Iron in PDB 5n5e: Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
Protein crystallography data
The structure of Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175, PDB code: 5n5e
was solved by
J.Marles-Wright,
D.He,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.19 /
2.03
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.853,
110.057,
136.271,
90.00,
91.22,
90.00
|
R / Rfree (%)
|
17.4 /
20.2
|
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Iron atom in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
(pdb code 5n5e). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the
Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175, PDB code: 5n5e:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 1 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe101
b:19.0
occ:0.86
|
OE1
|
e:GLU62
|
1.8
|
25.6
|
1.0
|
OE2
|
K:GLU62
|
2.0
|
28.4
|
1.0
|
ND1
|
e:HIS65
|
2.1
|
19.9
|
1.0
|
OE2
|
e:GLU32
|
2.2
|
22.6
|
1.0
|
OE1
|
e:GLU32
|
2.2
|
23.7
|
1.0
|
O
|
e:HOH219
|
2.3
|
27.4
|
1.0
|
CD
|
e:GLU32
|
2.5
|
24.5
|
1.0
|
CD
|
e:GLU62
|
2.9
|
23.2
|
1.0
|
CD
|
K:GLU62
|
2.9
|
23.5
|
1.0
|
CE1
|
e:HIS65
|
3.0
|
22.4
|
1.0
|
HE1
|
e:HIS65
|
3.1
|
26.9
|
1.0
|
HA
|
e:GLU62
|
3.2
|
23.8
|
1.0
|
OE1
|
K:GLU62
|
3.2
|
25.4
|
1.0
|
CG
|
e:HIS65
|
3.3
|
23.2
|
1.0
|
HB2
|
e:HIS65
|
3.4
|
23.1
|
1.0
|
OE2
|
e:GLU62
|
3.6
|
25.2
|
1.0
|
HB3
|
e:GLU62
|
3.7
|
21.5
|
1.0
|
CB
|
e:HIS65
|
3.7
|
19.2
|
1.0
|
HB3
|
e:HIS65
|
3.7
|
23.1
|
1.0
|
O
|
e:HOH230
|
3.7
|
29.9
|
1.0
|
HH
|
K:TYR39
|
3.8
|
33.2
|
1.0
|
HE2
|
K:TYR39
|
3.9
|
30.3
|
1.0
|
HG13
|
K:VAL58
|
3.9
|
26.8
|
1.0
|
FE
|
e:FE102
|
4.0
|
16.1
|
0.9
|
CA
|
e:GLU62
|
4.0
|
19.8
|
1.0
|
CG
|
e:GLU32
|
4.0
|
20.4
|
1.0
|
CG
|
e:GLU62
|
4.1
|
21.7
|
1.0
|
CB
|
e:GLU62
|
4.1
|
17.9
|
1.0
|
HE1
|
K:HIS65
|
4.2
|
30.2
|
1.0
|
NE2
|
e:HIS65
|
4.2
|
25.9
|
1.0
|
O
|
K:HOH237
|
4.2
|
33.3
|
1.0
|
CD2
|
e:HIS65
|
4.3
|
25.7
|
1.0
|
CG
|
K:GLU62
|
4.3
|
20.5
|
1.0
|
HG11
|
K:VAL58
|
4.3
|
26.8
|
1.0
|
HG3
|
e:GLU32
|
4.4
|
24.4
|
1.0
|
HA
|
e:GLU32
|
4.4
|
22.3
|
1.0
|
HG12
|
K:VAL58
|
4.4
|
26.8
|
1.0
|
HG2
|
e:GLU32
|
4.4
|
24.4
|
1.0
|
CG1
|
K:VAL58
|
4.4
|
22.3
|
1.0
|
HG2
|
K:GLU62
|
4.5
|
24.6
|
1.0
|
HG3
|
K:GLU62
|
4.5
|
24.6
|
1.0
|
HG3
|
e:GLU62
|
4.6
|
26.0
|
1.0
|
OH
|
K:TYR39
|
4.6
|
27.7
|
1.0
|
HB3
|
e:GLU32
|
4.7
|
24.4
|
1.0
|
HG2
|
e:GLU62
|
4.7
|
26.0
|
1.0
|
CE2
|
K:TYR39
|
4.7
|
25.3
|
1.0
|
O
|
e:GLU62
|
4.8
|
17.3
|
1.0
|
CB
|
e:GLU32
|
4.8
|
20.3
|
1.0
|
N
|
e:GLU62
|
4.9
|
15.9
|
1.0
|
CE1
|
K:HIS65
|
4.9
|
25.1
|
1.0
|
HE2
|
e:HIS65
|
4.9
|
31.1
|
1.0
|
C
|
e:GLU62
|
4.9
|
15.5
|
1.0
|
HE2
|
e:PHE69
|
4.9
|
27.9
|
1.0
|
|
Iron binding site 2 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 2 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe102
b:16.1
occ:0.90
|
OE1
|
K:GLU62
|
1.9
|
25.4
|
1.0
|
OE2
|
e:GLU62
|
2.0
|
25.2
|
1.0
|
OE2
|
K:GLU32
|
2.1
|
18.6
|
1.0
|
OE1
|
K:GLU32
|
2.2
|
24.0
|
1.0
|
ND1
|
K:HIS65
|
2.2
|
24.6
|
1.0
|
O
|
e:HOH230
|
2.4
|
29.9
|
1.0
|
CD
|
K:GLU32
|
2.4
|
21.4
|
1.0
|
CD
|
e:GLU62
|
2.9
|
23.2
|
1.0
|
CD
|
K:GLU62
|
3.0
|
23.5
|
1.0
|
CE1
|
K:HIS65
|
3.1
|
25.1
|
1.0
|
HE1
|
K:HIS65
|
3.2
|
30.2
|
1.0
|
OE1
|
e:GLU62
|
3.3
|
25.6
|
1.0
|
HA
|
K:GLU62
|
3.3
|
25.2
|
1.0
|
CG
|
K:HIS65
|
3.3
|
19.0
|
1.0
|
HB2
|
K:HIS65
|
3.4
|
21.7
|
1.0
|
OE2
|
K:GLU62
|
3.7
|
28.4
|
1.0
|
HB3
|
K:HIS65
|
3.7
|
21.7
|
1.0
|
CB
|
K:HIS65
|
3.7
|
18.1
|
1.0
|
HH
|
e:TYR39
|
3.7
|
26.8
|
1.0
|
HB3
|
K:GLU62
|
3.7
|
27.3
|
1.0
|
HE2
|
e:TYR39
|
3.8
|
27.1
|
1.0
|
HG13
|
e:VAL58
|
3.8
|
21.2
|
1.0
|
O
|
e:HOH219
|
3.9
|
27.4
|
1.0
|
O
|
e:HOH227
|
3.9
|
33.2
|
1.0
|
CG
|
K:GLU32
|
4.0
|
18.7
|
1.0
|
FE
|
e:FE101
|
4.0
|
19.0
|
0.9
|
CA
|
K:GLU62
|
4.1
|
21.0
|
1.0
|
CG
|
K:GLU62
|
4.1
|
20.5
|
1.0
|
CB
|
K:GLU62
|
4.1
|
22.8
|
1.0
|
HE1
|
e:HIS65
|
4.2
|
26.9
|
1.0
|
HG11
|
e:VAL58
|
4.3
|
21.2
|
1.0
|
NE2
|
K:HIS65
|
4.3
|
24.4
|
1.0
|
CG
|
e:GLU62
|
4.3
|
21.7
|
1.0
|
HA
|
K:GLU32
|
4.3
|
21.5
|
1.0
|
HG12
|
e:VAL58
|
4.3
|
21.2
|
1.0
|
CG1
|
e:VAL58
|
4.3
|
17.7
|
1.0
|
HG2
|
K:GLU32
|
4.3
|
22.4
|
1.0
|
HG3
|
K:GLU32
|
4.4
|
22.4
|
1.0
|
CD2
|
K:HIS65
|
4.4
|
22.2
|
1.0
|
HG3
|
e:GLU62
|
4.5
|
26.0
|
1.0
|
HG2
|
e:GLU62
|
4.5
|
26.0
|
1.0
|
OH
|
e:TYR39
|
4.5
|
22.4
|
1.0
|
HB3
|
K:GLU32
|
4.6
|
22.8
|
1.0
|
HG3
|
K:GLU62
|
4.6
|
24.6
|
1.0
|
CE2
|
e:TYR39
|
4.6
|
22.6
|
1.0
|
CB
|
K:GLU32
|
4.8
|
19.0
|
1.0
|
HG2
|
K:GLU62
|
4.8
|
24.6
|
1.0
|
O
|
K:GLU62
|
4.8
|
18.7
|
1.0
|
HE2
|
K:PHE69
|
4.9
|
25.0
|
1.0
|
CE1
|
e:HIS65
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 3 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 3 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:17.4
occ:0.95
|
OE1
|
A:GLU62
|
1.9
|
29.1
|
1.0
|
OE1
|
Z:GLU62
|
2.0
|
24.0
|
1.0
|
OE1
|
A:GLU32
|
2.1
|
21.1
|
1.0
|
OE2
|
A:GLU32
|
2.1
|
23.8
|
1.0
|
ND1
|
A:HIS65
|
2.2
|
22.7
|
1.0
|
O
|
Z:HOH231
|
2.3
|
30.4
|
1.0
|
CD
|
A:GLU32
|
2.4
|
19.4
|
1.0
|
CD
|
A:GLU62
|
3.0
|
22.4
|
1.0
|
CE1
|
A:HIS65
|
3.1
|
26.8
|
1.0
|
CD
|
Z:GLU62
|
3.1
|
24.6
|
1.0
|
HE1
|
A:HIS65
|
3.2
|
32.2
|
1.0
|
HA
|
A:GLU62
|
3.2
|
23.7
|
1.0
|
CG
|
A:HIS65
|
3.3
|
20.2
|
1.0
|
HB2
|
A:HIS65
|
3.3
|
26.8
|
1.0
|
OE2
|
Z:GLU62
|
3.4
|
28.1
|
1.0
|
OE2
|
A:GLU62
|
3.6
|
29.5
|
1.0
|
HH
|
Z:TYR39
|
3.6
|
29.3
|
1.0
|
HB3
|
A:GLU62
|
3.6
|
24.7
|
1.0
|
HB3
|
A:HIS65
|
3.6
|
26.8
|
1.0
|
CB
|
A:HIS65
|
3.6
|
22.3
|
1.0
|
HE2
|
Z:TYR39
|
3.8
|
24.7
|
1.0
|
O
|
A:HOH222
|
3.9
|
32.2
|
1.0
|
HG13
|
Z:VAL58
|
3.9
|
25.1
|
1.0
|
CG
|
A:GLU32
|
3.9
|
20.4
|
1.0
|
O
|
Z:HOH232
|
4.0
|
35.0
|
1.0
|
FE
|
A:FE102
|
4.0
|
18.1
|
0.9
|
CA
|
A:GLU62
|
4.0
|
19.8
|
1.0
|
CG
|
A:GLU62
|
4.1
|
21.7
|
1.0
|
CB
|
A:GLU62
|
4.1
|
20.6
|
1.0
|
NE2
|
A:HIS65
|
4.2
|
26.0
|
1.0
|
HG11
|
Z:VAL58
|
4.3
|
25.1
|
1.0
|
HA
|
A:GLU32
|
4.3
|
21.4
|
1.0
|
HG2
|
A:GLU32
|
4.3
|
24.5
|
1.0
|
HG3
|
A:GLU32
|
4.3
|
24.5
|
1.0
|
HE1
|
Z:HIS65
|
4.3
|
21.9
|
1.0
|
CD2
|
A:HIS65
|
4.4
|
22.7
|
1.0
|
HG12
|
Z:VAL58
|
4.4
|
25.1
|
1.0
|
CG1
|
Z:VAL58
|
4.4
|
20.9
|
1.0
|
CG
|
Z:GLU62
|
4.4
|
21.4
|
1.0
|
OH
|
Z:TYR39
|
4.5
|
24.4
|
1.0
|
HG3
|
Z:GLU62
|
4.6
|
25.7
|
1.0
|
HG3
|
A:GLU62
|
4.6
|
26.0
|
1.0
|
HB3
|
A:GLU32
|
4.6
|
18.7
|
1.0
|
HG2
|
Z:GLU62
|
4.6
|
25.7
|
1.0
|
CE2
|
Z:TYR39
|
4.6
|
20.6
|
1.0
|
CB
|
A:GLU32
|
4.7
|
15.6
|
1.0
|
HG2
|
A:GLU62
|
4.7
|
26.0
|
1.0
|
HE2
|
A:PHE69
|
4.8
|
22.0
|
1.0
|
O
|
A:GLU62
|
4.8
|
19.0
|
1.0
|
C
|
A:GLU62
|
5.0
|
18.2
|
1.0
|
N
|
A:GLU62
|
5.0
|
19.7
|
1.0
|
HE2
|
A:HIS65
|
5.0
|
31.2
|
1.0
|
CA
|
A:GLU32
|
5.0
|
17.9
|
1.0
|
|
Iron binding site 4 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 4 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe102
b:18.1
occ:0.94
|
OE2
|
Z:GLU62
|
1.8
|
28.1
|
1.0
|
OE2
|
A:GLU62
|
1.9
|
29.5
|
1.0
|
OE1
|
Z:GLU32
|
2.2
|
23.7
|
1.0
|
ND1
|
Z:HIS65
|
2.2
|
20.6
|
1.0
|
OE2
|
Z:GLU32
|
2.2
|
24.7
|
1.0
|
O
|
A:HOH222
|
2.3
|
32.2
|
1.0
|
CD
|
Z:GLU32
|
2.5
|
18.1
|
1.0
|
CD
|
A:GLU62
|
2.9
|
22.4
|
1.0
|
CD
|
Z:GLU62
|
2.9
|
24.6
|
1.0
|
CE1
|
Z:HIS65
|
3.0
|
18.3
|
1.0
|
HE1
|
Z:HIS65
|
3.1
|
21.9
|
1.0
|
OE1
|
A:GLU62
|
3.3
|
29.1
|
1.0
|
HA
|
Z:GLU62
|
3.3
|
24.8
|
1.0
|
CG
|
Z:HIS65
|
3.3
|
20.3
|
1.0
|
HB2
|
Z:HIS65
|
3.4
|
24.5
|
1.0
|
OE1
|
Z:GLU62
|
3.5
|
24.0
|
1.0
|
O
|
Z:HOH231
|
3.6
|
30.4
|
1.0
|
HB3
|
Z:GLU62
|
3.7
|
24.6
|
1.0
|
CB
|
Z:HIS65
|
3.7
|
20.4
|
1.0
|
HB3
|
Z:HIS65
|
3.8
|
24.5
|
1.0
|
HH
|
A:TYR39
|
3.8
|
28.2
|
1.0
|
HE2
|
A:TYR39
|
3.8
|
26.2
|
1.0
|
HG13
|
A:VAL58
|
3.8
|
26.0
|
1.0
|
FE
|
A:FE101
|
4.0
|
17.4
|
0.9
|
CG
|
Z:GLU32
|
4.0
|
20.2
|
1.0
|
CG
|
Z:GLU62
|
4.1
|
21.4
|
1.0
|
CA
|
Z:GLU62
|
4.1
|
20.7
|
1.0
|
HE1
|
A:HIS65
|
4.1
|
32.2
|
1.0
|
CB
|
Z:GLU62
|
4.1
|
20.5
|
1.0
|
NE2
|
Z:HIS65
|
4.2
|
24.1
|
1.0
|
O
|
A:HOH217
|
4.3
|
33.4
|
1.0
|
CG
|
A:GLU62
|
4.3
|
21.7
|
1.0
|
HG11
|
A:VAL58
|
4.3
|
26.0
|
1.0
|
HG12
|
A:VAL58
|
4.3
|
26.0
|
1.0
|
HA
|
Z:GLU32
|
4.4
|
24.9
|
1.0
|
CG1
|
A:VAL58
|
4.4
|
21.7
|
1.0
|
CD2
|
Z:HIS65
|
4.4
|
21.9
|
1.0
|
HG3
|
Z:GLU32
|
4.4
|
24.2
|
1.0
|
HG2
|
Z:GLU32
|
4.4
|
24.2
|
1.0
|
HG2
|
A:GLU62
|
4.4
|
26.0
|
1.0
|
HG3
|
A:GLU62
|
4.5
|
26.0
|
1.0
|
HG3
|
Z:GLU62
|
4.6
|
25.7
|
1.0
|
OH
|
A:TYR39
|
4.6
|
23.5
|
1.0
|
HB3
|
Z:GLU32
|
4.6
|
24.6
|
1.0
|
CE2
|
A:TYR39
|
4.7
|
21.8
|
1.0
|
HG2
|
Z:GLU62
|
4.7
|
25.7
|
1.0
|
CB
|
Z:GLU32
|
4.8
|
20.5
|
1.0
|
CE1
|
A:HIS65
|
4.8
|
26.8
|
1.0
|
HE2
|
Z:PHE69
|
4.9
|
24.5
|
1.0
|
O
|
Z:GLU62
|
4.9
|
18.6
|
1.0
|
HE2
|
Z:HIS65
|
4.9
|
28.9
|
1.0
|
N
|
Z:GLU62
|
5.0
|
21.9
|
1.0
|
|
Iron binding site 5 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 5 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe101
b:21.5
occ:1.00
|
OE1
|
B:GLU62
|
1.9
|
24.6
|
1.0
|
OE2
|
Y:GLU62
|
2.0
|
22.1
|
1.0
|
OE1
|
B:GLU32
|
2.2
|
20.8
|
1.0
|
OE2
|
B:GLU32
|
2.2
|
23.6
|
1.0
|
ND1
|
B:HIS65
|
2.2
|
18.7
|
1.0
|
O
|
Y:HOH239
|
2.4
|
29.4
|
1.0
|
CD
|
B:GLU32
|
2.5
|
22.4
|
1.0
|
CD
|
Y:GLU62
|
3.0
|
21.3
|
1.0
|
CD
|
B:GLU62
|
3.1
|
23.5
|
1.0
|
CE1
|
B:HIS65
|
3.1
|
22.0
|
1.0
|
HE1
|
B:HIS65
|
3.2
|
26.4
|
1.0
|
HA
|
B:GLU62
|
3.2
|
17.1
|
1.0
|
OE1
|
Y:GLU62
|
3.3
|
20.4
|
1.0
|
CG
|
B:HIS65
|
3.3
|
18.9
|
1.0
|
HB2
|
B:HIS65
|
3.4
|
19.1
|
1.0
|
HB3
|
B:HIS65
|
3.6
|
19.1
|
1.0
|
CB
|
B:HIS65
|
3.7
|
15.9
|
1.0
|
HH
|
Y:TYR39
|
3.7
|
27.2
|
1.0
|
HB3
|
B:GLU62
|
3.7
|
16.9
|
1.0
|
OE2
|
B:GLU62
|
3.7
|
23.8
|
1.0
|
O
|
B:HOH244
|
3.8
|
28.7
|
1.0
|
HE2
|
Y:TYR39
|
3.8
|
24.2
|
1.0
|
HG13
|
Y:VAL58
|
3.9
|
22.6
|
1.0
|
CG
|
B:GLU32
|
4.0
|
19.1
|
1.0
|
CA
|
B:GLU62
|
4.1
|
14.3
|
1.0
|
FE
|
B:FE102
|
4.1
|
20.5
|
1.0
|
O
|
Y:HOH247
|
4.1
|
31.6
|
1.0
|
CB
|
B:GLU62
|
4.1
|
14.1
|
1.0
|
CG
|
B:GLU62
|
4.2
|
20.4
|
1.0
|
HE1
|
Y:HIS65
|
4.2
|
27.6
|
1.0
|
HG11
|
Y:VAL58
|
4.3
|
22.6
|
1.0
|
NE2
|
B:HIS65
|
4.3
|
21.7
|
1.0
|
HG12
|
Y:VAL58
|
4.3
|
22.6
|
1.0
|
HA
|
B:GLU32
|
4.3
|
20.7
|
1.0
|
CG
|
Y:GLU62
|
4.3
|
18.0
|
1.0
|
CG1
|
Y:VAL58
|
4.3
|
18.8
|
1.0
|
CD2
|
B:HIS65
|
4.4
|
24.4
|
1.0
|
HG3
|
B:GLU32
|
4.4
|
23.0
|
1.0
|
HG2
|
B:GLU32
|
4.4
|
23.0
|
1.0
|
OH
|
Y:TYR39
|
4.5
|
22.6
|
1.0
|
HG3
|
Y:GLU62
|
4.5
|
21.6
|
1.0
|
HG2
|
Y:GLU62
|
4.6
|
21.6
|
1.0
|
HB3
|
B:GLU32
|
4.6
|
19.7
|
1.0
|
HG3
|
B:GLU62
|
4.7
|
24.5
|
1.0
|
CE2
|
Y:TYR39
|
4.7
|
20.2
|
1.0
|
HE2
|
B:PHE69
|
4.8
|
22.4
|
1.0
|
CB
|
B:GLU32
|
4.8
|
16.4
|
1.0
|
O
|
B:GLU62
|
4.8
|
15.0
|
1.0
|
HG2
|
B:GLU62
|
4.8
|
24.5
|
1.0
|
CE1
|
Y:HIS65
|
5.0
|
23.0
|
1.0
|
N
|
B:GLU62
|
5.0
|
17.6
|
1.0
|
|
Iron binding site 6 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 6 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
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 Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe102
b:20.5
occ:1.00
|
OE1
|
Y:GLU62
|
1.9
|
20.4
|
1.0
|
OE2
|
B:GLU62
|
2.1
|
23.8
|
1.0
|
OE2
|
Y:GLU32
|
2.1
|
22.9
|
1.0
|
OE1
|
Y:GLU32
|
2.1
|
23.9
|
1.0
|
ND1
|
Y:HIS65
|
2.2
|
19.1
|
1.0
|
CD
|
Y:GLU32
|
2.4
|
20.6
|
1.0
|
O
|
B:HOH244
|
2.4
|
28.7
|
1.0
|
CD
|
B:GLU62
|
3.0
|
23.5
|
1.0
|
CE1
|
Y:HIS65
|
3.0
|
23.0
|
1.0
|
CD
|
Y:GLU62
|
3.1
|
21.3
|
1.0
|
HE1
|
Y:HIS65
|
3.2
|
27.6
|
1.0
|
HA
|
Y:GLU62
|
3.2
|
22.2
|
1.0
|
CG
|
Y:HIS65
|
3.2
|
19.9
|
1.0
|
HB2
|
Y:HIS65
|
3.3
|
22.3
|
1.0
|
OE1
|
B:GLU62
|
3.3
|
24.6
|
1.0
|
HB3
|
Y:HIS65
|
3.6
|
22.3
|
1.0
|
CB
|
Y:HIS65
|
3.6
|
18.6
|
1.0
|
HB3
|
Y:GLU62
|
3.7
|
18.5
|
1.0
|
HH
|
B:TYR39
|
3.7
|
23.8
|
1.0
|
OE2
|
Y:GLU62
|
3.7
|
22.1
|
1.0
|
HE2
|
B:TYR39
|
3.8
|
20.9
|
1.0
|
O
|
Y:HOH239
|
3.8
|
29.4
|
1.0
|
HG13
|
B:VAL58
|
3.8
|
21.5
|
1.0
|
CG
|
Y:GLU32
|
3.9
|
19.3
|
1.0
|
CA
|
Y:GLU62
|
4.1
|
18.5
|
1.0
|
FE
|
B:FE101
|
4.1
|
21.5
|
1.0
|
CB
|
Y:GLU62
|
4.1
|
15.4
|
1.0
|
CG
|
Y:GLU62
|
4.1
|
18.0
|
1.0
|
NE2
|
Y:HIS65
|
4.2
|
19.3
|
1.0
|
HG11
|
B:VAL58
|
4.2
|
21.5
|
1.0
|
O
|
B:HOH247
|
4.2
|
32.3
|
1.0
|
HG3
|
Y:GLU32
|
4.3
|
23.2
|
1.0
|
HA
|
Y:GLU32
|
4.3
|
22.2
|
1.0
|
CD2
|
Y:HIS65
|
4.3
|
19.6
|
1.0
|
HE1
|
B:HIS65
|
4.3
|
26.4
|
1.0
|
HG2
|
Y:GLU32
|
4.3
|
23.2
|
1.0
|
HG12
|
B:VAL58
|
4.3
|
21.5
|
1.0
|
CG1
|
B:VAL58
|
4.3
|
17.9
|
1.0
|
CG
|
B:GLU62
|
4.4
|
20.4
|
1.0
|
OH
|
B:TYR39
|
4.5
|
19.8
|
1.0
|
HB3
|
Y:GLU32
|
4.6
|
18.5
|
1.0
|
HG3
|
B:GLU62
|
4.6
|
24.5
|
1.0
|
HG2
|
B:GLU62
|
4.6
|
24.5
|
1.0
|
HG3
|
Y:GLU62
|
4.6
|
21.6
|
1.0
|
CE2
|
B:TYR39
|
4.7
|
17.4
|
1.0
|
CB
|
Y:GLU32
|
4.7
|
15.4
|
1.0
|
O
|
Y:GLU62
|
4.8
|
18.0
|
1.0
|
HE2
|
Y:PHE69
|
4.8
|
21.8
|
1.0
|
HG2
|
Y:GLU62
|
4.8
|
21.6
|
1.0
|
HE2
|
Y:HIS65
|
5.0
|
23.1
|
1.0
|
N
|
Y:GLU62
|
5.0
|
17.1
|
1.0
|
C
|
Y:GLU62
|
5.0
|
16.7
|
1.0
|
|
Iron binding site 7 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 7 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:19.9
occ:0.94
|
OE1
|
C:GLU62
|
1.9
|
24.8
|
1.0
|
OE2
|
H:GLU62
|
2.0
|
28.9
|
1.0
|
OE2
|
C:GLU32
|
2.1
|
22.1
|
1.0
|
ND1
|
C:HIS65
|
2.1
|
23.4
|
1.0
|
OE1
|
C:GLU32
|
2.2
|
27.4
|
1.0
|
O
|
C:HOH230
|
2.4
|
34.2
|
1.0
|
CD
|
C:GLU32
|
2.5
|
22.9
|
1.0
|
CD
|
H:GLU62
|
2.9
|
25.4
|
1.0
|
CE1
|
C:HIS65
|
3.0
|
23.8
|
1.0
|
CD
|
C:GLU62
|
3.1
|
24.3
|
1.0
|
HE1
|
C:HIS65
|
3.1
|
28.6
|
1.0
|
CG
|
C:HIS65
|
3.2
|
24.7
|
1.0
|
OE1
|
H:GLU62
|
3.3
|
24.0
|
1.0
|
HA
|
C:GLU62
|
3.3
|
23.9
|
1.0
|
HB2
|
C:HIS65
|
3.3
|
26.2
|
1.0
|
HB3
|
C:HIS65
|
3.6
|
26.2
|
1.0
|
CB
|
C:HIS65
|
3.6
|
21.8
|
1.0
|
OE2
|
C:GLU62
|
3.7
|
28.2
|
1.0
|
HH
|
H:TYR39
|
3.7
|
28.9
|
1.0
|
HE2
|
H:TYR39
|
3.8
|
27.6
|
1.0
|
HB3
|
C:GLU62
|
3.8
|
22.4
|
1.0
|
HG13
|
H:VAL58
|
3.8
|
32.8
|
1.0
|
O
|
C:HOH228
|
3.9
|
28.2
|
1.0
|
CG
|
C:GLU32
|
4.0
|
22.2
|
1.0
|
CA
|
C:GLU62
|
4.1
|
19.9
|
1.0
|
FE
|
C:FE102
|
4.1
|
23.6
|
1.0
|
NE2
|
C:HIS65
|
4.2
|
26.7
|
1.0
|
CB
|
C:GLU62
|
4.2
|
18.7
|
1.0
|
CG
|
C:GLU62
|
4.2
|
21.8
|
1.0
|
HG11
|
H:VAL58
|
4.2
|
32.8
|
1.0
|
O
|
H:HOH239
|
4.2
|
36.7
|
1.0
|
CD2
|
C:HIS65
|
4.3
|
26.2
|
1.0
|
CG
|
H:GLU62
|
4.3
|
25.2
|
1.0
|
HG12
|
H:VAL58
|
4.3
|
32.8
|
1.0
|
CG1
|
H:VAL58
|
4.3
|
27.3
|
1.0
|
HE1
|
H:HIS65
|
4.3
|
30.3
|
1.0
|
HG3
|
C:GLU32
|
4.3
|
26.7
|
1.0
|
HG2
|
C:GLU32
|
4.4
|
26.7
|
1.0
|
HA
|
C:GLU32
|
4.4
|
28.9
|
1.0
|
HG3
|
H:GLU62
|
4.5
|
30.2
|
1.0
|
HG2
|
H:GLU62
|
4.5
|
30.2
|
1.0
|
OH
|
H:TYR39
|
4.5
|
24.0
|
1.0
|
CE2
|
H:TYR39
|
4.6
|
23.0
|
1.0
|
HB3
|
C:GLU32
|
4.7
|
27.3
|
1.0
|
HG3
|
C:GLU62
|
4.7
|
26.2
|
1.0
|
HE2
|
C:PHE69
|
4.7
|
25.7
|
1.0
|
CB
|
C:GLU32
|
4.8
|
22.8
|
1.0
|
O
|
C:GLU62
|
4.8
|
21.6
|
1.0
|
HG2
|
C:GLU62
|
4.8
|
26.2
|
1.0
|
HE2
|
C:HIS65
|
4.9
|
32.0
|
1.0
|
|
Iron binding site 8 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 8 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe102
b:23.6
occ:1.00
|
OE1
|
H:GLU62
|
1.9
|
24.0
|
1.0
|
OE2
|
C:GLU62
|
2.1
|
28.2
|
1.0
|
OE1
|
H:GLU32
|
2.1
|
24.7
|
1.0
|
OE2
|
H:GLU32
|
2.1
|
24.2
|
1.0
|
ND1
|
H:HIS65
|
2.2
|
22.3
|
1.0
|
O
|
C:HOH228
|
2.4
|
28.2
|
1.0
|
CD
|
H:GLU32
|
2.4
|
21.5
|
1.0
|
CD
|
H:GLU62
|
3.0
|
25.4
|
1.0
|
CD
|
C:GLU62
|
3.1
|
24.3
|
1.0
|
CE1
|
H:HIS65
|
3.1
|
25.2
|
1.0
|
HA
|
H:GLU62
|
3.2
|
26.6
|
1.0
|
HE1
|
H:HIS65
|
3.2
|
30.3
|
1.0
|
CG
|
H:HIS65
|
3.3
|
22.5
|
1.0
|
HB2
|
H:HIS65
|
3.3
|
25.7
|
1.0
|
OE1
|
C:GLU62
|
3.4
|
24.8
|
1.0
|
HB3
|
H:HIS65
|
3.6
|
25.7
|
1.0
|
CB
|
H:HIS65
|
3.6
|
21.4
|
1.0
|
HB3
|
H:GLU62
|
3.7
|
22.1
|
1.0
|
HH
|
C:TYR39
|
3.7
|
26.3
|
1.0
|
OE2
|
H:GLU62
|
3.7
|
28.9
|
1.0
|
HE2
|
C:TYR39
|
3.8
|
24.1
|
1.0
|
O
|
C:HOH230
|
3.9
|
34.2
|
1.0
|
HG13
|
C:VAL58
|
3.9
|
23.8
|
1.0
|
CG
|
H:GLU32
|
3.9
|
20.3
|
1.0
|
CA
|
H:GLU62
|
4.0
|
22.2
|
1.0
|
CB
|
H:GLU62
|
4.1
|
18.4
|
1.0
|
CG
|
H:GLU62
|
4.1
|
25.2
|
1.0
|
FE
|
C:FE101
|
4.1
|
19.9
|
0.9
|
HE1
|
C:HIS65
|
4.2
|
28.6
|
1.0
|
NE2
|
H:HIS65
|
4.3
|
25.4
|
1.0
|
O
|
C:HOH223
|
4.3
|
31.4
|
1.0
|
HG3
|
H:GLU32
|
4.3
|
24.4
|
1.0
|
HA
|
H:GLU32
|
4.3
|
21.6
|
1.0
|
HG11
|
C:VAL58
|
4.3
|
23.8
|
1.0
|
HG2
|
H:GLU32
|
4.3
|
24.4
|
1.0
|
CD2
|
H:HIS65
|
4.4
|
24.3
|
1.0
|
HG12
|
C:VAL58
|
4.4
|
23.8
|
1.0
|
CG1
|
C:VAL58
|
4.4
|
19.8
|
1.0
|
CG
|
C:GLU62
|
4.4
|
21.8
|
1.0
|
OH
|
C:TYR39
|
4.5
|
21.9
|
1.0
|
HB3
|
H:GLU32
|
4.5
|
23.7
|
1.0
|
HG3
|
C:GLU62
|
4.6
|
26.2
|
1.0
|
HG2
|
C:GLU62
|
4.6
|
26.2
|
1.0
|
HG3
|
H:GLU62
|
4.6
|
30.2
|
1.0
|
CE2
|
C:TYR39
|
4.7
|
20.1
|
1.0
|
CB
|
H:GLU32
|
4.7
|
19.8
|
1.0
|
O
|
H:GLU62
|
4.7
|
21.7
|
1.0
|
HE2
|
H:PHE69
|
4.7
|
26.4
|
1.0
|
HG2
|
H:GLU62
|
4.8
|
30.2
|
1.0
|
C
|
H:GLU62
|
4.9
|
19.9
|
1.0
|
N
|
H:GLU62
|
4.9
|
16.9
|
1.0
|
CE1
|
C:HIS65
|
5.0
|
23.8
|
1.0
|
|
Iron binding site 9 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 9 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe101
b:19.0
occ:0.93
|
OE1
|
D:GLU62
|
1.9
|
27.6
|
1.0
|
OE2
|
J:GLU62
|
2.0
|
26.4
|
1.0
|
OE1
|
D:GLU32
|
2.1
|
21.2
|
1.0
|
OE2
|
D:GLU32
|
2.1
|
24.8
|
1.0
|
ND1
|
D:HIS65
|
2.2
|
23.6
|
1.0
|
O
|
J:HOH220
|
2.3
|
28.8
|
1.0
|
CD
|
D:GLU32
|
2.4
|
23.6
|
1.0
|
CD
|
J:GLU62
|
3.0
|
24.3
|
1.0
|
CD
|
D:GLU62
|
3.0
|
21.7
|
1.0
|
CE1
|
D:HIS65
|
3.1
|
23.7
|
1.0
|
HE1
|
D:HIS65
|
3.2
|
28.4
|
1.0
|
HA
|
D:GLU62
|
3.2
|
25.1
|
1.0
|
CG
|
D:HIS65
|
3.2
|
20.5
|
1.0
|
HB2
|
D:HIS65
|
3.3
|
25.7
|
1.0
|
OE1
|
J:GLU62
|
3.3
|
25.9
|
1.0
|
HB3
|
D:HIS65
|
3.6
|
25.7
|
1.0
|
CB
|
D:HIS65
|
3.6
|
21.4
|
1.0
|
OE2
|
D:GLU62
|
3.7
|
27.1
|
1.0
|
HB3
|
D:GLU62
|
3.7
|
22.6
|
1.0
|
HH
|
J:TYR39
|
3.7
|
30.9
|
1.0
|
O
|
D:HOH231
|
3.8
|
27.8
|
1.0
|
HE2
|
J:TYR39
|
3.8
|
24.8
|
1.0
|
HG13
|
J:VAL58
|
3.8
|
25.3
|
1.0
|
CG
|
D:GLU32
|
3.9
|
21.8
|
1.0
|
O
|
J:HOH243
|
4.0
|
36.0
|
1.0
|
CA
|
D:GLU62
|
4.1
|
20.9
|
1.0
|
FE
|
D:FE102
|
4.1
|
20.4
|
0.9
|
CB
|
D:GLU62
|
4.1
|
18.8
|
1.0
|
CG
|
D:GLU62
|
4.1
|
24.9
|
1.0
|
HG11
|
J:VAL58
|
4.2
|
25.3
|
1.0
|
NE2
|
D:HIS65
|
4.2
|
26.7
|
1.0
|
HE1
|
J:HIS65
|
4.2
|
27.6
|
1.0
|
HG12
|
J:VAL58
|
4.3
|
25.3
|
1.0
|
HG3
|
D:GLU32
|
4.3
|
26.2
|
1.0
|
CG1
|
J:VAL58
|
4.3
|
21.1
|
1.0
|
HA
|
D:GLU32
|
4.3
|
24.2
|
1.0
|
CG
|
J:GLU62
|
4.3
|
18.1
|
1.0
|
CD2
|
D:HIS65
|
4.3
|
23.4
|
1.0
|
HG2
|
D:GLU32
|
4.3
|
26.2
|
1.0
|
HG3
|
J:GLU62
|
4.5
|
21.7
|
1.0
|
OH
|
J:TYR39
|
4.5
|
25.8
|
1.0
|
HG2
|
J:GLU62
|
4.5
|
21.7
|
1.0
|
HB3
|
D:GLU32
|
4.6
|
18.7
|
1.0
|
HG3
|
D:GLU62
|
4.6
|
29.8
|
1.0
|
CE2
|
J:TYR39
|
4.7
|
20.7
|
1.0
|
CB
|
D:GLU32
|
4.7
|
15.6
|
1.0
|
HG2
|
D:GLU62
|
4.8
|
29.8
|
1.0
|
O
|
D:GLU62
|
4.8
|
21.2
|
1.0
|
HE2
|
D:PHE69
|
4.9
|
28.4
|
1.0
|
N
|
D:GLU62
|
5.0
|
22.4
|
1.0
|
C
|
D:GLU62
|
5.0
|
19.9
|
1.0
|
CE1
|
J:HIS65
|
5.0
|
23.0
|
1.0
|
|
Iron binding site 10 out
of 30 in 5n5e
Go back to
Iron Binding Sites List in 5n5e
Iron binding site 10 out
of 30 in the Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Crystal Structure of Encapsulated Ferritin Domain From Pyrococcus Furiosus PFC_05175 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe102
b:20.4
occ:0.94
|
OE2
|
D:GLU62
|
1.9
|
27.1
|
1.0
|
OE1
|
J:GLU62
|
1.9
|
25.9
|
1.0
|
OE1
|
J:GLU32
|
2.2
|
25.7
|
1.0
|
OE2
|
J:GLU32
|
2.2
|
25.8
|
1.0
|
ND1
|
J:HIS65
|
2.2
|
23.6
|
1.0
|
O
|
D:HOH231
|
2.4
|
27.8
|
1.0
|
CD
|
J:GLU32
|
2.5
|
19.8
|
1.0
|
CD
|
D:GLU62
|
2.9
|
21.7
|
1.0
|
CE1
|
J:HIS65
|
3.0
|
23.0
|
1.0
|
CD
|
J:GLU62
|
3.0
|
24.3
|
1.0
|
HE1
|
J:HIS65
|
3.1
|
27.6
|
1.0
|
HA
|
J:GLU62
|
3.2
|
21.4
|
1.0
|
CG
|
J:HIS65
|
3.3
|
21.0
|
1.0
|
OE1
|
D:GLU62
|
3.3
|
27.6
|
1.0
|
HB2
|
J:HIS65
|
3.4
|
25.2
|
1.0
|
HB3
|
J:GLU62
|
3.7
|
22.5
|
1.0
|
HB3
|
J:HIS65
|
3.7
|
25.2
|
1.0
|
HH
|
D:TYR39
|
3.7
|
27.0
|
1.0
|
CB
|
J:HIS65
|
3.7
|
21.0
|
1.0
|
OE2
|
J:GLU62
|
3.7
|
26.4
|
1.0
|
O
|
J:HOH220
|
3.7
|
28.8
|
1.0
|
HE2
|
D:TYR39
|
3.8
|
23.2
|
1.0
|
HG13
|
D:VAL58
|
3.8
|
26.7
|
1.0
|
CG
|
J:GLU32
|
4.0
|
22.3
|
1.0
|
O
|
D:HOH232
|
4.1
|
32.2
|
1.0
|
CA
|
J:GLU62
|
4.1
|
17.8
|
1.0
|
FE
|
D:FE101
|
4.1
|
19.0
|
0.9
|
CB
|
J:GLU62
|
4.1
|
18.7
|
1.0
|
CG
|
J:GLU62
|
4.1
|
18.1
|
1.0
|
NE2
|
J:HIS65
|
4.2
|
26.5
|
1.0
|
HG11
|
D:VAL58
|
4.2
|
26.7
|
1.0
|
CG
|
D:GLU62
|
4.3
|
24.9
|
1.0
|
HE1
|
D:HIS65
|
4.3
|
28.4
|
1.0
|
CG1
|
D:VAL58
|
4.3
|
22.2
|
1.0
|
HA
|
J:GLU32
|
4.3
|
23.8
|
1.0
|
HG12
|
D:VAL58
|
4.3
|
26.7
|
1.0
|
CD2
|
J:HIS65
|
4.4
|
24.5
|
1.0
|
HG3
|
J:GLU32
|
4.4
|
26.8
|
1.0
|
HG2
|
J:GLU32
|
4.4
|
26.8
|
1.0
|
HG3
|
D:GLU62
|
4.5
|
29.8
|
1.0
|
HG2
|
D:GLU62
|
4.5
|
29.8
|
1.0
|
OH
|
D:TYR39
|
4.5
|
22.5
|
1.0
|
HG3
|
J:GLU62
|
4.6
|
21.7
|
1.0
|
CE2
|
D:TYR39
|
4.6
|
19.3
|
1.0
|
HB3
|
J:GLU32
|
4.6
|
23.4
|
1.0
|
CB
|
J:GLU32
|
4.8
|
19.5
|
1.0
|
O
|
J:GLU62
|
4.8
|
19.2
|
1.0
|
HG2
|
J:GLU62
|
4.8
|
21.7
|
1.0
|
HE2
|
J:PHE69
|
4.8
|
27.1
|
1.0
|
HE2
|
J:HIS65
|
5.0
|
31.8
|
1.0
|
C
|
J:GLU62
|
5.0
|
19.9
|
1.0
|
N
|
J:GLU62
|
5.0
|
17.7
|
1.0
|
|
Reference:
D.He,
C.Piergentili,
J.Ross,
E.Tarrant,
L.R.Tuck,
C.L.Mackay,
Z.Mciver,
K.J.Waldron,
D.J.Clarke,
J.Marles-Wright.
Conservation of the Structural and Functional Architecture of Encapsulated Ferritins in Bacteria and Archaea. Biochem.J. V. 476 975 2019.
ISSN: ESSN 1470-8728
PubMed: 30837306
DOI: 10.1042/BCJ20180922
Page generated: Tue Aug 6 06:03:17 2024
|