Iron in PDB 3oa8: Diheme Soxax
Protein crystallography data
The structure of Diheme Soxax, PDB code: 3oa8
was solved by
M.J.Maher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
35.31 /
1.77
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.172,
74.629,
74.295,
110.02,
108.08,
108.54
|
|
R / Rfree (%)
|
18.3 /
23
|
Iron Binding Sites:
The binding sites of Iron atom in the Diheme Soxax
(pdb code 3oa8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Diheme Soxax, PDB code: 3oa8:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 1 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:17.2
occ:1.00
|
FE
|
A:HEC401
|
0.0
|
17.2
|
1.0
|
|
NC
|
A:HEC401
|
2.0
|
15.4
|
1.0
|
|
NA
|
A:HEC401
|
2.0
|
14.4
|
1.0
|
|
NB
|
A:HEC401
|
2.0
|
15.9
|
1.0
|
|
ND
|
A:HEC401
|
2.0
|
16.8
|
1.0
|
|
NE2
|
A:HIS187
|
2.1
|
15.5
|
1.0
|
|
SD
|
A:CSS236
|
2.2
|
18.0
|
0.5
|
|
SG
|
A:CSS236
|
2.7
|
20.0
|
0.5
|
|
C1C
|
A:HEC401
|
3.0
|
16.4
|
1.0
|
|
C4B
|
A:HEC401
|
3.0
|
15.6
|
1.0
|
|
C4C
|
A:HEC401
|
3.0
|
16.8
|
1.0
|
|
C4D
|
A:HEC401
|
3.0
|
21.5
|
1.0
|
|
C1A
|
A:HEC401
|
3.0
|
18.1
|
1.0
|
|
C1B
|
A:HEC401
|
3.0
|
17.1
|
1.0
|
|
C4A
|
A:HEC401
|
3.1
|
15.5
|
1.0
|
|
C1D
|
A:HEC401
|
3.1
|
19.1
|
1.0
|
|
CE1
|
A:HIS187
|
3.1
|
16.5
|
1.0
|
|
CD2
|
A:HIS187
|
3.1
|
15.3
|
1.0
|
|
SG
|
A:CSS236
|
3.3
|
17.6
|
0.5
|
|
CHC
|
A:HEC401
|
3.3
|
16.5
|
1.0
|
|
CHA
|
A:HEC401
|
3.4
|
19.9
|
1.0
|
|
CHD
|
A:HEC401
|
3.4
|
20.3
|
1.0
|
|
CHB
|
A:HEC401
|
3.4
|
18.9
|
1.0
|
|
CB
|
A:CSS236
|
3.8
|
20.0
|
0.5
|
|
ND1
|
A:HIS187
|
4.2
|
13.8
|
1.0
|
|
C3C
|
A:HEC401
|
4.2
|
18.6
|
1.0
|
|
C2C
|
A:HEC401
|
4.2
|
16.0
|
1.0
|
|
C3B
|
A:HEC401
|
4.2
|
16.7
|
1.0
|
|
C2B
|
A:HEC401
|
4.2
|
18.1
|
1.0
|
|
CG
|
A:HIS187
|
4.3
|
16.7
|
1.0
|
|
C2A
|
A:HEC401
|
4.3
|
16.9
|
1.0
|
|
C3D
|
A:HEC401
|
4.3
|
21.8
|
1.0
|
|
C3A
|
A:HEC401
|
4.3
|
17.8
|
1.0
|
|
C2D
|
A:HEC401
|
4.3
|
22.7
|
1.0
|
|
CB
|
A:CSS236
|
4.5
|
19.2
|
0.5
|
|
OE1
|
A:GLN239
|
5.0
|
39.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 2 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.8
occ:1.00
|
FE
|
B:HEC401
|
0.0
|
16.8
|
1.0
|
|
NB
|
B:HEC401
|
2.0
|
17.8
|
1.0
|
|
NA
|
B:HEC401
|
2.0
|
15.0
|
1.0
|
|
NC
|
B:HEC401
|
2.0
|
15.3
|
1.0
|
|
NE2
|
B:HIS129
|
2.1
|
16.7
|
1.0
|
|
ND
|
B:HEC401
|
2.1
|
16.2
|
1.0
|
|
SD
|
B:MET178
|
2.4
|
15.5
|
1.0
|
|
C1B
|
B:HEC401
|
3.0
|
15.1
|
1.0
|
|
C4B
|
B:HEC401
|
3.0
|
14.7
|
1.0
|
|
C1D
|
B:HEC401
|
3.1
|
15.3
|
1.0
|
|
C1A
|
B:HEC401
|
3.1
|
13.7
|
1.0
|
|
CD2
|
B:HIS129
|
3.1
|
16.6
|
1.0
|
|
C1C
|
B:HEC401
|
3.1
|
13.4
|
1.0
|
|
C4C
|
B:HEC401
|
3.1
|
13.8
|
1.0
|
|
CE1
|
B:HIS129
|
3.1
|
16.2
|
1.0
|
|
C4A
|
B:HEC401
|
3.1
|
17.1
|
1.0
|
|
C4D
|
B:HEC401
|
3.1
|
15.8
|
1.0
|
|
CE
|
B:MET178
|
3.3
|
16.0
|
1.0
|
|
CHD
|
B:HEC401
|
3.4
|
13.1
|
1.0
|
|
CHB
|
B:HEC401
|
3.4
|
14.4
|
1.0
|
|
CHA
|
B:HEC401
|
3.4
|
13.2
|
1.0
|
|
CHC
|
B:HEC401
|
3.4
|
14.8
|
1.0
|
|
CG
|
B:MET178
|
3.4
|
14.8
|
1.0
|
|
CB
|
B:MET178
|
4.0
|
13.6
|
1.0
|
|
ND1
|
B:HIS129
|
4.2
|
16.9
|
1.0
|
|
CG
|
B:HIS129
|
4.2
|
16.5
|
1.0
|
|
C2B
|
B:HEC401
|
4.2
|
14.8
|
1.0
|
|
C3B
|
B:HEC401
|
4.3
|
16.4
|
1.0
|
|
C2C
|
B:HEC401
|
4.3
|
13.1
|
1.0
|
|
C3C
|
B:HEC401
|
4.3
|
12.6
|
1.0
|
|
C3A
|
B:HEC401
|
4.3
|
15.9
|
1.0
|
|
C2A
|
B:HEC401
|
4.3
|
15.9
|
1.0
|
|
C2D
|
B:HEC401
|
4.3
|
14.3
|
1.0
|
|
C3D
|
B:HEC401
|
4.3
|
15.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 3 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:18.8
occ:1.00
|
FE
|
C:HEC401
|
0.0
|
18.8
|
1.0
|
|
NA
|
C:HEC401
|
2.0
|
16.3
|
1.0
|
|
NC
|
C:HEC401
|
2.0
|
20.7
|
1.0
|
|
NB
|
C:HEC401
|
2.0
|
18.7
|
1.0
|
|
ND
|
C:HEC401
|
2.1
|
20.1
|
1.0
|
|
NE2
|
C:HIS187
|
2.1
|
17.8
|
1.0
|
|
SD
|
C:CSS236
|
2.2
|
18.2
|
0.5
|
|
SG
|
C:CSS236
|
2.6
|
21.1
|
0.5
|
|
C1A
|
C:HEC401
|
3.0
|
18.7
|
1.0
|
|
C4B
|
C:HEC401
|
3.0
|
18.0
|
1.0
|
|
C1B
|
C:HEC401
|
3.0
|
18.8
|
1.0
|
|
C4A
|
C:HEC401
|
3.0
|
18.8
|
1.0
|
|
C4D
|
C:HEC401
|
3.0
|
21.9
|
1.0
|
|
C1C
|
C:HEC401
|
3.1
|
19.2
|
1.0
|
|
C4C
|
C:HEC401
|
3.1
|
20.5
|
1.0
|
|
CE1
|
C:HIS187
|
3.1
|
17.2
|
1.0
|
|
CD2
|
C:HIS187
|
3.1
|
17.1
|
1.0
|
|
C1D
|
C:HEC401
|
3.1
|
20.1
|
1.0
|
|
SG
|
C:CSS236
|
3.2
|
23.0
|
0.5
|
|
CHA
|
C:HEC401
|
3.3
|
18.9
|
1.0
|
|
CHC
|
C:HEC401
|
3.4
|
19.3
|
1.0
|
|
CHB
|
C:HEC401
|
3.4
|
19.2
|
1.0
|
|
CHD
|
C:HEC401
|
3.5
|
21.7
|
1.0
|
|
CB
|
C:CSS236
|
3.6
|
20.7
|
0.5
|
|
ND1
|
C:HIS187
|
4.2
|
15.3
|
1.0
|
|
C2A
|
C:HEC401
|
4.2
|
18.1
|
1.0
|
|
CG
|
C:HIS187
|
4.2
|
14.7
|
1.0
|
|
C2B
|
C:HEC401
|
4.2
|
19.3
|
1.0
|
|
C3A
|
C:HEC401
|
4.2
|
17.0
|
1.0
|
|
C3B
|
C:HEC401
|
4.3
|
17.9
|
1.0
|
|
C2C
|
C:HEC401
|
4.3
|
18.5
|
1.0
|
|
C3C
|
C:HEC401
|
4.3
|
20.3
|
1.0
|
|
C3D
|
C:HEC401
|
4.3
|
22.5
|
1.0
|
|
CB
|
C:CSS236
|
4.4
|
20.7
|
0.5
|
|
C2D
|
C:HEC401
|
4.4
|
23.1
|
1.0
|
|
OE1
|
C:GLN239
|
4.7
|
35.4
|
1.0
|
|
CA
|
C:CSS236
|
4.9
|
20.8
|
0.5
|
|
CA
|
C:CSS236
|
5.0
|
21.1
|
0.5
|
|
Iron binding site 4 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 4 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:16.4
occ:1.00
|
FE
|
D:HEC401
|
0.0
|
16.4
|
1.0
|
|
NB
|
D:HEC401
|
2.0
|
13.0
|
1.0
|
|
NE2
|
D:HIS129
|
2.0
|
15.6
|
1.0
|
|
NA
|
D:HEC401
|
2.0
|
15.6
|
1.0
|
|
NC
|
D:HEC401
|
2.0
|
15.2
|
1.0
|
|
ND
|
D:HEC401
|
2.1
|
15.8
|
1.0
|
|
SD
|
D:MET178
|
2.4
|
16.1
|
1.0
|
|
CE1
|
D:HIS129
|
3.0
|
14.8
|
1.0
|
|
C1B
|
D:HEC401
|
3.0
|
15.8
|
1.0
|
|
CD2
|
D:HIS129
|
3.0
|
15.6
|
1.0
|
|
C4A
|
D:HEC401
|
3.0
|
17.3
|
1.0
|
|
C4B
|
D:HEC401
|
3.0
|
15.9
|
1.0
|
|
C1C
|
D:HEC401
|
3.1
|
12.9
|
1.0
|
|
C4C
|
D:HEC401
|
3.1
|
15.4
|
1.0
|
|
C1D
|
D:HEC401
|
3.1
|
16.8
|
1.0
|
|
C1A
|
D:HEC401
|
3.1
|
15.6
|
1.0
|
|
C4D
|
D:HEC401
|
3.1
|
17.3
|
1.0
|
|
CG
|
D:MET178
|
3.3
|
13.6
|
1.0
|
|
CE
|
D:MET178
|
3.3
|
17.5
|
1.0
|
|
CHB
|
D:HEC401
|
3.3
|
17.1
|
1.0
|
|
CHD
|
D:HEC401
|
3.4
|
16.4
|
1.0
|
|
CHC
|
D:HEC401
|
3.4
|
16.7
|
1.0
|
|
CHA
|
D:HEC401
|
3.5
|
14.8
|
1.0
|
|
CB
|
D:MET178
|
4.0
|
15.1
|
1.0
|
|
ND1
|
D:HIS129
|
4.1
|
15.9
|
1.0
|
|
CG
|
D:HIS129
|
4.1
|
16.4
|
1.0
|
|
C2B
|
D:HEC401
|
4.2
|
14.5
|
1.0
|
|
C3B
|
D:HEC401
|
4.2
|
14.9
|
1.0
|
|
C3A
|
D:HEC401
|
4.3
|
15.1
|
1.0
|
|
C2C
|
D:HEC401
|
4.3
|
14.8
|
1.0
|
|
C2A
|
D:HEC401
|
4.3
|
15.6
|
1.0
|
|
C3C
|
D:HEC401
|
4.3
|
15.1
|
1.0
|
|
C2D
|
D:HEC401
|
4.3
|
16.5
|
1.0
|
|
C3D
|
D:HEC401
|
4.3
|
16.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 5 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:18.5
occ:1.00
|
FE
|
E:HEC401
|
0.0
|
18.5
|
1.0
|
|
NB
|
E:HEC401
|
2.0
|
16.3
|
1.0
|
|
NA
|
E:HEC401
|
2.0
|
15.6
|
1.0
|
|
NC
|
E:HEC401
|
2.0
|
16.8
|
1.0
|
|
ND
|
E:HEC401
|
2.1
|
18.4
|
1.0
|
|
NE2
|
E:HIS187
|
2.1
|
15.6
|
1.0
|
|
SD
|
E:CSS236
|
2.3
|
25.3
|
0.5
|
|
SG
|
E:CSS236
|
2.3
|
15.2
|
0.5
|
|
C1B
|
E:HEC401
|
3.0
|
18.1
|
1.0
|
|
C4A
|
E:HEC401
|
3.0
|
17.5
|
1.0
|
|
C4B
|
E:HEC401
|
3.0
|
17.2
|
1.0
|
|
C1A
|
E:HEC401
|
3.0
|
16.7
|
1.0
|
|
C1C
|
E:HEC401
|
3.0
|
17.1
|
1.0
|
|
CD2
|
E:HIS187
|
3.1
|
17.9
|
1.0
|
|
C4D
|
E:HEC401
|
3.1
|
21.4
|
1.0
|
|
C4C
|
E:HEC401
|
3.1
|
19.5
|
1.0
|
|
C1D
|
E:HEC401
|
3.1
|
17.7
|
1.0
|
|
CE1
|
E:HIS187
|
3.1
|
17.4
|
1.0
|
|
SG
|
E:CSS236
|
3.1
|
26.3
|
0.5
|
|
CHB
|
E:HEC401
|
3.4
|
14.9
|
1.0
|
|
CHA
|
E:HEC401
|
3.4
|
19.5
|
1.0
|
|
CHC
|
E:HEC401
|
3.4
|
17.6
|
1.0
|
|
CHD
|
E:HEC401
|
3.5
|
19.1
|
1.0
|
|
CB
|
E:CSS236
|
3.6
|
18.9
|
0.5
|
|
CB
|
E:CSS236
|
4.1
|
22.7
|
0.5
|
|
ND1
|
E:HIS187
|
4.2
|
14.1
|
1.0
|
|
CG
|
E:HIS187
|
4.2
|
16.6
|
1.0
|
|
C3B
|
E:HEC401
|
4.2
|
17.1
|
1.0
|
|
C2B
|
E:HEC401
|
4.2
|
18.1
|
1.0
|
|
C3A
|
E:HEC401
|
4.2
|
17.6
|
1.0
|
|
C2A
|
E:HEC401
|
4.3
|
15.2
|
1.0
|
|
C2C
|
E:HEC401
|
4.3
|
18.4
|
1.0
|
|
C3C
|
E:HEC401
|
4.3
|
17.5
|
1.0
|
|
C3D
|
E:HEC401
|
4.3
|
22.5
|
1.0
|
|
C2D
|
E:HEC401
|
4.3
|
20.8
|
1.0
|
|
O
|
E:HOH374
|
4.8
|
47.9
|
1.0
|
|
CA
|
E:CSS236
|
4.8
|
22.9
|
0.5
|
|
CA
|
E:CSS236
|
4.8
|
20.1
|
0.5
|
|
NH2
|
E:ARG232
|
4.8
|
22.9
|
1.0
|
|
NE
|
E:ARG232
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 3oa8
Go back to
Iron Binding Sites List in 3oa8
Iron binding site 6 out
of 6 in the Diheme Soxax
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Diheme Soxax within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:17.8
occ:1.00
|
FE
|
F:HEC401
|
0.0
|
17.8
|
1.0
|
|
NC
|
F:HEC401
|
2.0
|
15.2
|
1.0
|
|
NB
|
F:HEC401
|
2.0
|
16.7
|
1.0
|
|
NE2
|
F:HIS129
|
2.0
|
16.5
|
1.0
|
|
NA
|
F:HEC401
|
2.1
|
18.4
|
1.0
|
|
ND
|
F:HEC401
|
2.1
|
17.4
|
1.0
|
|
SD
|
F:MET178
|
2.3
|
18.3
|
1.0
|
|
CE1
|
F:HIS129
|
3.0
|
14.2
|
1.0
|
|
C4C
|
F:HEC401
|
3.0
|
16.5
|
1.0
|
|
C1B
|
F:HEC401
|
3.0
|
16.9
|
1.0
|
|
C1D
|
F:HEC401
|
3.0
|
16.6
|
1.0
|
|
C1C
|
F:HEC401
|
3.0
|
15.4
|
1.0
|
|
C1A
|
F:HEC401
|
3.1
|
16.7
|
1.0
|
|
C4B
|
F:HEC401
|
3.1
|
18.5
|
1.0
|
|
C4A
|
F:HEC401
|
3.1
|
18.8
|
1.0
|
|
CD2
|
F:HIS129
|
3.1
|
17.0
|
1.0
|
|
C4D
|
F:HEC401
|
3.1
|
16.1
|
1.0
|
|
CG
|
F:MET178
|
3.3
|
16.4
|
1.0
|
|
CHD
|
F:HEC401
|
3.4
|
17.4
|
1.0
|
|
CHA
|
F:HEC401
|
3.4
|
18.1
|
1.0
|
|
CHB
|
F:HEC401
|
3.4
|
18.0
|
1.0
|
|
CHC
|
F:HEC401
|
3.4
|
18.2
|
1.0
|
|
CE
|
F:MET178
|
3.4
|
17.1
|
1.0
|
|
CB
|
F:MET178
|
3.9
|
17.0
|
1.0
|
|
ND1
|
F:HIS129
|
4.1
|
14.5
|
1.0
|
|
CG
|
F:HIS129
|
4.2
|
18.0
|
1.0
|
|
C3C
|
F:HEC401
|
4.2
|
17.3
|
1.0
|
|
C2C
|
F:HEC401
|
4.3
|
16.3
|
1.0
|
|
C2B
|
F:HEC401
|
4.3
|
18.2
|
1.0
|
|
C3B
|
F:HEC401
|
4.3
|
20.5
|
1.0
|
|
C2D
|
F:HEC401
|
4.3
|
16.2
|
1.0
|
|
C3A
|
F:HEC401
|
4.3
|
19.5
|
1.0
|
|
C2A
|
F:HEC401
|
4.3
|
18.8
|
1.0
|
|
C3D
|
F:HEC401
|
4.3
|
17.7
|
1.0
|
|
Reference:
J.Kilmartin,
M.J.Maher,
K.Krusong,
G.R.Hanson,
P.V.Bernhardt,
M.Riley,
U.Kappler.
Diheme Soxax Proteins - Insights Into Structure and Function of the Active Site To Be Published.
Page generated: Sun Dec 13 15:15:41 2020
|
