Manganese in PDB 1n8f: Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
Enzymatic activity of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
All present enzymatic activity of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep:
4.1.2.15;
Protein crystallography data
The structure of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep, PDB code: 1n8f
was solved by
I.A.Shumilin,
R.Bauerle,
R.H.Kretsinger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.75
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
213.224,
53.277,
150.245,
90.00,
116.90,
90.00
|
R / Rfree (%)
|
20.9 /
23.7
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
(pdb code 1n8f). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep, PDB code: 1n8f:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1n8f
Go back to
Manganese Binding Sites List in 1n8f
Manganese binding site 1 out
of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn351
b:28.9
occ:1.00
|
OE2
|
A:GLU302
|
2.1
|
29.5
|
1.0
|
OD2
|
A:ASP326
|
2.1
|
28.5
|
1.0
|
O
|
A:HOH5416
|
2.4
|
35.6
|
1.0
|
NE2
|
A:HIS268
|
2.4
|
23.4
|
1.0
|
SG
|
A:CYS61
|
2.6
|
27.3
|
1.0
|
CD
|
A:GLU302
|
3.0
|
26.3
|
1.0
|
CG
|
A:ASP326
|
3.1
|
29.6
|
1.0
|
O1
|
A:PEP1396
|
3.1
|
32.7
|
1.0
|
OE1
|
A:GLU302
|
3.2
|
27.9
|
1.0
|
CD2
|
A:HIS268
|
3.3
|
25.5
|
1.0
|
CE1
|
A:HIS268
|
3.4
|
23.6
|
1.0
|
CB
|
A:ASP326
|
3.5
|
29.0
|
1.0
|
CB
|
A:CYS61
|
3.6
|
27.3
|
1.0
|
C1
|
A:PEP1396
|
3.9
|
28.8
|
1.0
|
NZ
|
A:LYS97
|
4.0
|
24.5
|
1.0
|
OD1
|
A:ASP326
|
4.2
|
28.8
|
1.0
|
NH2
|
A:ARG92
|
4.2
|
26.1
|
1.0
|
CA
|
A:CYS61
|
4.3
|
26.4
|
1.0
|
O
|
A:HOH5427
|
4.3
|
27.2
|
1.0
|
O
|
A:HOH5552
|
4.3
|
43.3
|
1.0
|
CG
|
A:GLU302
|
4.4
|
27.1
|
1.0
|
CG
|
A:HIS268
|
4.4
|
26.0
|
1.0
|
ND1
|
A:HIS268
|
4.4
|
25.4
|
1.0
|
C2
|
A:PEP1396
|
4.4
|
27.9
|
1.0
|
O
|
A:HOH5566
|
4.5
|
43.7
|
1.0
|
O
|
A:HOH5525
|
4.5
|
46.1
|
1.0
|
O2'
|
A:PEP1396
|
4.6
|
26.8
|
1.0
|
O
|
A:CYS61
|
4.8
|
25.2
|
1.0
|
CA
|
A:ASP326
|
4.8
|
30.3
|
1.0
|
CE
|
A:LYS97
|
4.8
|
25.3
|
1.0
|
N
|
A:ASP326
|
4.9
|
30.5
|
1.0
|
C
|
A:CYS61
|
4.9
|
27.3
|
1.0
|
C3
|
A:PEP1396
|
4.9
|
29.8
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1n8f
Go back to
Manganese Binding Sites List in 1n8f
Manganese binding site 2 out
of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn351
b:19.5
occ:1.00
|
OE2
|
B:GLU302
|
2.1
|
17.8
|
1.0
|
O
|
B:HOH2376
|
2.1
|
20.5
|
1.0
|
OD2
|
B:ASP326
|
2.1
|
16.9
|
1.0
|
NE2
|
B:HIS268
|
2.3
|
12.9
|
1.0
|
SG
|
B:CYS61
|
2.6
|
15.7
|
1.0
|
CD
|
B:GLU302
|
2.9
|
11.7
|
1.0
|
OE1
|
B:GLU302
|
3.1
|
15.1
|
1.0
|
CG
|
B:ASP326
|
3.1
|
21.6
|
1.0
|
CD2
|
B:HIS268
|
3.2
|
16.9
|
1.0
|
O1
|
B:PEP1397
|
3.2
|
21.1
|
1.0
|
CE1
|
B:HIS268
|
3.2
|
19.2
|
1.0
|
CB
|
B:ASP326
|
3.5
|
17.0
|
1.0
|
CB
|
B:CYS61
|
3.6
|
16.8
|
1.0
|
C1
|
B:PEP1397
|
3.9
|
23.3
|
1.0
|
NZ
|
B:LYS97
|
4.0
|
19.8
|
1.0
|
O
|
B:HOH2548
|
4.1
|
31.5
|
1.0
|
OD1
|
B:ASP326
|
4.2
|
19.3
|
1.0
|
CA
|
B:CYS61
|
4.2
|
15.3
|
1.0
|
O
|
B:HOH2505
|
4.3
|
31.6
|
1.0
|
O
|
B:HOH2386
|
4.3
|
18.7
|
1.0
|
ND1
|
B:HIS268
|
4.3
|
15.5
|
1.0
|
CG
|
B:GLU302
|
4.3
|
15.7
|
1.0
|
CG
|
B:HIS268
|
4.4
|
17.0
|
1.0
|
NH2
|
B:ARG92
|
4.4
|
15.0
|
1.0
|
C2
|
B:PEP1397
|
4.4
|
21.2
|
1.0
|
O
|
B:HOH2561
|
4.5
|
39.2
|
1.0
|
O2'
|
B:PEP1397
|
4.6
|
18.9
|
1.0
|
CE
|
B:LYS97
|
4.8
|
18.4
|
1.0
|
CA
|
B:ASP326
|
4.8
|
16.8
|
1.0
|
C3
|
B:PEP1397
|
4.8
|
19.1
|
1.0
|
O
|
B:CYS61
|
4.8
|
14.2
|
1.0
|
N
|
B:ASP326
|
4.9
|
17.4
|
1.0
|
C
|
B:CYS61
|
4.9
|
17.3
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1n8f
Go back to
Manganese Binding Sites List in 1n8f
Manganese binding site 3 out
of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn351
b:31.5
occ:1.00
|
OD2
|
C:ASP326
|
2.0
|
25.7
|
1.0
|
OE2
|
C:GLU302
|
2.1
|
31.0
|
1.0
|
O
|
C:HOH3451
|
2.4
|
39.1
|
1.0
|
NE2
|
C:HIS268
|
2.4
|
31.0
|
1.0
|
SG
|
C:CYS61
|
2.6
|
31.3
|
1.0
|
O1
|
C:PEP1398
|
2.9
|
37.2
|
1.0
|
CD
|
C:GLU302
|
2.9
|
30.4
|
1.0
|
CG
|
C:ASP326
|
3.1
|
31.3
|
1.0
|
OE1
|
C:GLU302
|
3.1
|
30.3
|
1.0
|
CE1
|
C:HIS268
|
3.3
|
30.7
|
1.0
|
CD2
|
C:HIS268
|
3.3
|
30.6
|
1.0
|
CB
|
C:ASP326
|
3.4
|
31.3
|
1.0
|
CB
|
C:CYS61
|
3.7
|
32.0
|
1.0
|
C1
|
C:PEP1398
|
3.7
|
36.8
|
1.0
|
NZ
|
C:LYS97
|
4.0
|
29.1
|
1.0
|
OD1
|
C:ASP326
|
4.2
|
27.9
|
1.0
|
C2
|
C:PEP1398
|
4.2
|
36.2
|
1.0
|
NH2
|
C:ARG92
|
4.2
|
31.7
|
1.0
|
CA
|
C:CYS61
|
4.3
|
31.2
|
1.0
|
CG
|
C:GLU302
|
4.3
|
31.6
|
1.0
|
O
|
C:HOH3462
|
4.4
|
32.7
|
1.0
|
ND1
|
C:HIS268
|
4.4
|
29.6
|
1.0
|
CG
|
C:HIS268
|
4.4
|
30.8
|
1.0
|
O2'
|
C:PEP1398
|
4.4
|
36.5
|
1.0
|
C3
|
C:PEP1398
|
4.7
|
35.0
|
1.0
|
CE
|
C:LYS97
|
4.7
|
27.8
|
1.0
|
O2
|
C:PEP1398
|
4.7
|
36.0
|
1.0
|
O
|
C:CYS61
|
4.7
|
30.3
|
1.0
|
CA
|
C:ASP326
|
4.8
|
33.0
|
1.0
|
N
|
C:ASP326
|
4.9
|
32.4
|
1.0
|
C
|
C:CYS61
|
4.9
|
32.1
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1n8f
Go back to
Manganese Binding Sites List in 1n8f
Manganese binding site 4 out
of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn351
b:23.5
occ:1.00
|
OE2
|
D:GLU302
|
2.1
|
23.2
|
1.0
|
OD2
|
D:ASP326
|
2.1
|
25.4
|
1.0
|
O
|
D:HOH4414
|
2.2
|
29.4
|
1.0
|
NE2
|
D:HIS268
|
2.3
|
19.7
|
1.0
|
SG
|
D:CYS61
|
2.6
|
20.2
|
1.0
|
CD
|
D:GLU302
|
3.0
|
20.2
|
1.0
|
CG
|
D:ASP326
|
3.1
|
21.6
|
1.0
|
OE1
|
D:GLU302
|
3.1
|
23.7
|
1.0
|
CE1
|
D:HIS268
|
3.2
|
24.3
|
1.0
|
O1
|
D:PEP1399
|
3.2
|
29.3
|
1.0
|
CD2
|
D:HIS268
|
3.3
|
23.3
|
1.0
|
CB
|
D:ASP326
|
3.5
|
21.7
|
1.0
|
CB
|
D:CYS61
|
3.6
|
20.9
|
1.0
|
C1
|
D:PEP1399
|
3.9
|
30.3
|
1.0
|
NZ
|
D:LYS97
|
4.0
|
20.2
|
1.0
|
O
|
D:HOH4542
|
4.1
|
47.3
|
1.0
|
O
|
D:HOH4368
|
4.2
|
32.1
|
1.0
|
OD1
|
D:ASP326
|
4.2
|
25.2
|
1.0
|
CA
|
D:CYS61
|
4.2
|
20.7
|
1.0
|
NH2
|
D:ARG92
|
4.3
|
20.7
|
1.0
|
O
|
D:HOH4426
|
4.3
|
28.2
|
1.0
|
ND1
|
D:HIS268
|
4.3
|
22.2
|
1.0
|
CG
|
D:GLU302
|
4.4
|
23.8
|
1.0
|
C2
|
D:PEP1399
|
4.4
|
30.6
|
1.0
|
CG
|
D:HIS268
|
4.4
|
23.1
|
1.0
|
O
|
D:HOH4550
|
4.5
|
44.9
|
1.0
|
O2'
|
D:PEP1399
|
4.7
|
30.5
|
1.0
|
CA
|
D:ASP326
|
4.8
|
21.2
|
1.0
|
C3
|
D:PEP1399
|
4.8
|
27.1
|
1.0
|
N
|
D:ASP326
|
4.8
|
20.3
|
1.0
|
CE
|
D:LYS97
|
4.8
|
21.0
|
1.0
|
O
|
D:CYS61
|
4.9
|
18.5
|
1.0
|
C
|
D:CYS61
|
4.9
|
21.6
|
1.0
|
O
|
D:HOH4451
|
5.0
|
38.0
|
1.0
|
O2
|
D:PEP1399
|
5.0
|
28.4
|
1.0
|
|
Reference:
I.A.Shumilin,
R.Bauerle,
R.H.Kretsinger.
The High-Resolution Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase Reveals A Twist in the Plane of Bound Phosphoenolpyruvate Biochemistry V. 42 3766 2003.
ISSN: ISSN 0006-2960
PubMed: 12667068
DOI: 10.1021/BI027257P
Page generated: Sat Oct 5 11:50:10 2024
|