Iron in PDB 1pj0: Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;
Protein crystallography data
The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0
was solved by
W.C.Voegtli,
M.Sommerhalter,
L.Saleh,
J.Baldwin,
J.M.Bollinger Jr.,
A.C.Rosenzweig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.32 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.000,
84.400,
114.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.4 /
23.6
|
Other elements in 1pj0:
The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
(pdb code 1pj0). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1pj0
Go back to
Iron Binding Sites List in 1pj0
Iron binding site 1 out
of 4 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe376
b:20.6
occ:1.00
|
OE2
|
A:GLU238
|
2.0
|
19.8
|
1.0
|
ND1
|
A:HIS118
|
2.1
|
12.8
|
1.0
|
OE1
|
A:GLU115
|
2.1
|
16.0
|
1.0
|
OE1
|
A:GLU84
|
2.2
|
14.3
|
1.0
|
OE2
|
A:GLU84
|
2.3
|
14.9
|
1.0
|
CD
|
A:GLU84
|
2.5
|
13.9
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
13.0
|
1.0
|
CD
|
A:GLU238
|
3.2
|
18.8
|
1.0
|
CG
|
A:HIS118
|
3.2
|
13.1
|
1.0
|
CD
|
A:GLU115
|
3.2
|
15.3
|
1.0
|
CB
|
A:HIS118
|
3.6
|
13.7
|
1.0
|
OE2
|
A:GLU115
|
3.7
|
16.5
|
1.0
|
OE1
|
A:GLU238
|
3.8
|
19.2
|
1.0
|
CZ
|
A:PHE208
|
3.8
|
19.2
|
1.0
|
FE
|
A:FE377
|
4.0
|
14.1
|
1.0
|
CG
|
A:GLU84
|
4.0
|
13.6
|
1.0
|
NE2
|
A:HIS118
|
4.1
|
13.0
|
1.0
|
CE2
|
A:PHE208
|
4.2
|
19.0
|
1.0
|
CA
|
A:GLU115
|
4.2
|
14.2
|
1.0
|
CG2
|
A:ILE234
|
4.2
|
13.8
|
1.0
|
CD2
|
A:HIS118
|
4.3
|
12.8
|
1.0
|
CG
|
A:GLU238
|
4.3
|
17.2
|
1.0
|
CE1
|
A:PHE208
|
4.3
|
18.8
|
1.0
|
CG
|
A:GLU115
|
4.4
|
14.4
|
1.0
|
CB
|
A:GLU115
|
4.4
|
14.1
|
1.0
|
O
|
A:HOH437
|
4.6
|
23.5
|
1.0
|
CE1
|
A:HIS241
|
4.8
|
14.0
|
1.0
|
O
|
A:GLU115
|
4.8
|
14.2
|
1.0
|
CB
|
A:GLU84
|
4.9
|
13.5
|
1.0
|
ND1
|
A:HIS241
|
4.9
|
14.0
|
1.0
|
CD2
|
A:PHE208
|
4.9
|
19.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 1pj0
Go back to
Iron Binding Sites List in 1pj0
Iron binding site 2 out
of 4 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe377
b:14.1
occ:1.00
|
OE1
|
A:GLU238
|
1.9
|
19.2
|
1.0
|
OE2
|
A:GLU115
|
2.0
|
16.5
|
1.0
|
OE1
|
A:GLU204
|
2.0
|
20.8
|
1.0
|
ND1
|
A:HIS241
|
2.1
|
14.0
|
1.0
|
CD
|
A:GLU204
|
2.8
|
19.9
|
1.0
|
CD
|
A:GLU115
|
2.8
|
15.3
|
1.0
|
OE2
|
A:GLU204
|
2.8
|
21.8
|
1.0
|
CD
|
A:GLU238
|
2.9
|
18.8
|
1.0
|
OE1
|
A:GLU115
|
3.1
|
16.0
|
1.0
|
CE1
|
A:HIS241
|
3.1
|
14.0
|
1.0
|
CG
|
A:HIS241
|
3.1
|
14.2
|
1.0
|
OE2
|
A:GLU238
|
3.2
|
19.8
|
1.0
|
CB
|
A:HIS241
|
3.4
|
14.5
|
1.0
|
NE1
|
A:TRP111
|
3.6
|
15.3
|
1.0
|
CE2
|
A:PHE208
|
3.9
|
19.0
|
1.0
|
FE
|
A:FE376
|
4.0
|
20.6
|
1.0
|
CD1
|
A:TRP111
|
4.1
|
14.6
|
1.0
|
CG
|
A:GLU115
|
4.1
|
14.4
|
1.0
|
NE2
|
A:HIS241
|
4.2
|
13.7
|
1.0
|
CG
|
A:GLU204
|
4.2
|
19.4
|
1.0
|
CD2
|
A:HIS241
|
4.2
|
13.9
|
1.0
|
CG
|
A:GLU238
|
4.3
|
17.2
|
1.0
|
CA
|
A:GLU238
|
4.3
|
16.2
|
1.0
|
CD2
|
A:PHE208
|
4.4
|
19.1
|
1.0
|
CB
|
A:GLU238
|
4.6
|
16.4
|
1.0
|
CZ
|
A:PHE208
|
4.7
|
19.2
|
1.0
|
CE2
|
A:TRP111
|
4.8
|
15.0
|
1.0
|
CB
|
A:GLU204
|
4.8
|
17.8
|
1.0
|
CA
|
A:HIS241
|
4.9
|
14.6
|
1.0
|
N
|
A:GLU238
|
5.0
|
16.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 1pj0
Go back to
Iron Binding Sites List in 1pj0
Iron binding site 3 out
of 4 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe376
b:20.9
occ:1.00
|
ND1
|
B:HIS118
|
2.0
|
13.4
|
1.0
|
OE2
|
B:GLU238
|
2.0
|
18.7
|
1.0
|
OE2
|
B:GLU84
|
2.1
|
15.2
|
1.0
|
OE1
|
B:GLU115
|
2.1
|
15.6
|
1.0
|
OE1
|
B:GLU84
|
2.3
|
16.7
|
1.0
|
CD
|
B:GLU84
|
2.5
|
16.0
|
1.0
|
CE1
|
B:HIS118
|
2.9
|
13.8
|
1.0
|
CG
|
B:HIS118
|
3.1
|
13.0
|
1.0
|
CD
|
B:GLU238
|
3.2
|
16.8
|
1.0
|
CD
|
B:GLU115
|
3.2
|
14.9
|
1.0
|
CB
|
B:HIS118
|
3.6
|
13.2
|
1.0
|
OE1
|
B:GLU238
|
3.7
|
17.4
|
1.0
|
OE2
|
B:GLU115
|
3.7
|
16.6
|
1.0
|
CZ
|
B:PHE208
|
3.9
|
23.0
|
1.0
|
FE
|
B:FE377
|
3.9
|
14.1
|
1.0
|
CG
|
B:GLU84
|
4.0
|
15.4
|
1.0
|
NE2
|
B:HIS118
|
4.1
|
13.4
|
1.0
|
CE2
|
B:PHE208
|
4.2
|
23.7
|
1.0
|
CD2
|
B:HIS118
|
4.2
|
13.1
|
1.0
|
CG2
|
B:ILE234
|
4.2
|
15.7
|
1.0
|
CA
|
B:GLU115
|
4.2
|
12.7
|
1.0
|
CG
|
B:GLU115
|
4.4
|
14.2
|
1.0
|
CG
|
B:GLU238
|
4.4
|
15.7
|
1.0
|
CB
|
B:GLU115
|
4.4
|
13.0
|
1.0
|
CE1
|
B:PHE208
|
4.4
|
22.7
|
1.0
|
O
|
B:HOH431
|
4.7
|
24.7
|
1.0
|
CE1
|
B:HIS241
|
4.7
|
11.6
|
1.0
|
ND1
|
B:HIS241
|
4.8
|
11.3
|
1.0
|
CB
|
B:GLU84
|
4.9
|
14.7
|
1.0
|
O
|
B:GLU115
|
4.9
|
12.1
|
1.0
|
CD2
|
B:PHE208
|
5.0
|
22.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 1pj0
Go back to
Iron Binding Sites List in 1pj0
Iron binding site 4 out
of 4 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe377
b:14.1
occ:1.00
|
OE1
|
B:GLU238
|
1.9
|
17.4
|
1.0
|
OE1
|
B:GLU204
|
2.0
|
22.1
|
1.0
|
OE2
|
B:GLU115
|
2.0
|
16.6
|
1.0
|
ND1
|
B:HIS241
|
2.1
|
11.3
|
1.0
|
CD
|
B:GLU204
|
2.7
|
20.4
|
1.0
|
OE2
|
B:GLU204
|
2.8
|
21.9
|
1.0
|
CD
|
B:GLU115
|
2.8
|
14.9
|
1.0
|
CD
|
B:GLU238
|
2.9
|
16.8
|
1.0
|
OE1
|
B:GLU115
|
3.0
|
15.6
|
1.0
|
CE1
|
B:HIS241
|
3.1
|
11.6
|
1.0
|
CG
|
B:HIS241
|
3.1
|
12.3
|
1.0
|
OE2
|
B:GLU238
|
3.3
|
18.7
|
1.0
|
CB
|
B:HIS241
|
3.4
|
13.6
|
1.0
|
NE1
|
B:TRP111
|
3.7
|
11.7
|
1.0
|
CE2
|
B:PHE208
|
3.9
|
23.7
|
1.0
|
FE
|
B:FE376
|
3.9
|
20.9
|
1.0
|
CD1
|
B:TRP111
|
4.2
|
11.4
|
1.0
|
CG
|
B:GLU204
|
4.2
|
20.3
|
1.0
|
CG
|
B:GLU115
|
4.2
|
14.2
|
1.0
|
NE2
|
B:HIS241
|
4.2
|
10.6
|
1.0
|
CD2
|
B:HIS241
|
4.2
|
11.7
|
1.0
|
CG
|
B:GLU238
|
4.2
|
15.7
|
1.0
|
CA
|
B:GLU238
|
4.3
|
14.2
|
1.0
|
CD2
|
B:PHE208
|
4.4
|
22.6
|
1.0
|
CB
|
B:GLU238
|
4.6
|
14.9
|
1.0
|
CB
|
B:GLU204
|
4.8
|
18.6
|
1.0
|
CZ
|
B:PHE208
|
4.8
|
23.0
|
1.0
|
CE2
|
B:TRP111
|
4.9
|
12.2
|
1.0
|
CA
|
B:HIS241
|
5.0
|
13.8
|
1.0
|
N
|
B:GLU238
|
5.0
|
14.3
|
1.0
|
|
Reference:
W.C.Voegtli,
M.Sommerhalter,
L.Saleh,
J.Baldwin,
J.M.Bollinger Jr.,
A.C.Rosenzweig.
Variable Coordination Geometries at the Diiron(II) Active Site of Ribonucleotide Reductase R2. J.Am.Chem.Soc. V. 125 15822 2003.
ISSN: ISSN 0002-7863
PubMed: 14677973
DOI: 10.1021/JA0370387
Page generated: Sat Aug 3 13:08:59 2024
|