Iron in PDB 6qo8: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions:
1.17.4.1;
Protein crystallography data
The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions, PDB code: 6qo8
was solved by
K.Grave,
M.Hogbom,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.90 /
1.32
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.558,
61.456,
95.794,
90.00,
106.59,
90.00
|
R / Rfree (%)
|
13.4 /
16.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
(pdb code 6qo8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions, PDB code: 6qo8:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qo8
Go back to
Iron Binding Sites List in 6qo8
Iron binding site 1 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:7.8
occ:1.00
|
OD1
|
A:ASP62
|
1.9
|
11.0
|
1.0
|
OE2
|
A:GLU195
|
2.0
|
11.2
|
1.0
|
OE2
|
A:GLU93
|
2.0
|
10.4
|
1.0
|
ND1
|
A:HIS96
|
2.1
|
9.6
|
1.0
|
CG
|
A:ASP62
|
2.7
|
10.2
|
1.0
|
CD
|
A:GLU195
|
2.8
|
9.6
|
1.0
|
OD2
|
A:ASP62
|
2.9
|
12.1
|
1.0
|
CD
|
A:GLU93
|
3.0
|
9.3
|
1.0
|
CE1
|
A:HIS96
|
3.0
|
10.3
|
1.0
|
HA
|
A:GLU93
|
3.0
|
9.2
|
1.0
|
OE1
|
A:GLU195
|
3.0
|
11.3
|
1.0
|
HE1
|
A:HIS96
|
3.1
|
12.3
|
1.0
|
CG
|
A:HIS96
|
3.2
|
8.9
|
1.0
|
HB2
|
A:HIS96
|
3.2
|
11.0
|
1.0
|
HZ
|
A:PHE165
|
3.5
|
13.7
|
1.0
|
OE1
|
A:GLU93
|
3.5
|
11.4
|
1.0
|
HG23
|
A:ILE191
|
3.5
|
13.2
|
1.0
|
CB
|
A:HIS96
|
3.6
|
9.2
|
1.0
|
HB3
|
A:HIS96
|
3.6
|
11.0
|
1.0
|
HB3
|
A:GLU93
|
3.9
|
10.2
|
1.0
|
CA
|
A:GLU93
|
3.9
|
7.7
|
1.0
|
FE
|
A:FE2402
|
3.9
|
7.8
|
1.0
|
CZ
|
A:PHE165
|
4.0
|
11.4
|
1.0
|
CG
|
A:GLU93
|
4.1
|
8.9
|
1.0
|
CB
|
A:GLU93
|
4.1
|
8.5
|
1.0
|
NE2
|
A:HIS96
|
4.1
|
10.5
|
1.0
|
CB
|
A:ASP62
|
4.1
|
9.7
|
1.0
|
CG
|
A:GLU195
|
4.2
|
10.6
|
1.0
|
HA
|
A:ASP62
|
4.2
|
10.9
|
1.0
|
CD2
|
A:HIS96
|
4.2
|
10.0
|
1.0
|
HE1
|
A:HIS198
|
4.3
|
11.8
|
1.0
|
CG2
|
A:ILE191
|
4.3
|
11.0
|
1.0
|
HB3
|
A:ASP62
|
4.3
|
11.6
|
1.0
|
HG2
|
A:GLU195
|
4.4
|
12.7
|
1.0
|
HG21
|
A:ILE191
|
4.4
|
13.2
|
1.0
|
HE2
|
A:PHE165
|
4.4
|
12.9
|
1.0
|
HG3
|
A:GLU195
|
4.5
|
12.7
|
1.0
|
CE2
|
A:PHE165
|
4.5
|
10.8
|
1.0
|
HG22
|
A:ILE191
|
4.5
|
13.2
|
1.0
|
HH
|
A:TYR100
|
4.6
|
13.7
|
0.7
|
O
|
A:GLU93
|
4.6
|
9.3
|
1.0
|
HG3
|
A:GLU93
|
4.6
|
10.7
|
1.0
|
HG2
|
A:GLU93
|
4.6
|
10.7
|
1.0
|
CE1
|
A:PHE165
|
4.7
|
11.8
|
1.0
|
N
|
A:GLU93
|
4.7
|
8.5
|
1.0
|
HE1
|
A:PHE165
|
4.7
|
14.1
|
1.0
|
O
|
A:MET92
|
4.8
|
8.8
|
1.0
|
C
|
A:GLU93
|
4.8
|
8.9
|
1.0
|
CA
|
A:ASP62
|
4.8
|
9.1
|
1.0
|
HB2
|
A:ASP62
|
4.8
|
11.6
|
1.0
|
HE2
|
A:HIS96
|
4.9
|
12.6
|
1.0
|
CE1
|
A:HIS198
|
4.9
|
9.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 6qo8
Go back to
Iron Binding Sites List in 6qo8
Iron binding site 2 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:7.8
occ:1.00
|
OE1
|
A:GLU93
|
2.0
|
11.4
|
1.0
|
OE1
|
A:GLU161
|
2.0
|
10.7
|
1.0
|
OE1
|
A:GLU195
|
2.0
|
11.3
|
1.0
|
ND1
|
A:HIS198
|
2.1
|
9.7
|
1.0
|
OE2
|
A:GLU161
|
2.5
|
11.6
|
1.0
|
CD
|
A:GLU161
|
2.6
|
9.8
|
1.0
|
CD
|
A:GLU93
|
2.8
|
9.3
|
1.0
|
CE1
|
A:HIS198
|
3.0
|
9.8
|
1.0
|
OE2
|
A:GLU93
|
3.0
|
10.4
|
1.0
|
CG
|
A:HIS198
|
3.1
|
9.0
|
1.0
|
HA
|
A:GLU195
|
3.1
|
11.2
|
1.0
|
CD
|
A:GLU195
|
3.1
|
9.6
|
1.0
|
HE1
|
A:HIS198
|
3.1
|
11.8
|
1.0
|
HB2
|
A:HIS198
|
3.2
|
11.8
|
1.0
|
HB3
|
A:HIS198
|
3.4
|
11.8
|
1.0
|
CB
|
A:HIS198
|
3.5
|
9.9
|
1.0
|
HG2
|
A:GLN65
|
3.7
|
13.7
|
1.0
|
HE2
|
A:PHE165
|
3.7
|
12.9
|
1.0
|
OE2
|
A:GLU195
|
3.8
|
11.2
|
1.0
|
FE
|
A:FE2401
|
3.9
|
7.8
|
1.0
|
CA
|
A:GLU195
|
4.0
|
9.3
|
1.0
|
CG
|
A:GLU161
|
4.0
|
10.2
|
1.0
|
HB3
|
A:GLU195
|
4.1
|
11.7
|
1.0
|
CG
|
A:GLU93
|
4.1
|
8.9
|
1.0
|
NE2
|
A:HIS198
|
4.1
|
10.5
|
1.0
|
HE3
|
A:MET70
|
4.1
|
16.4
|
1.0
|
CD2
|
A:HIS198
|
4.2
|
10.0
|
1.0
|
CG
|
A:GLU195
|
4.2
|
10.6
|
1.0
|
HE21
|
A:GLN65
|
4.3
|
15.4
|
1.0
|
HE1
|
A:HIS96
|
4.3
|
12.3
|
1.0
|
CB
|
A:GLU195
|
4.3
|
9.7
|
1.0
|
HG2
|
A:GLU93
|
4.3
|
10.7
|
1.0
|
HG3
|
A:GLU93
|
4.3
|
10.7
|
1.0
|
HB3
|
A:GLU161
|
4.4
|
11.7
|
1.0
|
HG3
|
A:GLU161
|
4.4
|
12.2
|
1.0
|
HZ
|
A:PHE165
|
4.5
|
13.7
|
1.0
|
HE2
|
A:MET70
|
4.5
|
16.4
|
1.0
|
CE2
|
A:PHE165
|
4.5
|
10.8
|
1.0
|
HA
|
A:GLU161
|
4.5
|
10.9
|
1.0
|
HG2
|
A:GLU161
|
4.5
|
12.2
|
1.0
|
CG
|
A:GLN65
|
4.6
|
11.4
|
1.0
|
HG3
|
A:GLN65
|
4.7
|
13.7
|
1.0
|
HG3
|
A:GLU195
|
4.7
|
12.7
|
1.0
|
N
|
A:GLU195
|
4.7
|
9.9
|
1.0
|
CE
|
A:MET70
|
4.7
|
13.7
|
1.0
|
CB
|
A:GLU161
|
4.7
|
9.8
|
1.0
|
HG2
|
A:GLU195
|
4.9
|
12.7
|
1.0
|
CZ
|
A:PHE165
|
4.9
|
11.4
|
1.0
|
HE2
|
A:HIS198
|
4.9
|
12.6
|
1.0
|
OD1
|
A:ASP62
|
4.9
|
11.0
|
1.0
|
O
|
A:GLU195
|
4.9
|
10.3
|
1.0
|
CE1
|
A:HIS96
|
5.0
|
10.3
|
1.0
|
HB3
|
A:MET89
|
5.0
|
10.3
|
1.0
|
O
|
A:ASP194
|
5.0
|
10.1
|
1.0
|
CA
|
A:HIS198
|
5.0
|
9.7
|
1.0
|
C
|
A:GLU195
|
5.0
|
10.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qo8
Go back to
Iron Binding Sites List in 6qo8
Iron binding site 3 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:7.6
occ:1.00
|
OE1
|
B:GLU93
|
2.0
|
11.4
|
1.0
|
OE1
|
B:GLU161
|
2.0
|
10.9
|
1.0
|
OE1
|
B:GLU195
|
2.1
|
11.6
|
1.0
|
ND1
|
B:HIS198
|
2.1
|
9.5
|
1.0
|
OE2
|
B:GLU161
|
2.5
|
12.2
|
1.0
|
CD
|
B:GLU161
|
2.6
|
10.2
|
1.0
|
CD
|
B:GLU93
|
2.8
|
9.0
|
1.0
|
OE2
|
B:GLU93
|
3.0
|
9.5
|
1.0
|
CE1
|
B:HIS198
|
3.0
|
10.2
|
1.0
|
CG
|
B:HIS198
|
3.1
|
8.8
|
1.0
|
CD
|
B:GLU195
|
3.1
|
9.2
|
1.0
|
HA
|
B:GLU195
|
3.2
|
11.3
|
1.0
|
HE1
|
B:HIS198
|
3.2
|
12.2
|
1.0
|
HB2
|
B:HIS198
|
3.2
|
10.7
|
1.0
|
HB3
|
B:HIS198
|
3.4
|
10.7
|
1.0
|
CB
|
B:HIS198
|
3.5
|
8.9
|
1.0
|
HE2
|
B:PHE165
|
3.7
|
13.3
|
1.0
|
HG2
|
B:GLN65
|
3.7
|
14.1
|
1.0
|
OE2
|
B:GLU195
|
3.8
|
10.7
|
1.0
|
FE
|
B:FE2403
|
3.9
|
7.5
|
1.0
|
CA
|
B:GLU195
|
4.0
|
9.4
|
1.0
|
CG
|
B:GLU161
|
4.1
|
10.3
|
1.0
|
HB3
|
B:GLU195
|
4.1
|
11.1
|
1.0
|
NE2
|
B:HIS198
|
4.1
|
9.6
|
1.0
|
CG
|
B:GLU93
|
4.1
|
9.6
|
1.0
|
CD2
|
B:HIS198
|
4.2
|
9.2
|
1.0
|
HE3
|
B:MET70
|
4.2
|
16.7
|
1.0
|
CG
|
B:GLU195
|
4.2
|
9.5
|
1.0
|
HE21
|
B:GLN65
|
4.3
|
15.9
|
1.0
|
HE1
|
B:HIS96
|
4.3
|
11.7
|
1.0
|
CB
|
B:GLU195
|
4.3
|
9.3
|
1.0
|
HG3
|
B:GLU93
|
4.3
|
11.5
|
1.0
|
HG2
|
B:GLU93
|
4.4
|
11.5
|
1.0
|
HB3
|
B:GLU161
|
4.4
|
11.7
|
1.0
|
HE2
|
B:MET70
|
4.4
|
16.7
|
1.0
|
HZ
|
B:PHE165
|
4.4
|
13.0
|
1.0
|
CE2
|
B:PHE165
|
4.5
|
11.1
|
1.0
|
HA
|
B:GLU161
|
4.5
|
10.3
|
1.0
|
HG3
|
B:GLU161
|
4.5
|
12.3
|
1.0
|
HG2
|
B:GLU161
|
4.5
|
12.3
|
1.0
|
CG
|
B:GLN65
|
4.6
|
11.7
|
1.0
|
HG3
|
B:GLN65
|
4.7
|
14.1
|
1.0
|
HG3
|
B:GLU195
|
4.7
|
11.4
|
1.0
|
CB
|
B:GLU161
|
4.7
|
9.8
|
1.0
|
N
|
B:GLU195
|
4.8
|
9.3
|
1.0
|
CE
|
B:MET70
|
4.8
|
13.9
|
1.0
|
CZ
|
B:PHE165
|
4.9
|
10.9
|
1.0
|
OD1
|
B:ASP62
|
4.9
|
11.2
|
1.0
|
HG2
|
B:GLU195
|
4.9
|
11.4
|
1.0
|
HE2
|
B:HIS198
|
4.9
|
11.5
|
1.0
|
O
|
B:GLU195
|
4.9
|
10.1
|
1.0
|
HB3
|
B:MET89
|
5.0
|
10.2
|
1.0
|
O
|
B:ASP194
|
5.0
|
9.4
|
1.0
|
CA
|
B:HIS198
|
5.0
|
8.9
|
1.0
|
CE1
|
B:HIS96
|
5.0
|
9.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qo8
Go back to
Iron Binding Sites List in 6qo8
Iron binding site 4 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:7.5
occ:1.00
|
OD1
|
B:ASP62
|
1.9
|
11.2
|
1.0
|
OE2
|
B:GLU195
|
2.0
|
10.7
|
1.0
|
OE2
|
B:GLU93
|
2.0
|
9.5
|
1.0
|
ND1
|
B:HIS96
|
2.1
|
8.9
|
1.0
|
CG
|
B:ASP62
|
2.7
|
9.6
|
1.0
|
CD
|
B:GLU195
|
2.8
|
9.2
|
1.0
|
OD2
|
B:ASP62
|
2.9
|
11.8
|
1.0
|
HA
|
B:GLU93
|
2.9
|
9.9
|
1.0
|
CE1
|
B:HIS96
|
2.9
|
9.8
|
1.0
|
CD
|
B:GLU93
|
3.0
|
9.0
|
1.0
|
HE1
|
B:HIS96
|
3.0
|
11.7
|
1.0
|
OE1
|
B:GLU195
|
3.0
|
11.6
|
1.0
|
CG
|
B:HIS96
|
3.2
|
8.2
|
1.0
|
HB2
|
B:HIS96
|
3.3
|
11.0
|
1.0
|
HZ
|
B:PHE165
|
3.5
|
13.0
|
1.0
|
OE1
|
B:GLU93
|
3.5
|
11.4
|
1.0
|
HG23
|
B:ILE191
|
3.6
|
12.2
|
1.0
|
CB
|
B:HIS96
|
3.6
|
9.1
|
1.0
|
HB3
|
B:HIS96
|
3.6
|
11.0
|
1.0
|
CA
|
B:GLU93
|
3.8
|
8.2
|
1.0
|
HB3
|
B:GLU93
|
3.8
|
10.4
|
1.0
|
FE
|
B:FE2402
|
3.9
|
7.6
|
1.0
|
CZ
|
B:PHE165
|
4.0
|
10.9
|
1.0
|
CG
|
B:GLU93
|
4.1
|
9.6
|
1.0
|
NE2
|
B:HIS96
|
4.1
|
9.6
|
1.0
|
CB
|
B:GLU93
|
4.1
|
8.7
|
1.0
|
CB
|
B:ASP62
|
4.1
|
9.4
|
1.0
|
CG
|
B:GLU195
|
4.2
|
9.5
|
1.0
|
HA
|
B:ASP62
|
4.2
|
10.9
|
1.0
|
CD2
|
B:HIS96
|
4.2
|
9.6
|
1.0
|
HE1
|
B:HIS198
|
4.3
|
12.2
|
1.0
|
HB3
|
B:ASP62
|
4.3
|
11.3
|
1.0
|
CG2
|
B:ILE191
|
4.3
|
10.2
|
1.0
|
HG2
|
B:GLU195
|
4.4
|
11.4
|
1.0
|
HG3
|
B:GLU195
|
4.4
|
11.4
|
1.0
|
HE2
|
B:PHE165
|
4.4
|
13.3
|
1.0
|
HG21
|
B:ILE191
|
4.5
|
12.2
|
1.0
|
CE2
|
B:PHE165
|
4.5
|
11.1
|
1.0
|
HG22
|
B:ILE191
|
4.5
|
12.2
|
1.0
|
HH
|
B:TYR100
|
4.6
|
13.6
|
0.6
|
O
|
B:GLU93
|
4.6
|
9.3
|
1.0
|
HG2
|
B:GLU93
|
4.7
|
11.5
|
1.0
|
N
|
B:GLU93
|
4.7
|
8.0
|
1.0
|
HG3
|
B:GLU93
|
4.7
|
11.5
|
1.0
|
CE1
|
B:PHE165
|
4.7
|
12.0
|
1.0
|
C
|
B:GLU93
|
4.7
|
8.5
|
1.0
|
HE1
|
B:PHE165
|
4.8
|
14.4
|
1.0
|
O
|
B:MET92
|
4.8
|
8.9
|
1.0
|
HB2
|
B:ASP62
|
4.8
|
11.3
|
1.0
|
CA
|
B:ASP62
|
4.8
|
9.1
|
1.0
|
HE2
|
B:HIS96
|
4.9
|
11.5
|
1.0
|
CE1
|
B:HIS198
|
4.9
|
10.2
|
1.0
|
ND1
|
B:HIS198
|
5.0
|
9.5
|
1.0
|
|
Reference:
K.Grave,
W.Lambert,
G.Berggren,
J.J.Griese,
M.D.Bennett,
D.T.Logan,
M.Hogbom.
Redox-Induced Structural Changes in the Di-Iron and Di-Manganese Forms of Bacillus Anthracis Ribonucleotide Reductase Subunit Nrdf Suggest A Mechanism For Gating of Radical Access. J.Biol.Inorg.Chem. V. 24 849 2019.
ISSN: ESSN 1432-1327
PubMed: 31410573
DOI: 10.1007/S00775-019-01703-Z
Page generated: Wed Aug 7 08:10:37 2024
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