Iron in PDB 6qob: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor:
1.17.4.1;
Protein crystallography data
The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor, PDB code: 6qob
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)
|
45.94 /
1.46
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.137,
60.377,
95.758,
90.00,
106.38,
90.00
|
R / Rfree (%)
|
17 /
19.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
(pdb code 6qob). 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 with Partially Oxidised Di-Iron Metallocofactor, PDB code: 6qob:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6qob
Go back to
Iron Binding Sites List in 6qob
Iron binding site 1 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:15.9
occ:0.80
|
O
|
A:HOH501
|
1.8
|
18.9
|
1.0
|
OE2
|
A:GLU161
|
1.9
|
12.9
|
0.5
|
OE1
|
A:GLU93
|
1.9
|
22.9
|
1.0
|
OE2
|
A:GLU195
|
2.1
|
34.6
|
1.0
|
OE2
|
A:GLU161
|
2.1
|
16.1
|
0.5
|
ND1
|
A:HIS198
|
2.2
|
15.3
|
1.0
|
O
|
A:HOH511
|
2.3
|
22.3
|
1.0
|
OE1
|
A:GLU161
|
2.7
|
23.6
|
0.5
|
CD
|
A:GLU161
|
2.7
|
19.3
|
0.5
|
CD
|
A:GLU93
|
2.7
|
21.0
|
1.0
|
OE2
|
A:GLU93
|
2.9
|
28.5
|
1.0
|
CD
|
A:GLU161
|
3.0
|
20.7
|
0.5
|
CE1
|
A:HIS198
|
3.1
|
19.1
|
1.0
|
CD
|
A:GLU195
|
3.1
|
28.4
|
0.2
|
HG2
|
A:GLU161
|
3.2
|
16.6
|
0.5
|
HE1
|
A:HIS198
|
3.2
|
23.0
|
1.0
|
FE
|
A:FE403
|
3.3
|
16.6
|
0.7
|
HA
|
A:GLU195
|
3.3
|
18.4
|
1.0
|
CG
|
A:HIS198
|
3.3
|
11.8
|
1.0
|
HB2
|
A:HIS198
|
3.5
|
16.2
|
1.0
|
OE1
|
A:GLU195
|
3.5
|
19.9
|
0.4
|
CG
|
A:GLU161
|
3.6
|
13.8
|
0.5
|
HG2
|
A:GLN65
|
3.6
|
20.4
|
1.0
|
HB3
|
A:HIS198
|
3.6
|
16.2
|
1.0
|
CB
|
A:HIS198
|
3.7
|
13.5
|
1.0
|
O
|
A:HOH505
|
3.8
|
33.1
|
1.0
|
HB3
|
A:GLU161
|
3.9
|
17.2
|
0.5
|
OE1
|
A:GLU161
|
4.0
|
20.7
|
0.5
|
HE1
|
A:HIS96
|
4.0
|
18.7
|
1.0
|
HE2
|
A:PHE165
|
4.1
|
20.1
|
0.4
|
O
|
A:HOH559
|
4.1
|
20.7
|
0.8
|
CG
|
A:GLU93
|
4.1
|
15.0
|
1.0
|
CG
|
A:GLU161
|
4.2
|
17.3
|
0.5
|
CA
|
A:GLU195
|
4.3
|
15.3
|
1.0
|
NE2
|
A:HIS198
|
4.3
|
14.3
|
1.0
|
OD1
|
A:ASP62
|
4.3
|
16.9
|
0.4
|
CB
|
A:GLU161
|
4.3
|
14.3
|
0.5
|
HG3
|
A:GLU161
|
4.4
|
16.6
|
0.5
|
HG3
|
A:GLU93
|
4.4
|
18.0
|
1.0
|
CG
|
A:GLU195
|
4.4
|
24.5
|
0.7
|
CD2
|
A:HIS198
|
4.4
|
13.6
|
1.0
|
HB3
|
A:GLU161
|
4.4
|
20.2
|
0.5
|
HG2
|
A:GLU93
|
4.4
|
18.0
|
1.0
|
HE21
|
A:GLN65
|
4.5
|
26.9
|
1.0
|
HA
|
A:GLU161
|
4.5
|
15.4
|
0.5
|
CG
|
A:GLN65
|
4.5
|
17.0
|
1.0
|
HB2
|
A:GLU195
|
4.6
|
23.3
|
1.0
|
HG2
|
A:GLU161
|
4.6
|
20.8
|
0.5
|
CE1
|
A:HIS96
|
4.6
|
15.6
|
1.0
|
HG3
|
A:GLU161
|
4.6
|
20.8
|
0.5
|
HG3
|
A:GLN65
|
4.7
|
20.4
|
1.0
|
OD1
|
A:ASP62
|
4.7
|
15.5
|
0.6
|
CB
|
A:GLU195
|
4.7
|
19.4
|
1.0
|
HG3
|
A:GLU195
|
4.7
|
29.4
|
0.6
|
ND1
|
A:HIS96
|
4.7
|
13.5
|
1.0
|
CE2
|
A:PHE165
|
4.7
|
16.8
|
0.3
|
HZ
|
A:PHE165
|
4.8
|
29.4
|
1.0
|
CB
|
A:GLU161
|
4.8
|
16.9
|
0.5
|
HA
|
A:GLU161
|
4.8
|
16.7
|
0.5
|
HE3
|
A:MET89
|
4.8
|
24.1
|
1.0
|
N
|
A:GLU195
|
4.9
|
14.5
|
1.0
|
OD2
|
A:ASP62
|
5.0
|
13.0
|
0.4
|
|
Iron binding site 2 out
of 4 in 6qob
Go back to
Iron Binding Sites List in 6qob
Iron binding site 2 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:16.6
occ:0.72
|
O
|
A:HOH559
|
1.9
|
20.7
|
0.8
|
OD2
|
A:ASP62
|
2.0
|
13.0
|
0.4
|
OE2
|
A:GLU93
|
2.0
|
28.5
|
1.0
|
ND1
|
A:HIS96
|
2.1
|
13.5
|
1.0
|
OD1
|
A:ASP62
|
2.1
|
15.5
|
0.6
|
O
|
A:HOH501
|
2.2
|
18.9
|
1.0
|
CG
|
A:ASP62
|
2.7
|
17.1
|
0.4
|
OD1
|
A:ASP62
|
2.8
|
16.9
|
0.4
|
CE1
|
A:HIS96
|
2.9
|
15.6
|
1.0
|
HE1
|
A:HIS96
|
3.0
|
18.7
|
1.0
|
O
|
A:HOH511
|
3.0
|
22.3
|
1.0
|
CG
|
A:ASP62
|
3.2
|
16.7
|
0.6
|
CD
|
A:GLU93
|
3.2
|
21.0
|
1.0
|
CG
|
A:HIS96
|
3.3
|
10.7
|
1.0
|
FE
|
A:FE402
|
3.3
|
15.9
|
0.8
|
HA
|
A:GLU93
|
3.3
|
13.1
|
1.0
|
OD2
|
A:ASP62
|
3.5
|
20.1
|
0.6
|
HB2
|
A:HIS96
|
3.5
|
13.4
|
1.0
|
HG23
|
A:ILE191
|
3.6
|
17.7
|
1.0
|
HB3
|
A:HIS96
|
3.7
|
13.4
|
1.0
|
OE1
|
A:GLU195
|
3.7
|
19.9
|
0.4
|
CB
|
A:HIS96
|
3.7
|
11.2
|
1.0
|
OE1
|
A:GLU93
|
3.7
|
22.9
|
1.0
|
HZ
|
A:PHE165
|
3.7
|
29.4
|
1.0
|
OE2
|
A:GLU195
|
3.9
|
34.6
|
1.0
|
CD
|
A:GLU195
|
4.0
|
28.4
|
0.2
|
CB
|
A:ASP62
|
4.1
|
15.8
|
0.4
|
CZ
|
A:PHE165
|
4.1
|
24.5
|
1.0
|
NE2
|
A:HIS96
|
4.1
|
13.5
|
1.0
|
HE1
|
A:HIS198
|
4.1
|
23.0
|
1.0
|
CA
|
A:GLU93
|
4.2
|
10.9
|
1.0
|
HB3
|
A:GLU93
|
4.2
|
15.3
|
1.0
|
HB3
|
A:ASP62
|
4.3
|
18.9
|
0.4
|
CD2
|
A:HIS96
|
4.3
|
15.0
|
1.0
|
CG
|
A:GLU93
|
4.4
|
15.0
|
1.0
|
CG2
|
A:ILE191
|
4.4
|
14.8
|
1.0
|
HB2
|
A:ASP62
|
4.5
|
18.9
|
0.4
|
HA
|
A:ASP62
|
4.5
|
15.5
|
0.6
|
CB
|
A:GLU93
|
4.5
|
12.8
|
1.0
|
HB2
|
A:GLU195
|
4.5
|
23.3
|
1.0
|
CB
|
A:ASP62
|
4.5
|
14.3
|
0.6
|
HG21
|
A:ILE191
|
4.5
|
17.7
|
1.0
|
HE2
|
A:PHE165
|
4.5
|
20.1
|
0.4
|
HG22
|
A:ILE191
|
4.6
|
17.7
|
1.0
|
CE2
|
A:PHE165
|
4.6
|
16.8
|
0.3
|
CE1
|
A:HIS198
|
4.7
|
19.1
|
1.0
|
ND1
|
A:HIS198
|
4.7
|
15.3
|
1.0
|
HB3
|
A:ASP62
|
4.7
|
17.1
|
0.6
|
CE1
|
A:PHE165
|
4.7
|
20.2
|
1.0
|
HA
|
A:ASP62
|
4.8
|
15.5
|
0.4
|
HE1
|
A:PHE165
|
4.8
|
24.3
|
1.0
|
HA
|
A:GLU195
|
4.9
|
18.4
|
1.0
|
HE2
|
A:HIS96
|
4.9
|
16.2
|
1.0
|
OE2
|
A:GLU161
|
4.9
|
16.1
|
0.5
|
HG2
|
A:GLU93
|
4.9
|
18.0
|
1.0
|
HG3
|
A:GLU93
|
5.0
|
18.0
|
1.0
|
O
|
A:GLU93
|
5.0
|
11.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 6qob
Go back to
Iron Binding Sites List in 6qob
Iron binding site 3 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe405
b:15.8
occ:0.77
|
O
|
B:HOH541
|
1.8
|
21.5
|
0.9
|
OE2
|
B:GLU93
|
2.1
|
25.8
|
1.0
|
OD1
|
B:ASP62
|
2.1
|
13.0
|
0.7
|
OD2
|
B:ASP62
|
2.1
|
16.6
|
0.3
|
ND1
|
B:HIS96
|
2.2
|
11.8
|
1.0
|
O
|
B:HOH501
|
2.3
|
18.8
|
1.0
|
CG
|
B:ASP62
|
2.7
|
16.3
|
0.3
|
OD1
|
B:ASP62
|
2.7
|
11.5
|
0.3
|
CE1
|
B:HIS96
|
3.0
|
12.9
|
1.0
|
HE1
|
B:HIS96
|
3.0
|
15.5
|
1.0
|
O
|
B:HOH525
|
3.1
|
23.3
|
1.0
|
CG
|
B:ASP62
|
3.2
|
19.5
|
0.7
|
CD
|
B:GLU93
|
3.2
|
16.8
|
1.0
|
CG
|
B:HIS96
|
3.3
|
10.2
|
1.0
|
HA
|
B:GLU93
|
3.3
|
12.5
|
1.0
|
FE
|
B:FE406
|
3.3
|
14.3
|
0.8
|
HB2
|
B:HIS96
|
3.5
|
12.5
|
1.0
|
HZ
|
B:PHE165
|
3.5
|
28.9
|
1.0
|
HG23
|
B:ILE191
|
3.6
|
15.1
|
1.0
|
OD2
|
B:ASP62
|
3.6
|
19.5
|
0.7
|
HB3
|
B:HIS96
|
3.7
|
12.5
|
1.0
|
CB
|
B:HIS96
|
3.7
|
10.4
|
1.0
|
OE1
|
B:GLU195
|
3.8
|
14.3
|
0.4
|
OE1
|
B:GLU93
|
3.8
|
21.5
|
1.0
|
OE2
|
B:GLU195
|
3.9
|
28.9
|
1.0
|
CZ
|
B:PHE165
|
4.0
|
24.1
|
1.0
|
CD
|
B:GLU195
|
4.1
|
14.5
|
0.3
|
CB
|
B:ASP62
|
4.1
|
13.4
|
0.3
|
HE2
|
B:PHE165
|
4.1
|
44.9
|
1.0
|
NE2
|
B:HIS96
|
4.2
|
12.7
|
1.0
|
HB3
|
B:GLU93
|
4.2
|
13.4
|
1.0
|
HE1
|
B:HIS198
|
4.2
|
15.7
|
1.0
|
CA
|
B:GLU93
|
4.2
|
10.4
|
1.0
|
HB3
|
B:ASP62
|
4.3
|
16.0
|
0.3
|
CE2
|
B:PHE165
|
4.3
|
37.4
|
1.0
|
CG2
|
B:ILE191
|
4.3
|
12.5
|
1.0
|
CD2
|
B:HIS96
|
4.3
|
13.3
|
1.0
|
CG
|
B:GLU93
|
4.4
|
13.7
|
1.0
|
CB
|
B:GLU93
|
4.4
|
11.1
|
1.0
|
HG22
|
B:ILE191
|
4.4
|
15.1
|
1.0
|
HA
|
B:ASP62
|
4.5
|
14.8
|
0.7
|
CB
|
B:ASP62
|
4.5
|
12.7
|
0.7
|
HB2
|
B:GLU195
|
4.5
|
19.1
|
1.0
|
HG21
|
B:ILE191
|
4.5
|
15.1
|
1.0
|
HB2
|
B:ASP62
|
4.5
|
16.0
|
0.3
|
HB3
|
B:ASP62
|
4.6
|
15.2
|
0.7
|
ND1
|
B:HIS198
|
4.7
|
15.3
|
1.0
|
CE1
|
B:HIS198
|
4.7
|
13.1
|
1.0
|
HA
|
B:ASP62
|
4.7
|
14.9
|
0.3
|
CE1
|
B:PHE165
|
4.8
|
20.0
|
1.0
|
O
|
B:GLU93
|
4.9
|
10.5
|
1.0
|
HE2
|
B:HIS96
|
4.9
|
15.3
|
1.0
|
HG2
|
B:GLU93
|
4.9
|
16.5
|
1.0
|
OE1
|
B:GLU161
|
4.9
|
14.4
|
0.5
|
HG3
|
B:GLU93
|
5.0
|
16.5
|
1.0
|
HA
|
B:GLU195
|
5.0
|
17.6
|
1.0
|
HE1
|
B:PHE165
|
5.0
|
24.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 6qob
Go back to
Iron Binding Sites List in 6qob
Iron binding site 4 out
of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor
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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe406
b:14.3
occ:0.83
|
OE1
|
B:GLU93
|
1.9
|
21.5
|
1.0
|
OE1
|
B:GLU161
|
1.9
|
14.1
|
0.6
|
O
|
B:HOH501
|
1.9
|
18.8
|
1.0
|
OE1
|
B:GLU161
|
2.0
|
14.4
|
0.5
|
OE2
|
B:GLU195
|
2.1
|
28.9
|
1.0
|
O
|
B:HOH525
|
2.2
|
23.3
|
1.0
|
ND1
|
B:HIS198
|
2.3
|
15.3
|
1.0
|
CD
|
B:GLU93
|
2.6
|
16.8
|
1.0
|
OE2
|
B:GLU93
|
2.8
|
25.8
|
1.0
|
CD
|
B:GLU161
|
2.8
|
22.3
|
0.5
|
OE2
|
B:GLU161
|
2.9
|
25.9
|
0.5
|
CD
|
B:GLU161
|
3.0
|
24.8
|
0.6
|
CD
|
B:GLU195
|
3.1
|
14.5
|
0.3
|
CE1
|
B:HIS198
|
3.1
|
13.1
|
1.0
|
HG2
|
B:GLU161
|
3.2
|
14.8
|
0.6
|
HE1
|
B:HIS198
|
3.2
|
15.7
|
1.0
|
FE
|
B:FE405
|
3.3
|
15.8
|
0.8
|
CG
|
B:HIS198
|
3.3
|
13.1
|
1.0
|
HA
|
B:GLU195
|
3.4
|
17.6
|
1.0
|
OE1
|
B:GLU195
|
3.5
|
14.3
|
0.4
|
HB2
|
B:HIS198
|
3.5
|
17.1
|
1.0
|
HB3
|
B:HIS198
|
3.6
|
17.1
|
1.0
|
CG
|
B:GLU161
|
3.6
|
12.3
|
0.6
|
HG2
|
B:GLN65
|
3.6
|
22.0
|
1.0
|
HE2
|
B:PHE165
|
3.7
|
44.9
|
1.0
|
CB
|
B:HIS198
|
3.7
|
14.2
|
1.0
|
HB3
|
B:GLU161
|
3.8
|
18.3
|
0.6
|
O
|
B:HOH541
|
4.0
|
21.5
|
0.9
|
OE2
|
B:GLU161
|
4.0
|
23.0
|
0.6
|
O
|
B:HOH503
|
4.0
|
29.5
|
1.0
|
CG
|
B:GLU93
|
4.1
|
13.7
|
1.0
|
HE1
|
B:HIS96
|
4.1
|
15.5
|
1.0
|
OD1
|
B:ASP62
|
4.3
|
11.5
|
0.3
|
CG
|
B:GLU161
|
4.3
|
13.9
|
0.5
|
CB
|
B:GLU161
|
4.3
|
15.3
|
0.6
|
NE2
|
B:HIS198
|
4.3
|
11.9
|
1.0
|
CA
|
B:GLU195
|
4.3
|
14.6
|
1.0
|
HG3
|
B:GLU93
|
4.3
|
16.5
|
1.0
|
HG2
|
B:GLU93
|
4.4
|
16.5
|
1.0
|
CG
|
B:GLU195
|
4.4
|
16.8
|
0.6
|
HB3
|
B:GLU161
|
4.4
|
15.7
|
0.5
|
HG3
|
B:GLU161
|
4.4
|
14.8
|
0.6
|
CD2
|
B:HIS198
|
4.4
|
12.6
|
1.0
|
HE21
|
B:GLN65
|
4.5
|
30.0
|
1.0
|
CE2
|
B:PHE165
|
4.5
|
37.4
|
1.0
|
HA
|
B:GLU161
|
4.5
|
17.1
|
0.5
|
HZ
|
B:PHE165
|
4.5
|
28.9
|
1.0
|
CG
|
B:GLN65
|
4.5
|
18.3
|
1.0
|
HB2
|
B:GLU195
|
4.6
|
19.1
|
1.0
|
HG3
|
B:GLU195
|
4.7
|
20.2
|
0.6
|
CB
|
B:GLU195
|
4.7
|
15.9
|
1.0
|
HG3
|
B:GLN65
|
4.7
|
22.0
|
1.0
|
CE1
|
B:HIS96
|
4.7
|
12.9
|
1.0
|
OD1
|
B:ASP62
|
4.7
|
13.0
|
0.7
|
HG2
|
B:GLU161
|
4.7
|
16.6
|
0.5
|
HG3
|
B:GLU161
|
4.8
|
16.6
|
0.5
|
ND1
|
B:HIS96
|
4.8
|
11.8
|
1.0
|
HA
|
B:GLU161
|
4.8
|
17.3
|
0.6
|
HE3
|
B:MET89
|
4.8
|
22.5
|
1.0
|
CB
|
B:GLU161
|
4.8
|
13.1
|
0.5
|
CZ
|
B:PHE165
|
4.9
|
24.1
|
1.0
|
N
|
B:GLU195
|
5.0
|
12.7
|
1.0
|
HB2
|
B:GLU161
|
5.0
|
18.3
|
0.6
|
|
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 08:11:31 2024
|