Iron in PDB 4lyu: Fifteen Minutes Iron Loaded Frog M Ferritin
Enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin
All present enzymatic activity of Fifteen Minutes Iron Loaded Frog M Ferritin:
1.16.3.1;
Protein crystallography data
The structure of Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu
was solved by
S.Mangani,
F.Di Pisa,
C.Pozzi,
P.Turano,
D.Lalli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.08 /
1.75
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
183.843,
183.843,
183.843,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
20.4
|
Other elements in 4lyu:
The structure of Fifteen Minutes Iron Loaded Frog M Ferritin also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Fifteen Minutes Iron Loaded Frog M Ferritin
(pdb code 4lyu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Fifteen Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyu:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 1 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:17.5
occ:0.70
|
OE1
|
A:GLU23
|
2.0
|
15.9
|
1.0
|
OE1
|
A:GLU58
|
2.0
|
19.7
|
1.0
|
O
|
A:HOH301
|
2.1
|
22.7
|
1.0
|
O
|
A:HOH302
|
2.1
|
18.4
|
1.0
|
ND1
|
A:HIS61
|
2.4
|
18.0
|
1.0
|
CD
|
A:GLU23
|
2.9
|
14.9
|
1.0
|
CD
|
A:GLU58
|
3.1
|
19.3
|
1.0
|
OE2
|
A:GLU23
|
3.1
|
16.7
|
1.0
|
CE1
|
A:HIS61
|
3.2
|
18.6
|
1.0
|
CG
|
A:HIS61
|
3.4
|
16.5
|
1.0
|
OE2
|
A:GLU58
|
3.6
|
21.6
|
1.0
|
O
|
A:HOH464
|
3.6
|
30.6
|
0.7
|
CB
|
A:HIS61
|
3.7
|
15.0
|
1.0
|
FE
|
A:FE2203
|
3.8
|
28.4
|
0.7
|
CG1
|
A:VAL106
|
4.0
|
11.1
|
1.0
|
OE1
|
A:GLN137
|
4.1
|
18.1
|
1.0
|
O
|
A:HOH424
|
4.3
|
20.5
|
1.0
|
CG
|
A:GLU23
|
4.3
|
13.3
|
1.0
|
CG
|
A:GLU58
|
4.4
|
16.8
|
1.0
|
NE2
|
A:HIS61
|
4.4
|
18.5
|
1.0
|
O
|
A:HOH413
|
4.4
|
25.4
|
1.0
|
CA
|
A:GLU58
|
4.5
|
13.8
|
1.0
|
CD2
|
A:HIS61
|
4.5
|
17.8
|
1.0
|
CB
|
A:GLU58
|
4.6
|
15.1
|
1.0
|
CB
|
A:GLU23
|
4.8
|
11.4
|
1.0
|
CD
|
A:GLN137
|
5.0
|
16.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 2 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:42.4
occ:0.40
|
ND1
|
A:HIS54
|
2.5
|
21.9
|
1.0
|
FE
|
A:FE2203
|
2.5
|
28.4
|
0.7
|
O
|
A:HOH413
|
2.8
|
25.4
|
1.0
|
OE2
|
A:GLU58
|
2.9
|
21.6
|
1.0
|
OE2
|
A:GLU103
|
3.0
|
19.9
|
1.0
|
CE1
|
A:HIS54
|
3.1
|
22.7
|
1.0
|
OD2
|
A:ASP140
|
3.4
|
21.9
|
1.0
|
OE2
|
A:GLU57
|
3.4
|
28.9
|
1.0
|
CG
|
A:HIS54
|
3.6
|
19.6
|
1.0
|
CD
|
A:GLU103
|
3.6
|
17.8
|
1.0
|
OE1
|
A:GLU103
|
3.8
|
19.1
|
1.0
|
CD
|
A:GLU57
|
3.9
|
26.7
|
1.0
|
CD
|
A:GLU58
|
3.9
|
19.3
|
1.0
|
CE2
|
A:TYR30
|
4.0
|
14.7
|
1.0
|
OE1
|
A:GLU57
|
4.0
|
30.6
|
1.0
|
CG
|
A:ASP140
|
4.1
|
18.4
|
1.0
|
OH
|
A:TYR30
|
4.1
|
18.2
|
1.0
|
CB
|
A:HIS54
|
4.1
|
16.2
|
1.0
|
CZ
|
A:TYR30
|
4.3
|
15.8
|
1.0
|
O
|
A:HOH301
|
4.3
|
22.7
|
1.0
|
NE2
|
A:HIS54
|
4.4
|
23.6
|
1.0
|
FE
|
A:FE2205
|
4.4
|
36.4
|
0.5
|
CG
|
A:GLU58
|
4.5
|
16.8
|
1.0
|
CB
|
A:ASP140
|
4.5
|
15.4
|
1.0
|
O
|
A:HIS54
|
4.6
|
12.6
|
1.0
|
CD2
|
A:HIS54
|
4.6
|
21.3
|
1.0
|
CA
|
A:HIS54
|
4.6
|
14.3
|
1.0
|
OE1
|
A:GLU58
|
4.8
|
19.7
|
1.0
|
CG
|
A:GLU57
|
4.8
|
22.8
|
1.0
|
CD2
|
A:TYR30
|
4.8
|
13.3
|
1.0
|
O
|
A:HOH464
|
4.9
|
30.6
|
0.7
|
OD1
|
A:ASP140
|
4.9
|
19.7
|
1.0
|
CG
|
A:GLU103
|
4.9
|
15.2
|
1.0
|
|
Iron binding site 3 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 3 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:28.4
occ:0.70
|
OE2
|
A:GLU58
|
1.8
|
21.6
|
1.0
|
O
|
A:HOH413
|
1.9
|
25.4
|
1.0
|
O
|
A:HOH301
|
2.1
|
22.7
|
1.0
|
OE2
|
A:GLU103
|
2.1
|
19.9
|
1.0
|
OE1
|
A:GLU103
|
2.4
|
19.1
|
1.0
|
FE
|
A:FE2202
|
2.5
|
42.4
|
0.4
|
O
|
A:HOH464
|
2.5
|
30.6
|
0.7
|
CD
|
A:GLU103
|
2.6
|
17.8
|
1.0
|
CD
|
A:GLU58
|
2.8
|
19.3
|
1.0
|
OE1
|
A:GLU58
|
3.3
|
19.7
|
1.0
|
FE
|
A:FE2201
|
3.8
|
17.5
|
0.7
|
NE2
|
A:GLN137
|
4.0
|
17.9
|
1.0
|
OE1
|
A:GLN137
|
4.1
|
18.1
|
1.0
|
CG
|
A:GLU58
|
4.1
|
16.8
|
1.0
|
CG
|
A:GLU103
|
4.1
|
15.2
|
1.0
|
OD2
|
A:ASP140
|
4.2
|
21.9
|
1.0
|
CE2
|
A:TYR30
|
4.3
|
14.7
|
1.0
|
CD
|
A:GLN137
|
4.4
|
16.6
|
1.0
|
OE2
|
A:GLU57
|
4.5
|
28.9
|
1.0
|
OH
|
A:TYR30
|
4.5
|
18.2
|
1.0
|
CE1
|
A:HIS61
|
4.7
|
18.6
|
1.0
|
ND1
|
A:HIS54
|
4.8
|
21.9
|
1.0
|
ND1
|
A:HIS61
|
4.8
|
18.0
|
1.0
|
O
|
A:HOH302
|
4.8
|
18.4
|
1.0
|
CZ
|
A:TYR30
|
4.9
|
15.8
|
1.0
|
CB
|
A:GLU103
|
4.9
|
13.4
|
1.0
|
|
Iron binding site 4 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 4 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe204
b:37.1
occ:0.50
|
OE2
|
A:GLU136
|
2.2
|
26.9
|
1.0
|
OE1
|
A:GLU136
|
2.2
|
27.9
|
1.0
|
CD
|
A:GLU136
|
2.5
|
25.5
|
1.0
|
NE2
|
A:HIS61
|
2.9
|
18.5
|
1.0
|
CD2
|
A:HIS61
|
3.6
|
17.8
|
1.0
|
O
|
A:HOH434
|
3.7
|
29.7
|
1.0
|
CG
|
A:GLU57
|
3.8
|
22.8
|
1.0
|
CG
|
A:GLU136
|
4.0
|
23.3
|
1.0
|
CE1
|
A:HIS61
|
4.1
|
18.6
|
1.0
|
CD
|
A:GLU57
|
4.2
|
26.7
|
1.0
|
OE2
|
A:GLU57
|
4.2
|
28.9
|
1.0
|
CB
|
A:GLU136
|
4.9
|
19.6
|
1.0
|
CG
|
A:HIS61
|
4.9
|
16.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 5 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe205
b:36.4
occ:0.50
|
O
|
A:HOH303
|
2.2
|
50.3
|
1.0
|
OD1
|
A:ASP140
|
2.4
|
19.7
|
1.0
|
OD2
|
A:ASP140
|
2.4
|
21.9
|
1.0
|
OE1
|
A:GLU57
|
2.5
|
30.6
|
1.0
|
OE2
|
A:GLU57
|
2.6
|
28.9
|
1.0
|
CG
|
A:ASP140
|
2.7
|
18.4
|
1.0
|
CD
|
A:GLU57
|
2.8
|
26.7
|
1.0
|
OE1
|
A:GLU136
|
3.3
|
27.9
|
1.0
|
CG
|
A:GLU136
|
3.7
|
23.3
|
1.0
|
CD
|
A:GLU136
|
4.0
|
25.5
|
1.0
|
CB
|
A:ASP140
|
4.2
|
15.4
|
1.0
|
CG
|
A:GLU57
|
4.3
|
22.8
|
1.0
|
CE1
|
A:HIS54
|
4.4
|
22.7
|
1.0
|
FE
|
A:FE2202
|
4.4
|
42.4
|
0.4
|
O
|
A:GLU136
|
4.6
|
14.9
|
1.0
|
O
|
A:HOH413
|
4.7
|
25.4
|
1.0
|
O
|
A:HOH438
|
4.7
|
31.5
|
1.0
|
ND1
|
A:HIS54
|
4.9
|
21.9
|
1.0
|
NE2
|
A:HIS54
|
4.9
|
23.6
|
1.0
|
|
Iron binding site 6 out
of 6 in 4lyu
Go back to
Iron Binding Sites List in 4lyu
Iron binding site 6 out
of 6 in the Fifteen Minutes Iron Loaded Frog M Ferritin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Fifteen Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe206
b:10.7
occ:0.25
|
CL
|
A:CL215
|
2.2
|
14.2
|
0.2
|
NE2
|
A:HIS169
|
2.3
|
9.9
|
1.0
|
O
|
A:HOH304
|
2.4
|
16.5
|
0.2
|
CE1
|
A:HIS169
|
3.1
|
10.1
|
1.0
|
CD2
|
A:HIS169
|
3.3
|
10.5
|
1.0
|
ND1
|
A:HIS169
|
4.3
|
10.3
|
1.0
|
CG
|
A:HIS169
|
4.4
|
10.1
|
1.0
|
|
Reference:
S.Mangani,
F.Di Pisa,
C.Pozzi,
P.Turano,
D.Lalli.
Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Mon Aug 5 06:29:35 2024
|