG
|
B:GLU302
|
4.5
|
24.0
|
1.0
|
O
|
B:HOH520
|
4.5
|
25.4
|
1.0
|
CG
|
B:HIS268
|
4.5
|
24.5
|
1.0
|
ND1
|
B:HIS268
|
4.6
|
28.2
|
1.0
|
CA
|
B:ASP326
|
4.9
|
23.3
|
1.0
|
CZ
|
B:ARG92
|
4.9
|
24.9
|
1.0
|
O
|
B:CYS61
|
4.9
|
24.1
|
1.0
|
N
|
B:ASP326
|
4.9
|
24.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7rue
Go back to
Manganese Binding Sites List in 7rue
Manganese binding site 3 out
of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn402
b:48.9
occ:1.00
|
OD2
|
C:ASP326
|
1.9
|
42.4
|
1.0
|
OE2
|
C:GLU302
|
2.2
|
48.8
|
1.0
|
NE2
|
C:HIS268
|
2.7
|
57.8
|
1.0
|
O03
|
C:7QH401
|
2.9
|
51.5
|
0.8
|
CG
|
C:ASP326
|
2.9
|
46.8
|
1.0
|
SG
|
C:CYS61
|
2.9
|
50.6
|
1.0
|
CD
|
C:GLU302
|
3.0
|
51.1
|
1.0
|
OE1
|
C:GLU302
|
3.0
|
51.2
|
1.0
|
CB
|
C:ASP326
|
3.3
|
51.0
|
1.0
|
CD2
|
C:HIS268
|
3.3
|
52.3
|
1.0
|
CB
|
C:CYS61
|
3.4
|
47.3
|
1.0
|
C04
|
C:7QH401
|
3.6
|
54.3
|
0.8
|
N02
|
C:7QH401
|
3.6
|
54.0
|
0.8
|
CE1
|
C:HIS268
|
3.9
|
56.7
|
1.0
|
N01
|
C:7QH401
|
3.9
|
58.3
|
0.8
|
OD1
|
C:ASP326
|
4.0
|
46.2
|
1.0
|
NH2
|
C:ARG92
|
4.1
|
50.0
|
1.0
|
CA
|
C:CYS61
|
4.2
|
48.4
|
1.0
|
NZ
|
C:LYS97
|
4.4
|
50.1
|
1.0
|
CG
|
C:GLU302
|
4.4
|
49.6
|
1.0
|
CG
|
C:HIS268
|
4.6
|
56.8
|
1.0
|
CA
|
C:ASP326
|
4.7
|
55.4
|
1.0
|
O
|
C:CYS61
|
4.8
|
55.1
|
1.0
|
NZ
|
C:LYS273
|
4.8
|
55.0
|
1.0
|
C
|
C:CYS61
|
4.8
|
51.9
|
1.0
|
ND1
|
C:HIS268
|
4.8
|
57.7
|
1.0
|
N03
|
C:7QH401
|
4.8
|
55.1
|
0.8
|
N
|
C:ASP326
|
4.8
|
53.2
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7rue
Go back to
Manganese Binding Sites List in 7rue
Manganese binding site 4 out
of 4 in the Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Dahp Synthase Complexed with Trifluoropyruvate Semicarbazone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn402
b:40.8
occ:1.00
|
OD2
|
D:ASP326
|
2.1
|
33.9
|
1.0
|
OE2
|
D:GLU302
|
2.2
|
37.0
|
1.0
|
O
|
D:HOH518
|
2.4
|
35.1
|
1.0
|
NE2
|
D:HIS268
|
2.6
|
43.0
|
1.0
|
SG
|
D:CYS61
|
2.7
|
29.4
|
1.0
|
CD
|
D:GLU302
|
3.0
|
30.7
|
1.0
|
OE1
|
D:GLU302
|
3.1
|
32.2
|
1.0
|
CG
|
D:ASP326
|
3.2
|
31.4
|
1.0
|
O03
|
D:7QH401
|
3.3
|
38.0
|
0.7
|
CD2
|
D:HIS268
|
3.3
|
41.5
|
1.0
|
CB
|
D:ASP326
|
3.6
|
27.5
|
1.0
|
CB
|
D:CYS61
|
3.6
|
29.3
|
1.0
|
CE1
|
D:HIS268
|
3.7
|
42.3
|
1.0
|
NZ
|
D:LYS97
|
4.0
|
28.0
|
1.0
|
C04
|
D:7QH401
|
4.2
|
40.1
|
0.7
|
CA
|
D:CYS61
|
4.3
|
30.1
|
1.0
|
OD1
|
D:ASP326
|
4.3
|
25.0
|
1.0
|
NH2
|
D:ARG92
|
4.3
|
32.3
|
1.0
|
CG
|
D:GLU302
|
4.4
|
30.7
|
1.0
|
N02
|
D:7QH401
|
4.5
|
42.3
|
0.7
|
CG
|
D:HIS268
|
4.6
|
41.0
|
1.0
|
ND1
|
D:HIS268
|
4.7
|
38.1
|
1.0
|
O
|
D:CYS61
|
4.7
|
32.5
|
1.0
|
O02
|
D:7QH401
|
4.8
|
52.9
|
0.7
|
CE
|
D:LYS97
|
4.8
|
39.8
|
1.0
|
CA
|
D:ASP326
|
4.9
|
24.9
|
1.0
|
C
|
D:CYS61
|
4.9
|
31.7
|
1.0
|
|
Reference:
M.Heimhalt,
P.Mukherjee,
R.A.Grainger,
R.Szabla,
C.Brown,
R.Turner,
M.S.Junop,
P.J.Berti.
An Inhibitor-in-Pieces Approach to Dahp Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
DOI: 10.1021/ACSINFECDIS.1C00462
Page generated: Sun Oct 6 10:29:59 2024
|