Iron in PDB 4itt: Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
Protein crystallography data
The structure of Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4itt
was solved by
S.Pfaffen,
M.E.P.Murphy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.55 /
2.10
|
Space group
|
P 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
175.283,
175.283,
175.283,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
22.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
(pdb code 4itt). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries, PDB code: 4itt:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 1 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
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 Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:34.7
occ:0.40
|
OE2
|
D:GLU48
|
2.1
|
41.6
|
1.0
|
OE2
|
D:GLU94
|
2.4
|
27.2
|
1.0
|
O
|
D:HOH399
|
2.5
|
36.8
|
1.0
|
CD
|
D:GLU48
|
2.9
|
32.1
|
1.0
|
OE1
|
D:GLU44
|
3.0
|
50.1
|
1.0
|
OE2
|
D:GLU130
|
3.1
|
46.7
|
1.0
|
CD
|
D:GLU94
|
3.3
|
23.8
|
1.0
|
OE1
|
D:GLU94
|
3.5
|
22.4
|
1.0
|
CD
|
D:GLU130
|
3.6
|
43.3
|
1.0
|
OE1
|
D:GLU48
|
3.6
|
45.8
|
1.0
|
CG
|
D:GLU48
|
3.7
|
27.5
|
1.0
|
CG
|
D:GLU130
|
3.9
|
37.0
|
1.0
|
OH
|
D:TYR22
|
3.9
|
18.4
|
1.0
|
CD
|
D:GLU44
|
4.0
|
47.7
|
1.0
|
CE1
|
D:TYR22
|
4.1
|
15.3
|
1.0
|
CZ
|
D:TYR22
|
4.3
|
17.0
|
1.0
|
ND2
|
D:ASN97
|
4.4
|
27.7
|
1.0
|
OE1
|
D:GLU130
|
4.5
|
39.1
|
1.0
|
CG
|
D:GLU94
|
4.6
|
21.1
|
1.0
|
OE2
|
D:GLU44
|
4.7
|
60.4
|
1.0
|
CB
|
D:GLU130
|
4.8
|
27.8
|
1.0
|
CE1
|
D:HIS51
|
4.8
|
29.2
|
1.0
|
CG
|
D:GLU44
|
4.9
|
39.4
|
1.0
|
OE1
|
D:GLN127
|
4.9
|
26.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 2 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
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 Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:37.1
occ:0.45
|
OE2
|
B:GLU48
|
1.9
|
49.2
|
1.0
|
OE2
|
B:GLU94
|
2.4
|
24.5
|
1.0
|
O
|
B:HOH386
|
2.8
|
50.9
|
1.0
|
OE1
|
B:GLU44
|
2.8
|
43.9
|
1.0
|
CD
|
B:GLU48
|
3.0
|
32.1
|
1.0
|
OE1
|
B:GLU130
|
3.2
|
60.5
|
1.0
|
CD
|
B:GLU94
|
3.2
|
29.4
|
1.0
|
OE1
|
B:GLU94
|
3.4
|
26.8
|
1.0
|
CD
|
B:GLU130
|
3.6
|
44.1
|
1.0
|
OE1
|
B:GLU47
|
3.8
|
73.2
|
1.0
|
OE1
|
B:GLU48
|
3.8
|
39.0
|
1.0
|
CD
|
B:GLU44
|
3.9
|
44.2
|
1.0
|
CG
|
B:GLU130
|
3.9
|
37.4
|
1.0
|
CG
|
B:GLU48
|
3.9
|
29.1
|
1.0
|
OH
|
B:TYR22
|
4.0
|
22.1
|
1.0
|
O
|
B:HOH398
|
4.1
|
60.2
|
1.0
|
CE1
|
B:TYR22
|
4.2
|
20.1
|
1.0
|
OE2
|
B:GLU44
|
4.4
|
54.3
|
1.0
|
CZ
|
B:TYR22
|
4.4
|
21.8
|
1.0
|
OE2
|
B:GLU130
|
4.4
|
53.4
|
1.0
|
ND2
|
B:ASN97
|
4.5
|
28.2
|
1.0
|
CG
|
B:GLU94
|
4.6
|
27.8
|
1.0
|
CB
|
B:GLU130
|
4.7
|
27.2
|
1.0
|
OE1
|
B:GLN127
|
4.7
|
25.6
|
1.0
|
CD
|
B:GLU47
|
4.8
|
59.3
|
1.0
|
CE1
|
B:HIS51
|
4.8
|
37.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 3 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
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 Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:39.1
occ:0.50
|
OE2
|
C:GLU48
|
2.3
|
38.9
|
1.0
|
OE2
|
C:GLU94
|
2.4
|
26.0
|
1.0
|
OE1
|
C:GLU44
|
2.9
|
47.5
|
1.0
|
OE2
|
C:GLU130
|
2.9
|
47.1
|
1.0
|
CD
|
C:GLU48
|
3.0
|
34.0
|
1.0
|
CD
|
C:GLU94
|
3.3
|
25.7
|
1.0
|
OE1
|
C:GLU94
|
3.5
|
25.2
|
1.0
|
CD
|
C:GLU130
|
3.6
|
41.3
|
1.0
|
OE1
|
C:GLU48
|
3.7
|
43.5
|
1.0
|
CG
|
C:GLU48
|
3.9
|
28.8
|
1.0
|
OH
|
C:TYR22
|
3.9
|
19.4
|
1.0
|
CD
|
C:GLU44
|
4.0
|
43.2
|
1.0
|
CE1
|
C:TYR22
|
4.0
|
17.1
|
1.0
|
CG
|
C:GLU130
|
4.0
|
38.8
|
1.0
|
O
|
C:HOH311
|
4.2
|
45.8
|
1.0
|
CZ
|
C:TYR22
|
4.3
|
18.7
|
1.0
|
O
|
C:HOH395
|
4.5
|
42.5
|
1.0
|
OE1
|
C:GLU130
|
4.6
|
42.4
|
1.0
|
OE2
|
C:GLU44
|
4.6
|
45.5
|
1.0
|
CG
|
C:GLU94
|
4.6
|
23.3
|
1.0
|
ND2
|
C:ASN97
|
4.7
|
35.1
|
1.0
|
CB
|
C:GLU130
|
4.7
|
27.2
|
1.0
|
OE1
|
C:GLN127
|
4.8
|
23.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 4 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
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 Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:41.7
occ:0.50
|
OE2
|
E:GLU48
|
2.0
|
41.3
|
1.0
|
O
|
E:HOH387
|
2.3
|
30.0
|
1.0
|
OE2
|
E:GLU94
|
2.6
|
30.3
|
1.0
|
OE1
|
E:GLU44
|
2.8
|
45.9
|
1.0
|
CD
|
E:GLU48
|
3.1
|
32.2
|
1.0
|
OE1
|
E:GLU130
|
3.4
|
57.3
|
1.0
|
CD
|
E:GLU94
|
3.4
|
28.1
|
1.0
|
CG
|
E:GLU130
|
3.4
|
43.7
|
1.0
|
CD
|
E:GLU130
|
3.4
|
50.3
|
1.0
|
OE1
|
E:GLU94
|
3.5
|
26.0
|
1.0
|
CD
|
E:GLU44
|
3.9
|
46.4
|
1.0
|
CG
|
E:GLU48
|
3.9
|
28.9
|
1.0
|
OE1
|
E:GLU48
|
4.0
|
35.1
|
1.0
|
OH
|
E:TYR22
|
4.2
|
21.9
|
1.0
|
OE2
|
E:GLU130
|
4.2
|
43.1
|
1.0
|
CE1
|
E:TYR22
|
4.3
|
18.1
|
1.0
|
OE2
|
E:GLU44
|
4.4
|
53.7
|
1.0
|
CZ
|
E:TYR22
|
4.6
|
17.1
|
1.0
|
CE1
|
E:HIS51
|
4.6
|
30.5
|
1.0
|
CB
|
E:GLU130
|
4.7
|
29.4
|
1.0
|
ND2
|
E:ASN97
|
4.7
|
26.0
|
1.0
|
OE1
|
E:GLN127
|
4.8
|
26.7
|
1.0
|
CG
|
E:GLU94
|
4.8
|
26.2
|
1.0
|
ND1
|
E:HIS51
|
4.9
|
30.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 5 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:37.0
occ:0.45
|
OE2
|
G:GLU48
|
2.1
|
39.6
|
1.0
|
O
|
G:HOH404
|
2.3
|
43.2
|
1.0
|
OE2
|
G:GLU94
|
2.4
|
25.8
|
1.0
|
O
|
G:HOH411
|
2.7
|
44.8
|
1.0
|
OE1
|
G:GLU44
|
2.7
|
45.2
|
1.0
|
CD
|
G:GLU48
|
3.1
|
31.1
|
1.0
|
CD
|
G:GLU94
|
3.3
|
23.3
|
1.0
|
OE1
|
G:GLU130
|
3.4
|
47.1
|
1.0
|
OE1
|
G:GLU94
|
3.6
|
24.1
|
1.0
|
CD
|
G:GLU130
|
3.7
|
40.2
|
1.0
|
OH
|
G:TYR22
|
3.9
|
16.3
|
1.0
|
OE1
|
G:GLU48
|
3.9
|
34.6
|
1.0
|
CD
|
G:GLU44
|
3.9
|
43.5
|
1.0
|
CG
|
G:GLU130
|
3.9
|
33.8
|
1.0
|
OE2
|
G:GLU47
|
4.0
|
62.2
|
1.0
|
CG
|
G:GLU48
|
4.0
|
28.6
|
1.0
|
CE1
|
G:TYR22
|
4.2
|
14.6
|
1.0
|
O
|
G:HOH405
|
4.2
|
46.0
|
1.0
|
CZ
|
G:TYR22
|
4.4
|
16.1
|
1.0
|
OE2
|
G:GLU130
|
4.5
|
54.2
|
1.0
|
CE1
|
G:HIS51
|
4.6
|
32.9
|
1.0
|
CB
|
G:GLU130
|
4.6
|
25.9
|
1.0
|
CG
|
G:GLU94
|
4.7
|
21.1
|
1.0
|
O
|
G:HOH412
|
4.7
|
53.0
|
1.0
|
OE2
|
G:GLU44
|
4.8
|
48.2
|
1.0
|
ND2
|
G:ASN97
|
4.8
|
14.2
|
0.5
|
CG
|
G:GLU44
|
4.8
|
32.4
|
1.0
|
OE1
|
G:GLN127
|
4.9
|
21.2
|
1.0
|
CD
|
G:GLU47
|
4.9
|
53.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 4itt
Go back to
Iron Binding Sites List in 4itt
Iron binding site 6 out
of 6 in the Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Iron Soaked (5 Min) Ferritin From Pseudo- Nitzschia Multiseries within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe201
b:46.6
occ:0.50
|
OE2
|
H:GLU94
|
2.5
|
26.9
|
1.0
|
OE1
|
H:GLU48
|
2.8
|
36.1
|
1.0
|
OE2
|
H:GLU48
|
2.9
|
46.0
|
1.0
|
CD
|
H:GLU48
|
2.9
|
32.0
|
1.0
|
OE1
|
H:GLU44
|
3.1
|
47.5
|
1.0
|
CD
|
H:GLU94
|
3.3
|
25.2
|
1.0
|
OE1
|
H:GLU94
|
3.5
|
23.4
|
1.0
|
OE1
|
H:GLU130
|
3.8
|
51.2
|
1.0
|
CG
|
H:GLU48
|
3.9
|
31.4
|
1.0
|
CD
|
H:GLU130
|
3.9
|
46.3
|
1.0
|
CD
|
H:GLU44
|
4.0
|
46.9
|
1.0
|
OH
|
H:TYR22
|
4.0
|
20.8
|
1.0
|
CE1
|
H:TYR22
|
4.1
|
19.8
|
1.0
|
CG
|
H:GLU130
|
4.2
|
35.1
|
1.0
|
OE2
|
H:GLU44
|
4.2
|
57.8
|
1.0
|
CZ
|
H:TYR22
|
4.4
|
21.9
|
1.0
|
ND2
|
H:ASN97
|
4.4
|
43.3
|
1.0
|
OE2
|
H:GLU130
|
4.5
|
57.6
|
1.0
|
O
|
H:HOH313
|
4.5
|
38.6
|
1.0
|
OE1
|
H:GLN127
|
4.6
|
23.0
|
1.0
|
CG
|
H:GLU94
|
4.7
|
21.7
|
1.0
|
CE1
|
H:HIS51
|
4.7
|
26.1
|
1.0
|
CB
|
H:GLU130
|
4.8
|
25.7
|
1.0
|
ND1
|
H:HIS51
|
4.9
|
31.8
|
1.0
|
|
Reference:
S.Pfaffen,
R.Abdulqadir,
N.E.Le Brun,
M.E.Murphy.
Mechanism of Ferrous Iron Binding and Oxidation By Ferritin From A Pennate Diatom. J.Biol.Chem. V. 288 14917 2013.
ISSN: ISSN 0021-9258
PubMed: 23548912
DOI: 10.1074/JBC.M113.454496
Page generated: Mon Aug 5 04:14:59 2024
|