Iron in PDB 5u1a: Ferritin with Gc Mtre Loop 1 Inserted at HIS34
Enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34
All present enzymatic activity of Ferritin with Gc Mtre Loop 1 Inserted at HIS34:
1.16.3.2;
Protein crystallography data
The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a
was solved by
S.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.412,
128.412,
165.041,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.8 /
19.6
|
Other elements in 5u1a:
The structure of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
(pdb code 5u1a). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Ferritin with Gc Mtre Loop 1 Inserted at HIS34, PDB code: 5u1a:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 1 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:42.0
occ:1.00
|
O
|
D:HOH384
|
2.3
|
23.0
|
1.0
|
NE2
|
D:HIS164
|
2.4
|
32.6
|
1.0
|
NE2
|
A:HIS164
|
2.4
|
33.2
|
1.0
|
NE2
|
B:HIS164
|
2.6
|
32.7
|
1.0
|
O
|
B:HOH378
|
3.2
|
41.8
|
1.0
|
CE1
|
D:HIS164
|
3.3
|
30.7
|
1.0
|
CD2
|
A:HIS164
|
3.3
|
32.6
|
1.0
|
CD2
|
D:HIS164
|
3.4
|
29.0
|
1.0
|
CE1
|
A:HIS164
|
3.4
|
33.8
|
1.0
|
CD2
|
B:HIS164
|
3.5
|
33.8
|
1.0
|
CE1
|
B:HIS164
|
3.7
|
34.4
|
1.0
|
ND1
|
D:HIS164
|
4.4
|
27.9
|
1.0
|
CG
|
D:HIS164
|
4.5
|
29.0
|
1.0
|
CG
|
A:HIS164
|
4.5
|
30.8
|
1.0
|
CD1
|
B:LEU168
|
4.5
|
26.3
|
1.0
|
ND1
|
A:HIS164
|
4.5
|
28.6
|
1.0
|
CD1
|
A:LEU168
|
4.6
|
23.2
|
1.0
|
CG
|
B:HIS164
|
4.7
|
31.1
|
1.0
|
CD1
|
D:LEU168
|
4.7
|
24.6
|
1.0
|
ND1
|
B:HIS164
|
4.8
|
30.9
|
1.0
|
OD1
|
A:ASN163
|
5.0
|
40.6
|
1.0
|
OD1
|
B:ASN163
|
5.0
|
56.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 2 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe204
b:37.9
occ:0.25
|
O
|
E:HOH390
|
2.2
|
23.8
|
0.2
|
NE2
|
E:HIS164
|
2.4
|
36.2
|
1.0
|
O
|
E:HOH392
|
3.0
|
34.2
|
0.2
|
CE1
|
E:HIS164
|
3.3
|
36.0
|
1.0
|
CD2
|
E:HIS164
|
3.5
|
35.7
|
1.0
|
ND1
|
E:HIS164
|
4.4
|
31.7
|
1.0
|
CG
|
E:HIS164
|
4.6
|
31.6
|
1.0
|
OD1
|
E:ASN163
|
4.6
|
36.5
|
1.0
|
CD1
|
E:LEU168
|
4.9
|
24.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 3 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe206
b:37.5
occ:0.25
|
O
|
F:HOH413
|
2.0
|
13.7
|
0.2
|
O
|
F:HOH421
|
2.5
|
50.0
|
0.2
|
NE2
|
F:HIS164
|
2.5
|
39.9
|
1.0
|
CE1
|
F:HIS164
|
3.4
|
40.4
|
1.0
|
CD2
|
F:HIS164
|
3.5
|
38.9
|
1.0
|
ND1
|
F:HIS164
|
4.5
|
34.9
|
1.0
|
CG
|
F:HIS164
|
4.6
|
33.1
|
1.0
|
OD1
|
F:ASN163
|
4.7
|
47.7
|
1.0
|
CD1
|
F:LEU168
|
4.8
|
22.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 4 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe203
b:39.6
occ:1.00
|
NE2
|
G:HIS164
|
2.4
|
29.4
|
1.0
|
O
|
G:HOH415
|
2.4
|
26.3
|
1.0
|
NE2
|
J:HIS164
|
2.5
|
33.7
|
1.0
|
NE2
|
H:HIS164
|
2.7
|
36.7
|
1.0
|
O
|
J:HOH385
|
3.1
|
41.3
|
1.0
|
CD2
|
G:HIS164
|
3.3
|
30.9
|
1.0
|
CE1
|
G:HIS164
|
3.4
|
29.3
|
1.0
|
CD2
|
J:HIS164
|
3.4
|
32.2
|
1.0
|
CE1
|
J:HIS164
|
3.4
|
33.7
|
1.0
|
CD2
|
H:HIS164
|
3.5
|
36.0
|
1.0
|
CE1
|
H:HIS164
|
3.7
|
35.5
|
1.0
|
CD1
|
H:LEU168
|
4.5
|
26.0
|
1.0
|
CG
|
G:HIS164
|
4.5
|
29.4
|
1.0
|
ND1
|
G:HIS164
|
4.5
|
29.9
|
1.0
|
ND1
|
J:HIS164
|
4.5
|
30.2
|
1.0
|
CG
|
J:HIS164
|
4.6
|
30.4
|
1.0
|
CD1
|
G:LEU168
|
4.6
|
25.4
|
1.0
|
CG
|
H:HIS164
|
4.7
|
30.7
|
1.0
|
CD1
|
J:LEU168
|
4.7
|
26.7
|
1.0
|
ND1
|
H:HIS164
|
4.8
|
30.6
|
1.0
|
OD1
|
G:ASN163
|
4.8
|
41.2
|
1.0
|
OD1
|
H:ASN163
|
5.0
|
51.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 5 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe203
b:38.5
occ:0.25
|
NE2
|
K:HIS164
|
2.4
|
30.6
|
1.0
|
O
|
K:HOH420
|
2.5
|
26.3
|
0.2
|
CD2
|
K:HIS164
|
3.3
|
32.7
|
1.0
|
CE1
|
K:HIS164
|
3.4
|
32.2
|
1.0
|
ND1
|
K:HIS164
|
4.5
|
31.5
|
1.0
|
CG
|
K:HIS164
|
4.5
|
28.7
|
1.0
|
CD1
|
K:LEU168
|
4.8
|
23.6
|
1.0
|
OD1
|
K:ASN163
|
4.8
|
47.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 5u1a
Go back to
Iron Binding Sites List in 5u1a
Iron binding site 6 out
of 6 in the Ferritin with Gc Mtre Loop 1 Inserted at HIS34
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Ferritin with Gc Mtre Loop 1 Inserted at HIS34 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe206
b:42.7
occ:0.25
|
O
|
L:HOH412
|
2.3
|
21.3
|
0.2
|
NE2
|
L:HIS164
|
2.3
|
34.5
|
1.0
|
O
|
L:HOH422
|
2.6
|
48.1
|
0.2
|
CE1
|
L:HIS164
|
3.2
|
33.5
|
1.0
|
CD2
|
L:HIS164
|
3.4
|
35.1
|
1.0
|
ND1
|
L:HIS164
|
4.3
|
29.1
|
1.0
|
CG
|
L:HIS164
|
4.4
|
31.0
|
1.0
|
OD1
|
L:ASN163
|
4.7
|
43.4
|
1.0
|
CD1
|
L:LEU168
|
4.9
|
25.4
|
1.0
|
|
Reference:
L.Wang,
D.Xing,
A.Le Van,
A.E.Jerse,
S.Wang.
Structure-Based Design of Ferritin Nanoparticle Immunogens Displaying Antigenic Loops of Neisseria Gonorrhoeae. Febs Open Bio V. 7 1196 2017.
ISSN: ESSN 2211-5463
PubMed: 28781959
DOI: 10.1002/2211-5463.12267
Page generated: Tue Aug 6 09:44:20 2024
|