Iron in PDB 1rib: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Enzymatic activity of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
All present enzymatic activity of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2:
1.17.4.1;
Protein crystallography data
The structure of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2, PDB code: 1rib
was solved by
H.Eklund,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
7.00 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.300,
85.500,
115.700,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
n/a
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
(pdb code 1rib). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2, PDB code: 1rib:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1rib
Go back to
Iron Binding Sites List in 1rib
Iron binding site 1 out
of 4 in the Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:21.5
occ:0.90
|
FE1
|
A:FEO401
|
0.0
|
21.5
|
0.9
|
OE1
|
A:GLU115
|
1.8
|
18.0
|
1.0
|
O
|
A:HOH749
|
2.1
|
31.5
|
1.0
|
ND1
|
A:HIS118
|
2.1
|
7.3
|
1.0
|
OD2
|
A:ASP84
|
2.2
|
18.0
|
1.0
|
O
|
A:FEO401
|
2.2
|
34.9
|
1.0
|
OD1
|
A:ASP84
|
2.5
|
18.9
|
1.0
|
CG
|
A:ASP84
|
2.6
|
17.3
|
1.0
|
CD
|
A:GLU115
|
2.9
|
15.7
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
7.9
|
1.0
|
O
|
A:HOH522
|
3.1
|
30.9
|
1.0
|
CG
|
A:HIS118
|
3.2
|
9.0
|
1.0
|
OE2
|
A:GLU115
|
3.4
|
16.6
|
1.0
|
FE2
|
A:FEO401
|
3.4
|
12.9
|
1.0
|
CB
|
A:HIS118
|
3.8
|
13.2
|
1.0
|
OE1
|
A:GLU238
|
4.0
|
23.4
|
1.0
|
CB
|
A:ASP84
|
4.1
|
14.2
|
1.0
|
NE2
|
A:HIS118
|
4.2
|
9.0
|
1.0
|
CG
|
A:GLU115
|
4.2
|
15.5
|
1.0
|
CD2
|
A:HIS118
|
4.3
|
9.9
|
1.0
|
OE2
|
A:GLU238
|
4.4
|
17.4
|
1.0
|
CA
|
A:GLU115
|
4.4
|
13.7
|
1.0
|
CB
|
A:GLU115
|
4.5
|
14.5
|
1.0
|
CD
|
A:GLU238
|
4.5
|
20.9
|
1.0
|
CE2
|
A:PHE208
|
4.5
|
18.2
|
1.0
|
CZ
|
A:PHE208
|
4.5
|
17.4
|
1.0
|
CG2
|
A:ILE234
|
4.6
|
11.3
|
1.0
|
ND1
|
A:HIS241
|
4.7
|
9.8
|
1.0
|
CE1
|
A:HIS241
|
4.7
|
9.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 1rib
Go back to
Iron Binding Sites List in 1rib
Iron binding site 2 out
of 4 in the Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:12.9
occ:1.00
|
FE2
|
A:FEO401
|
0.0
|
12.9
|
1.0
|
OE2
|
A:GLU115
|
2.0
|
16.6
|
1.0
|
O
|
A:FEO401
|
2.1
|
34.9
|
1.0
|
OE2
|
A:GLU238
|
2.1
|
17.4
|
1.0
|
OE2
|
A:GLU204
|
2.1
|
22.3
|
1.0
|
O
|
A:HOH522
|
2.3
|
30.9
|
1.0
|
ND1
|
A:HIS241
|
2.3
|
9.8
|
1.0
|
CD
|
A:GLU115
|
2.9
|
15.7
|
1.0
|
CD
|
A:GLU238
|
3.1
|
20.9
|
1.0
|
OE1
|
A:GLU115
|
3.1
|
18.0
|
1.0
|
CD
|
A:GLU204
|
3.2
|
22.4
|
1.0
|
CE1
|
A:HIS241
|
3.2
|
9.3
|
1.0
|
CG
|
A:HIS241
|
3.3
|
11.8
|
1.0
|
FE1
|
A:FEO401
|
3.4
|
21.5
|
0.9
|
OE1
|
A:GLU238
|
3.6
|
23.4
|
1.0
|
CB
|
A:HIS241
|
3.7
|
10.0
|
1.0
|
CG
|
A:GLU204
|
3.9
|
20.5
|
1.0
|
NE1
|
A:TRP111
|
4.1
|
13.5
|
1.0
|
OE1
|
A:GLU204
|
4.1
|
25.6
|
1.0
|
O
|
A:HOH749
|
4.2
|
31.5
|
1.0
|
CG
|
A:GLU115
|
4.3
|
15.5
|
1.0
|
NE2
|
A:HIS241
|
4.4
|
12.4
|
1.0
|
OD1
|
A:ASP84
|
4.4
|
18.9
|
1.0
|
CG
|
A:GLU238
|
4.4
|
16.7
|
1.0
|
CD1
|
A:TRP111
|
4.4
|
13.3
|
1.0
|
CD2
|
A:HIS241
|
4.4
|
10.8
|
1.0
|
CA
|
A:GLU238
|
4.6
|
15.0
|
1.0
|
CB
|
A:GLU204
|
4.7
|
17.7
|
1.0
|
CE1
|
A:HIS118
|
4.9
|
7.9
|
1.0
|
CB
|
A:GLU238
|
4.9
|
13.5
|
1.0
|
ND1
|
A:HIS118
|
4.9
|
7.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 1rib
Go back to
Iron Binding Sites List in 1rib
Iron binding site 3 out
of 4 in the Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:22.9
occ:0.90
|
FE1
|
B:FEO402
|
0.0
|
22.9
|
0.9
|
O
|
B:FEO402
|
1.8
|
24.8
|
1.0
|
ND1
|
B:HIS118
|
2.0
|
9.6
|
1.0
|
OE1
|
B:GLU115
|
2.0
|
14.6
|
1.0
|
O
|
B:HOH712
|
2.1
|
31.4
|
1.0
|
OD2
|
B:ASP84
|
2.5
|
20.8
|
1.0
|
OD1
|
B:ASP84
|
2.6
|
22.0
|
1.0
|
CE1
|
B:HIS118
|
2.7
|
10.9
|
1.0
|
CG
|
B:ASP84
|
2.8
|
20.0
|
1.0
|
O
|
B:HOH640
|
3.1
|
24.9
|
1.0
|
CG
|
B:HIS118
|
3.1
|
10.6
|
1.0
|
CD
|
B:GLU115
|
3.1
|
13.9
|
1.0
|
FE2
|
B:FEO402
|
3.3
|
20.0
|
1.0
|
OE2
|
B:GLU115
|
3.6
|
17.3
|
1.0
|
OE2
|
B:GLU238
|
3.8
|
25.9
|
1.0
|
CB
|
B:HIS118
|
3.8
|
12.4
|
1.0
|
NE2
|
B:HIS118
|
3.9
|
10.4
|
1.0
|
CD2
|
B:HIS118
|
4.2
|
9.6
|
1.0
|
CB
|
B:ASP84
|
4.2
|
17.9
|
1.0
|
CG
|
B:GLU115
|
4.4
|
11.7
|
1.0
|
CA
|
B:GLU115
|
4.4
|
11.7
|
1.0
|
CD
|
B:GLU238
|
4.5
|
22.3
|
1.0
|
CG2
|
B:ILE234
|
4.5
|
8.1
|
1.0
|
OE1
|
B:GLU238
|
4.5
|
22.3
|
1.0
|
CZ
|
B:PHE208
|
4.5
|
19.8
|
1.0
|
CB
|
B:GLU115
|
4.6
|
10.8
|
1.0
|
CE1
|
B:HIS241
|
4.6
|
8.3
|
1.0
|
CE2
|
B:PHE208
|
4.6
|
23.1
|
1.0
|
ND1
|
B:HIS241
|
4.6
|
9.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1rib
Go back to
Iron Binding Sites List in 1rib
Iron binding site 4 out
of 4 in the Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:20.0
occ:1.00
|
FE2
|
B:FEO402
|
0.0
|
20.0
|
1.0
|
O
|
B:FEO402
|
1.9
|
24.8
|
1.0
|
OE2
|
B:GLU204
|
2.0
|
15.6
|
1.0
|
OE1
|
B:GLU238
|
2.1
|
22.3
|
1.0
|
O
|
B:HOH640
|
2.2
|
24.9
|
1.0
|
ND1
|
B:HIS241
|
2.4
|
9.5
|
1.0
|
OE2
|
B:GLU115
|
2.4
|
17.3
|
1.0
|
CD
|
B:GLU238
|
2.9
|
22.3
|
1.0
|
CD
|
B:GLU204
|
3.0
|
16.9
|
1.0
|
CD
|
B:GLU115
|
3.1
|
13.9
|
1.0
|
OE2
|
B:GLU238
|
3.1
|
25.9
|
1.0
|
OE1
|
B:GLU115
|
3.2
|
14.6
|
1.0
|
CE1
|
B:HIS241
|
3.2
|
8.3
|
1.0
|
FE1
|
B:FEO402
|
3.3
|
22.9
|
0.9
|
CG
|
B:HIS241
|
3.4
|
8.8
|
1.0
|
CG
|
B:GLU204
|
3.6
|
19.0
|
1.0
|
CB
|
B:HIS241
|
3.8
|
11.2
|
1.0
|
OE1
|
B:GLU204
|
4.0
|
16.3
|
1.0
|
NE1
|
B:TRP111
|
4.2
|
11.4
|
1.0
|
O
|
B:HOH712
|
4.2
|
31.4
|
1.0
|
CG
|
B:GLU238
|
4.3
|
19.7
|
1.0
|
NE2
|
B:HIS241
|
4.4
|
8.0
|
1.0
|
CB
|
B:GLU204
|
4.5
|
19.2
|
1.0
|
OD1
|
B:ASP84
|
4.5
|
22.0
|
1.0
|
CD2
|
B:HIS241
|
4.5
|
9.1
|
1.0
|
CG
|
B:GLU115
|
4.5
|
11.7
|
1.0
|
CA
|
B:GLU238
|
4.6
|
14.8
|
1.0
|
CE1
|
B:HIS118
|
4.7
|
10.9
|
1.0
|
CD1
|
B:TRP111
|
4.7
|
10.7
|
1.0
|
ND1
|
B:HIS118
|
4.7
|
9.6
|
1.0
|
NE2
|
B:GLN87
|
4.7
|
17.4
|
1.0
|
CB
|
B:GLU238
|
5.0
|
16.8
|
1.0
|
|
Reference:
P.Nordlund,
H.Eklund.
Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2. J.Mol.Biol. V. 232 123 1993.
ISSN: ISSN 0022-2836
PubMed: 8331655
DOI: 10.1006/JMBI.1993.1374
Page generated: Sat Aug 3 14:15:52 2024
|