Iron in PDB 1rnr: Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
Enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
All present enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein:
1.17.4.1;
Protein crystallography data
The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr
was solved by
A.Aberg,
P.Nordlund,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.100,
85.300,
115.700,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
n/a
|
Other elements in 1rnr:
The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
(pdb code 1rnr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1rnr
Go back to
Iron Binding Sites List in 1rnr
Iron binding site 1 out
of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:23.6
occ:0.70
|
OE1
|
A:GLU115
|
1.9
|
15.7
|
1.0
|
OD1
|
A:ASP84
|
1.9
|
22.8
|
1.0
|
OE2
|
A:DAH208
|
2.0
|
51.6
|
1.0
|
OZ
|
A:DAH208
|
2.2
|
53.0
|
1.0
|
ND1
|
A:HIS118
|
2.4
|
9.4
|
1.0
|
OE2
|
A:GLU238
|
2.8
|
28.8
|
1.0
|
CE2
|
A:DAH208
|
2.9
|
51.8
|
1.0
|
CZ
|
A:DAH208
|
2.9
|
52.4
|
1.0
|
CG
|
A:ASP84
|
3.0
|
23.6
|
1.0
|
CD
|
A:GLU115
|
3.0
|
12.4
|
1.0
|
CG
|
A:HIS118
|
3.3
|
9.6
|
1.0
|
OD2
|
A:ASP84
|
3.4
|
28.5
|
1.0
|
CE1
|
A:HIS118
|
3.5
|
8.7
|
1.0
|
OE2
|
A:GLU115
|
3.5
|
15.5
|
1.0
|
FE
|
A:FE402
|
3.6
|
15.8
|
1.0
|
CB
|
A:HIS118
|
3.7
|
12.6
|
1.0
|
CD
|
A:GLU238
|
3.9
|
27.6
|
1.0
|
CD2
|
A:DAH208
|
4.2
|
48.8
|
1.0
|
CG
|
A:GLU115
|
4.2
|
11.5
|
1.0
|
CE1
|
A:DAH208
|
4.3
|
51.0
|
1.0
|
CB
|
A:ASP84
|
4.3
|
20.6
|
1.0
|
CA
|
A:GLU115
|
4.4
|
11.1
|
1.0
|
CD2
|
A:HIS118
|
4.5
|
10.6
|
1.0
|
CB
|
A:GLU115
|
4.5
|
8.1
|
1.0
|
NE2
|
A:HIS118
|
4.5
|
8.0
|
1.0
|
CG2
|
A:ILE234
|
4.6
|
11.6
|
1.0
|
OE1
|
A:GLU238
|
4.7
|
32.5
|
1.0
|
CG
|
A:GLU238
|
4.7
|
24.5
|
1.0
|
CA
|
A:ASP84
|
4.8
|
18.7
|
1.0
|
O
|
A:GLU115
|
4.9
|
13.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 1rnr
Go back to
Iron Binding Sites List in 1rnr
Iron binding site 2 out
of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:15.8
occ:1.00
|
OE2
|
A:GLU238
|
1.9
|
28.8
|
1.0
|
OE2
|
A:GLU204
|
2.0
|
26.2
|
1.0
|
OE2
|
A:GLU115
|
2.0
|
15.5
|
1.0
|
OE1
|
A:GLU238
|
2.3
|
32.5
|
1.0
|
ND1
|
A:HIS241
|
2.4
|
14.0
|
1.0
|
CD
|
A:GLU238
|
2.4
|
27.6
|
1.0
|
CD
|
A:GLU115
|
3.0
|
12.4
|
1.0
|
CD
|
A:GLU204
|
3.1
|
26.2
|
1.0
|
OE1
|
A:GLU115
|
3.2
|
15.7
|
1.0
|
OZ
|
A:DAH208
|
3.3
|
53.0
|
1.0
|
CE1
|
A:HIS241
|
3.3
|
11.3
|
1.0
|
CG
|
A:HIS241
|
3.4
|
15.1
|
1.0
|
CZ
|
A:DAH208
|
3.6
|
52.4
|
1.0
|
FE
|
A:FE401
|
3.6
|
23.6
|
0.7
|
CB
|
A:HIS241
|
3.7
|
14.6
|
1.0
|
OE1
|
A:GLU204
|
3.8
|
30.2
|
1.0
|
CG
|
A:GLU238
|
3.9
|
24.5
|
1.0
|
CE1
|
A:DAH208
|
4.0
|
51.0
|
1.0
|
CG
|
A:GLU204
|
4.0
|
27.0
|
1.0
|
CE2
|
A:DAH208
|
4.1
|
51.8
|
1.0
|
NE1
|
A:TRP111
|
4.2
|
8.8
|
1.0
|
OE2
|
A:DAH208
|
4.3
|
51.6
|
1.0
|
CG
|
A:GLU115
|
4.4
|
11.5
|
1.0
|
NE2
|
A:HIS241
|
4.4
|
13.1
|
1.0
|
CD2
|
A:HIS241
|
4.5
|
13.3
|
1.0
|
CD1
|
A:TRP111
|
4.6
|
9.8
|
1.0
|
CA
|
A:GLU238
|
4.7
|
14.5
|
1.0
|
CB
|
A:GLU238
|
4.8
|
17.3
|
1.0
|
CB
|
A:GLU204
|
4.8
|
24.6
|
1.0
|
CD1
|
A:DAH208
|
4.8
|
48.2
|
1.0
|
ND1
|
A:HIS118
|
4.9
|
9.4
|
1.0
|
CE1
|
A:HIS118
|
5.0
|
8.7
|
1.0
|
CD2
|
A:DAH208
|
5.0
|
48.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 1rnr
Go back to
Iron Binding Sites List in 1rnr
Iron binding site 3 out
of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:17.0
occ:0.70
|
OD1
|
B:ASP84
|
2.0
|
26.4
|
1.0
|
OZ
|
B:DAH208
|
2.0
|
44.4
|
1.0
|
OE2
|
B:DAH208
|
2.1
|
42.0
|
1.0
|
ND1
|
B:HIS118
|
2.3
|
8.4
|
1.0
|
OE1
|
B:GLU115
|
2.3
|
22.2
|
1.0
|
OE2
|
B:GLU238
|
2.4
|
27.6
|
1.0
|
CZ
|
B:DAH208
|
2.7
|
43.5
|
1.0
|
CE2
|
B:DAH208
|
2.8
|
42.8
|
1.0
|
CG
|
B:ASP84
|
2.9
|
27.6
|
1.0
|
CE1
|
B:HIS118
|
3.1
|
5.5
|
1.0
|
OD2
|
B:ASP84
|
3.2
|
32.0
|
1.0
|
CG
|
B:HIS118
|
3.4
|
7.2
|
1.0
|
FE
|
B:FE402
|
3.5
|
20.0
|
1.0
|
CD
|
B:GLU115
|
3.5
|
20.0
|
1.0
|
CD
|
B:GLU238
|
3.5
|
26.5
|
1.0
|
CB
|
B:HIS118
|
3.9
|
9.8
|
1.0
|
CE1
|
B:DAH208
|
4.0
|
43.7
|
1.0
|
OE2
|
B:GLU115
|
4.0
|
24.2
|
1.0
|
CD2
|
B:DAH208
|
4.1
|
41.2
|
1.0
|
OE1
|
B:GLU238
|
4.2
|
28.8
|
1.0
|
NE2
|
B:HIS118
|
4.3
|
6.2
|
1.0
|
CB
|
B:ASP84
|
4.3
|
22.3
|
1.0
|
CG
|
B:GLU238
|
4.4
|
24.7
|
1.0
|
CD2
|
B:HIS118
|
4.5
|
4.6
|
1.0
|
CG2
|
B:ILE234
|
4.5
|
10.2
|
1.0
|
CA
|
B:GLU115
|
4.6
|
11.1
|
1.0
|
CG
|
B:GLU115
|
4.7
|
16.9
|
1.0
|
ND1
|
B:HIS241
|
4.8
|
9.3
|
1.0
|
CA
|
B:ASP84
|
4.8
|
20.6
|
1.0
|
CB
|
B:GLU115
|
4.8
|
12.7
|
1.0
|
CE1
|
B:HIS241
|
4.9
|
7.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 1rnr
Go back to
Iron Binding Sites List in 1rnr
Iron binding site 4 out
of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:20.0
occ:1.00
|
OE2
|
B:GLU204
|
1.9
|
24.1
|
1.0
|
OE1
|
B:GLU238
|
1.9
|
28.8
|
1.0
|
OE2
|
B:GLU238
|
2.1
|
27.6
|
1.0
|
ND1
|
B:HIS241
|
2.3
|
9.3
|
1.0
|
CD
|
B:GLU238
|
2.3
|
26.5
|
1.0
|
OE2
|
B:GLU115
|
2.3
|
24.2
|
1.0
|
CD
|
B:GLU204
|
3.0
|
24.9
|
1.0
|
OE1
|
B:GLU115
|
3.0
|
22.2
|
1.0
|
CD
|
B:GLU115
|
3.1
|
20.0
|
1.0
|
OZ
|
B:DAH208
|
3.1
|
44.4
|
1.0
|
CE1
|
B:HIS241
|
3.2
|
7.1
|
1.0
|
CG
|
B:HIS241
|
3.3
|
12.0
|
1.0
|
FE
|
B:FE401
|
3.5
|
17.0
|
0.7
|
CZ
|
B:DAH208
|
3.6
|
43.5
|
1.0
|
CB
|
B:HIS241
|
3.7
|
15.2
|
1.0
|
CG
|
B:GLU204
|
3.7
|
27.0
|
1.0
|
CG
|
B:GLU238
|
3.9
|
24.7
|
1.0
|
CE1
|
B:DAH208
|
3.9
|
43.7
|
1.0
|
OE1
|
B:GLU204
|
3.9
|
26.8
|
1.0
|
NE1
|
B:TRP111
|
4.0
|
10.8
|
1.0
|
NE2
|
B:HIS241
|
4.4
|
8.5
|
1.0
|
CE2
|
B:DAH208
|
4.4
|
42.8
|
1.0
|
CD1
|
B:TRP111
|
4.4
|
9.5
|
1.0
|
CD2
|
B:HIS241
|
4.4
|
10.8
|
1.0
|
CG
|
B:GLU115
|
4.5
|
16.9
|
1.0
|
CB
|
B:GLU204
|
4.6
|
25.2
|
1.0
|
CA
|
B:GLU238
|
4.7
|
16.6
|
1.0
|
CB
|
B:GLU238
|
4.7
|
19.5
|
1.0
|
OE2
|
B:DAH208
|
4.7
|
42.0
|
1.0
|
CE1
|
B:HIS118
|
4.8
|
5.5
|
1.0
|
OE1
|
B:GLN87
|
4.8
|
19.0
|
1.0
|
CD1
|
B:DAH208
|
4.8
|
42.1
|
1.0
|
ND1
|
B:HIS118
|
4.9
|
8.4
|
1.0
|
OD1
|
B:ASP84
|
5.0
|
26.4
|
1.0
|
|
Reference:
A.Aberg,
M.Ormo,
P.Nordlund,
B.M.Sjoberg.
Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein. Biochemistry V. 32 9845 1993.
ISSN: ISSN 0006-2960
PubMed: 8373782
DOI: 10.1021/BI00088A040
Page generated: Sat Aug 3 14:16:44 2024
|