Iron in PDB 6qo7: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced):
1.17.4.1;
Protein crystallography data
The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced), PDB code: 6qo7
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)
|
41.82 /
1.63
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.293,
59.958,
95.360,
90.00,
107.11,
90.00
|
R / Rfree (%)
|
15.9 /
19.2
|
Other elements in 6qo7:
The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
(pdb code 6qo7). 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 Aerobically Soaked with Ferrous Ions (Photo-Reduced), PDB code: 6qo7:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qo7
Go back to
Iron Binding Sites List in 6qo7
Iron binding site 1 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:15.3
occ:1.00
|
OE1
|
A:GLU93
|
2.1
|
21.6
|
1.0
|
OE1
|
A:GLU161
|
2.1
|
22.6
|
1.0
|
ND1
|
A:HIS198
|
2.1
|
13.9
|
1.0
|
OE2
|
A:GLU195
|
2.1
|
18.6
|
1.0
|
OE2
|
A:GLU161
|
2.4
|
18.2
|
1.0
|
CD
|
A:GLU161
|
2.5
|
19.2
|
1.0
|
CD
|
A:GLU93
|
2.8
|
22.9
|
1.0
|
OE2
|
A:GLU93
|
2.9
|
19.9
|
1.0
|
CE1
|
A:HIS198
|
3.0
|
13.6
|
1.0
|
HE1
|
A:HIS198
|
3.1
|
16.3
|
1.0
|
HA
|
A:GLU195
|
3.2
|
16.7
|
1.0
|
CG
|
A:HIS198
|
3.2
|
13.9
|
1.0
|
HB2
|
A:HIS198
|
3.2
|
13.5
|
1.0
|
CD
|
A:GLU195
|
3.2
|
25.4
|
1.0
|
HB3
|
A:HIS198
|
3.4
|
13.5
|
1.0
|
CB
|
A:HIS198
|
3.5
|
11.3
|
1.0
|
HE2
|
A:PHE165
|
3.7
|
21.3
|
1.0
|
HG2
|
A:GLN65
|
3.7
|
26.0
|
1.0
|
FE
|
A:FE2402
|
3.9
|
17.8
|
1.0
|
OE1
|
A:GLU195
|
3.9
|
20.6
|
1.0
|
CG
|
A:GLU161
|
4.0
|
18.5
|
1.0
|
CA
|
A:GLU195
|
4.1
|
13.9
|
1.0
|
HB3
|
A:GLU195
|
4.1
|
20.1
|
1.0
|
HE3
|
A:MET70
|
4.1
|
32.8
|
1.0
|
HE1
|
A:HIS96
|
4.1
|
20.5
|
1.0
|
NE2
|
A:HIS198
|
4.2
|
13.2
|
1.0
|
CG
|
A:GLU93
|
4.2
|
15.4
|
1.0
|
HE21
|
A:GLN65
|
4.3
|
26.8
|
1.0
|
CD2
|
A:HIS198
|
4.3
|
14.7
|
1.0
|
CG
|
A:GLU195
|
4.3
|
23.9
|
1.0
|
CB
|
A:GLU195
|
4.3
|
16.8
|
1.0
|
HG2
|
A:GLU93
|
4.4
|
18.5
|
1.0
|
HB3
|
A:GLU161
|
4.4
|
17.3
|
1.0
|
HG3
|
A:GLU93
|
4.4
|
18.5
|
1.0
|
HG3
|
A:GLU161
|
4.4
|
22.2
|
1.0
|
HE2
|
A:MET70
|
4.5
|
32.8
|
1.0
|
HG2
|
A:GLU161
|
4.5
|
22.2
|
1.0
|
CE2
|
A:PHE165
|
4.5
|
17.7
|
1.0
|
HA
|
A:GLU161
|
4.5
|
15.8
|
1.0
|
HZ
|
A:PHE165
|
4.5
|
18.9
|
1.0
|
CG
|
A:GLN65
|
4.6
|
21.7
|
1.0
|
CE
|
A:MET70
|
4.7
|
27.3
|
1.0
|
CB
|
A:GLU161
|
4.7
|
14.4
|
1.0
|
N
|
A:GLU195
|
4.8
|
14.6
|
1.0
|
HG3
|
A:GLN65
|
4.9
|
26.0
|
1.0
|
CE1
|
A:HIS96
|
4.9
|
17.1
|
1.0
|
HG3
|
A:GLU195
|
4.9
|
28.6
|
1.0
|
HG2
|
A:GLU195
|
4.9
|
28.6
|
1.0
|
HE2
|
A:HIS198
|
4.9
|
15.9
|
1.0
|
HB3
|
A:MET89
|
4.9
|
15.0
|
1.0
|
CZ
|
A:PHE165
|
4.9
|
15.8
|
1.0
|
O
|
A:GLU195
|
5.0
|
13.7
|
1.0
|
HE1
|
A:MET70
|
5.0
|
32.8
|
1.0
|
CA
|
A:HIS198
|
5.0
|
14.5
|
1.0
|
OD1
|
A:ASP62
|
5.0
|
19.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 6qo7
Go back to
Iron Binding Sites List in 6qo7
Iron binding site 2 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:17.8
occ:1.00
|
OD1
|
A:ASP62
|
2.0
|
19.7
|
1.0
|
ND1
|
A:HIS96
|
2.0
|
14.1
|
1.0
|
OE1
|
A:GLU195
|
2.0
|
20.6
|
1.0
|
OE2
|
A:GLU93
|
2.2
|
19.9
|
1.0
|
CD
|
A:GLU195
|
2.7
|
25.4
|
1.0
|
CG
|
A:ASP62
|
2.8
|
14.4
|
1.0
|
OE2
|
A:GLU195
|
2.8
|
18.6
|
1.0
|
CE1
|
A:HIS96
|
2.9
|
17.1
|
1.0
|
HE1
|
A:HIS96
|
3.0
|
20.5
|
1.0
|
OD2
|
A:ASP62
|
3.0
|
20.6
|
1.0
|
HA
|
A:GLU93
|
3.0
|
17.2
|
1.0
|
CD
|
A:GLU93
|
3.1
|
22.9
|
1.0
|
CG
|
A:HIS96
|
3.2
|
13.3
|
1.0
|
HB2
|
A:HIS96
|
3.3
|
18.5
|
1.0
|
HZ
|
A:PHE165
|
3.5
|
18.9
|
1.0
|
HG23
|
A:ILE191
|
3.6
|
17.1
|
1.0
|
CB
|
A:HIS96
|
3.6
|
15.4
|
1.0
|
HB3
|
A:HIS96
|
3.6
|
18.5
|
1.0
|
OE1
|
A:GLU93
|
3.7
|
21.6
|
1.0
|
FE
|
A:FE2401
|
3.9
|
15.3
|
1.0
|
CA
|
A:GLU93
|
3.9
|
14.3
|
1.0
|
O
|
A:HOH501
|
3.9
|
39.0
|
1.0
|
CZ
|
A:PHE165
|
4.0
|
15.8
|
1.0
|
HB3
|
A:GLU93
|
4.0
|
16.2
|
1.0
|
NE2
|
A:HIS96
|
4.0
|
13.8
|
1.0
|
CG
|
A:GLU195
|
4.1
|
23.9
|
1.0
|
CD2
|
A:HIS96
|
4.2
|
13.5
|
1.0
|
CB
|
A:ASP62
|
4.2
|
15.7
|
1.0
|
CG
|
A:GLU93
|
4.2
|
15.4
|
1.0
|
CB
|
A:GLU93
|
4.2
|
13.5
|
1.0
|
HA
|
A:ASP62
|
4.3
|
16.0
|
1.0
|
CG2
|
A:ILE191
|
4.3
|
14.2
|
1.0
|
HG2
|
A:GLU195
|
4.3
|
28.6
|
1.0
|
HE2
|
A:PHE165
|
4.3
|
21.3
|
1.0
|
HE1
|
A:HIS198
|
4.4
|
16.3
|
1.0
|
HG3
|
A:GLU195
|
4.4
|
28.6
|
1.0
|
CE2
|
A:PHE165
|
4.4
|
17.7
|
1.0
|
HG21
|
A:ILE191
|
4.4
|
17.1
|
1.0
|
HB3
|
A:ASP62
|
4.4
|
18.9
|
1.0
|
HG22
|
A:ILE191
|
4.5
|
17.1
|
1.0
|
O
|
A:GLU93
|
4.6
|
13.2
|
1.0
|
CE1
|
A:PHE165
|
4.7
|
13.6
|
1.0
|
HG2
|
A:GLU93
|
4.8
|
18.5
|
1.0
|
N
|
A:GLU93
|
4.8
|
12.9
|
1.0
|
HH
|
A:TYR100
|
4.8
|
40.0
|
1.0
|
HE1
|
A:PHE165
|
4.8
|
16.3
|
1.0
|
HE2
|
A:HIS96
|
4.8
|
16.6
|
1.0
|
C
|
A:GLU93
|
4.8
|
13.4
|
1.0
|
CA
|
A:ASP62
|
4.8
|
13.3
|
1.0
|
HG3
|
A:GLU93
|
4.8
|
18.5
|
1.0
|
HB2
|
A:ASP62
|
4.8
|
18.9
|
1.0
|
O
|
A:MET92
|
4.8
|
12.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qo7
Go back to
Iron Binding Sites List in 6qo7
Iron binding site 3 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.1
occ:1.00
|
OD1
|
B:ASP62
|
2.0
|
21.7
|
1.0
|
OE2
|
B:GLU195
|
2.1
|
20.9
|
1.0
|
ND1
|
B:HIS96
|
2.1
|
12.6
|
1.0
|
OE2
|
B:GLU93
|
2.2
|
18.9
|
1.0
|
CD
|
B:GLU195
|
2.7
|
22.2
|
1.0
|
CG
|
B:ASP62
|
2.8
|
20.2
|
1.0
|
OE1
|
B:GLU195
|
2.8
|
18.3
|
1.0
|
CE1
|
B:HIS96
|
2.9
|
13.5
|
1.0
|
OD2
|
B:ASP62
|
3.0
|
22.2
|
1.0
|
HA
|
B:GLU93
|
3.0
|
14.3
|
1.0
|
HE1
|
B:HIS96
|
3.0
|
16.2
|
1.0
|
CD
|
B:GLU93
|
3.1
|
17.1
|
1.0
|
CG
|
B:HIS96
|
3.2
|
13.4
|
1.0
|
HB2
|
B:HIS96
|
3.3
|
19.1
|
1.0
|
HG23
|
B:ILE191
|
3.5
|
15.5
|
1.0
|
CB
|
B:HIS96
|
3.6
|
15.9
|
1.0
|
HZ
|
B:PHE165
|
3.6
|
22.4
|
1.0
|
HB3
|
B:HIS96
|
3.6
|
19.1
|
1.0
|
OE1
|
B:GLU93
|
3.7
|
21.5
|
1.0
|
CA
|
B:GLU93
|
3.9
|
11.9
|
1.0
|
FE
|
B:FE2402
|
3.9
|
14.5
|
1.0
|
O
|
B:HOH502
|
3.9
|
29.9
|
1.0
|
HB3
|
B:GLU93
|
4.0
|
16.0
|
1.0
|
CZ
|
B:PHE165
|
4.0
|
18.7
|
1.0
|
NE2
|
B:HIS96
|
4.1
|
12.8
|
1.0
|
CG
|
B:GLU195
|
4.2
|
18.9
|
1.0
|
CB
|
B:ASP62
|
4.2
|
14.5
|
1.0
|
CG
|
B:GLU93
|
4.2
|
13.2
|
1.0
|
CB
|
B:GLU93
|
4.2
|
13.3
|
1.0
|
CD2
|
B:HIS96
|
4.2
|
12.6
|
1.0
|
HA
|
B:ASP62
|
4.3
|
17.5
|
1.0
|
HE2
|
B:PHE165
|
4.3
|
23.2
|
1.0
|
HE1
|
B:HIS198
|
4.3
|
14.1
|
1.0
|
CG2
|
B:ILE191
|
4.3
|
12.9
|
1.0
|
HG2
|
B:GLU195
|
4.4
|
22.7
|
1.0
|
HB3
|
B:ASP62
|
4.4
|
17.4
|
1.0
|
CE2
|
B:PHE165
|
4.4
|
19.3
|
1.0
|
HG3
|
B:GLU195
|
4.4
|
22.7
|
1.0
|
HG21
|
B:ILE191
|
4.5
|
15.5
|
1.0
|
HG22
|
B:ILE191
|
4.5
|
15.5
|
1.0
|
O
|
B:GLU93
|
4.6
|
13.4
|
1.0
|
N
|
B:GLU93
|
4.7
|
11.7
|
1.0
|
HG2
|
B:GLU93
|
4.8
|
15.9
|
1.0
|
C
|
B:GLU93
|
4.8
|
15.9
|
1.0
|
HB2
|
B:ASP62
|
4.8
|
17.4
|
1.0
|
HG3
|
B:GLU93
|
4.8
|
15.9
|
1.0
|
CE1
|
B:PHE165
|
4.8
|
15.2
|
1.0
|
O
|
B:MET92
|
4.8
|
12.0
|
1.0
|
CA
|
B:ASP62
|
4.8
|
14.6
|
1.0
|
HE2
|
B:HIS96
|
4.8
|
15.4
|
1.0
|
HE1
|
B:PHE165
|
4.9
|
18.2
|
1.0
|
CE1
|
B:HIS198
|
4.9
|
11.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qo7
Go back to
Iron Binding Sites List in 6qo7
Iron binding site 4 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)
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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:14.5
occ:1.00
|
OE2
|
B:GLU161
|
2.0
|
22.3
|
1.0
|
OE1
|
B:GLU93
|
2.1
|
21.5
|
1.0
|
ND1
|
B:HIS198
|
2.1
|
12.6
|
1.0
|
OE1
|
B:GLU195
|
2.1
|
18.3
|
1.0
|
OE1
|
B:GLU161
|
2.4
|
20.6
|
1.0
|
CD
|
B:GLU161
|
2.5
|
19.9
|
1.0
|
CD
|
B:GLU93
|
2.8
|
17.1
|
1.0
|
OE2
|
B:GLU93
|
2.9
|
18.9
|
1.0
|
CE1
|
B:HIS198
|
3.1
|
11.8
|
1.0
|
HA
|
B:GLU195
|
3.2
|
19.1
|
1.0
|
CG
|
B:HIS198
|
3.2
|
13.8
|
1.0
|
HE1
|
B:HIS198
|
3.2
|
14.1
|
1.0
|
HB2
|
B:HIS198
|
3.2
|
14.0
|
1.0
|
CD
|
B:GLU195
|
3.3
|
22.2
|
1.0
|
HB3
|
B:HIS198
|
3.4
|
14.0
|
1.0
|
CB
|
B:HIS198
|
3.5
|
11.7
|
1.0
|
HE2
|
B:PHE165
|
3.6
|
23.2
|
1.0
|
HG2
|
B:GLN65
|
3.7
|
34.5
|
1.0
|
FE
|
B:FE2401
|
3.9
|
16.1
|
1.0
|
OE2
|
B:GLU195
|
4.0
|
20.9
|
1.0
|
CG
|
B:GLU161
|
4.0
|
17.4
|
1.0
|
HB3
|
B:GLU195
|
4.0
|
18.7
|
1.0
|
CA
|
B:GLU195
|
4.0
|
15.9
|
1.0
|
CG
|
B:GLU93
|
4.2
|
13.2
|
1.0
|
NE2
|
B:HIS198
|
4.2
|
12.1
|
1.0
|
HE1
|
B:HIS96
|
4.2
|
16.2
|
1.0
|
CD2
|
B:HIS198
|
4.3
|
12.6
|
1.0
|
HE21
|
B:GLN65
|
4.3
|
29.3
|
1.0
|
HE3
|
B:MET70
|
4.3
|
40.1
|
1.0
|
HE2
|
B:MET70
|
4.3
|
40.1
|
1.0
|
HB3
|
B:GLU161
|
4.3
|
16.0
|
1.0
|
CB
|
B:GLU195
|
4.3
|
15.6
|
1.0
|
CG
|
B:GLU195
|
4.3
|
18.9
|
1.0
|
CE2
|
B:PHE165
|
4.4
|
19.3
|
1.0
|
HG2
|
B:GLU93
|
4.4
|
15.9
|
1.0
|
HG3
|
B:GLU161
|
4.4
|
20.9
|
1.0
|
HG3
|
B:GLU93
|
4.4
|
15.9
|
1.0
|
HG2
|
B:GLU161
|
4.5
|
20.9
|
1.0
|
HA
|
B:GLU161
|
4.5
|
18.2
|
1.0
|
HZ
|
B:PHE165
|
4.5
|
22.4
|
1.0
|
CG
|
B:GLN65
|
4.6
|
28.8
|
1.0
|
CB
|
B:GLU161
|
4.6
|
13.3
|
1.0
|
CE
|
B:MET70
|
4.7
|
33.4
|
1.0
|
N
|
B:GLU195
|
4.8
|
13.1
|
1.0
|
HG3
|
B:GLN65
|
4.9
|
34.5
|
1.0
|
CZ
|
B:PHE165
|
4.9
|
18.7
|
1.0
|
HG3
|
B:GLU195
|
4.9
|
22.7
|
1.0
|
OD1
|
B:ASP62
|
4.9
|
21.7
|
1.0
|
CE1
|
B:HIS96
|
4.9
|
13.5
|
1.0
|
HG2
|
B:GLU195
|
4.9
|
22.7
|
1.0
|
O
|
B:GLU195
|
4.9
|
12.8
|
1.0
|
HE2
|
B:HIS198
|
5.0
|
14.6
|
1.0
|
HB3
|
B:MET89
|
5.0
|
14.7
|
1.0
|
HE1
|
B:MET70
|
5.0
|
40.1
|
1.0
|
O
|
B:ASP194
|
5.0
|
14.6
|
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 08:09:10 2024
|