Iron in PDB 7ke3: Heavy Chain Ferritin with C-Terminal EBNA1 Epitope

Enzymatic activity of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope

All present enzymatic activity of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope:
1.16.3.1;

Protein crystallography data

The structure of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope, PDB code: 7ke3 was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 2.20
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 217.882, 217.882, 147.203, 90, 90, 90
R / Rfree (%) 24.1 / 27.1

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope (pdb code 7ke3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope, PDB code: 7ke3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 7ke3

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Iron binding site 1 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:30.5
occ:0.99
 OE2 A:GLU27 2.0 26.6 1.0
OE2 A:GLU62 2.0 23.4 1.0
ND1 A:HIS65 2.2 26.9 1.0
CD A:GLU62 2.8 25.1 1.0
CD A:GLU27 3.0 25.8 1.0
OE1 A:GLU62 3.1 32.4 1.0
CE1 A:HIS65 3.2 29.6 1.0
CG A:HIS65 3.2 28.0 1.0
OE1 A:GLU27 3.4 24.9 1.0
CB A:HIS65 3.5 21.1 1.0
OE1 A:GLN141 3.7 30.3 1.0
CG1 A:VAL110 4.1 22.6 1.0
CG A:GLU62 4.2 25.8 1.0
NE2 A:HIS65 4.3 35.1 1.0
CG A:GLU27 4.3 24.5 1.0
CA A:GLU62 4.3 25.8 1.0
CD2 A:HIS65 4.3 26.9 1.0
CB A:GLU62 4.5 23.8 1.0
CB A:GLU27 4.6 22.8 1.0
CD A:GLN141 4.7 25.5 1.0
O A:GLU62 4.8 27.1 1.0
CA A:HIS65 5.0 24.7 1.0

Iron binding site 2 out of 20 in 7ke3

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Iron binding site 2 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:35.0
occ:0.71
 OD1 A:ASP131 2.3 28.4 1.0
OE1 H:GLU134 2.5 29.6 1.0
OD1 H:ASP131 2.5 28.9 1.0
OE1 A:GLU134 2.6 32.5 1.0
CG A:ASP131 3.5 28.8 1.0
CG H:ASP131 3.7 28.5 1.0
CD H:GLU134 3.7 26.7 1.0
CD A:GLU134 3.8 30.4 1.0
CB A:ASP131 4.1 25.1 1.0
CB H:ASP131 4.3 29.2 1.0
OE2 H:GLU134 4.4 29.7 1.0
OE2 A:GLU134 4.5 26.9 1.0
CA A:ASP131 4.5 25.1 1.0
OD2 A:ASP131 4.5 29.5 1.0
OD2 H:ASP131 4.7 28.5 1.0
CA H:ASP131 4.7 25.6 1.0
CB H:GLU134 4.7 27.1 1.0
CG H:GLU134 4.8 27.6 1.0
CB A:GLU134 4.9 26.3 1.0
CG A:GLU134 5.0 27.0 1.0

Iron binding site 3 out of 20 in 7ke3

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Iron binding site 3 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.8
occ:0.87
 OE2 B:GLU62 1.9 31.0 1.0
OE2 B:GLU27 2.0 25.1 1.0
ND1 B:HIS65 2.2 29.0 1.0
CD B:GLU62 2.7 27.8 1.0
OE1 B:GLU62 2.9 35.9 1.0
CD B:GLU27 3.1 25.2 1.0
CE1 B:HIS65 3.1 34.5 1.0
CG B:HIS65 3.2 29.8 1.0
OE1 B:GLU27 3.5 23.3 1.0
CB B:HIS65 3.5 22.9 1.0
OE1 B:GLN141 3.7 29.5 1.0
CG B:GLU62 4.1 25.8 1.0
CG1 B:VAL110 4.1 19.9 1.0
NE2 B:HIS65 4.3 36.3 1.0
O B:HOH411 4.3 35.3 1.0
O B:HOH438 4.3 37.5 1.0
CD2 B:HIS65 4.3 29.2 1.0
CA B:GLU62 4.4 27.1 1.0
CG B:GLU27 4.4 24.1 1.0
CB B:GLU62 4.5 26.0 1.0
CD B:GLN141 4.7 25.1 1.0
CB B:GLU27 4.7 22.2 1.0
O B:GLU62 4.9 22.9 1.0

Iron binding site 4 out of 20 in 7ke3

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Iron binding site 4 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:25.9
occ:0.70
 NE2 B:HIS173 2.2 33.8 1.0
NE2 J:HIS173 2.2 33.8 1.0
NE2 D:HIS173 2.3 27.8 1.0
O D:HOH453 2.3 15.4 1.0
NE2 H:HIS173 2.3 31.6 1.0
CE1 J:HIS173 2.5 29.4 1.0
CE1 B:HIS173 2.6 29.8 1.0
CE1 D:HIS173 2.7 28.3 1.0
CE1 H:HIS173 2.7 31.4 1.0
CD2 B:HIS173 3.5 26.8 1.0
CD2 D:HIS173 3.6 26.2 1.0
CD2 J:HIS173 3.6 23.8 1.0
CD2 H:HIS173 3.6 29.1 1.0
ND1 J:HIS173 3.8 29.8 1.0
ND1 B:HIS173 3.9 31.4 1.0
ND1 D:HIS173 4.0 30.1 1.0
ND1 H:HIS173 4.0 31.2 1.0
CG J:HIS173 4.3 26.5 1.0
CG B:HIS173 4.4 27.5 1.0
CG D:HIS173 4.4 26.9 1.0
CG H:HIS173 4.5 27.4 1.0

Iron binding site 5 out of 20 in 7ke3

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Iron binding site 5 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:35.8
occ:0.66
 OE1 L:GLU134 2.3 31.4 1.0
OD1 L:ASP131 2.4 28.9 1.0
OE2 C:GLU134 2.4 33.6 1.0
OD1 J:ASP131 2.4 32.2 1.0
OE1 J:GLU134 3.1 34.2 1.0
OD1 C:ASP131 3.1 33.2 1.0
CG L:ASP131 3.5 28.2 1.0
CD L:GLU134 3.6 26.8 1.0
CD C:GLU134 3.6 30.6 1.0
CG J:ASP131 3.6 31.1 1.0
O L:HOH446 3.8 40.2 1.0
CB L:ASP131 4.1 27.1 1.0
CB J:ASP131 4.2 27.6 1.0
OE2 L:GLU134 4.2 28.7 1.0
OE1 C:GLU134 4.3 29.4 1.0
CG C:ASP131 4.3 33.6 1.0
CD J:GLU134 4.3 28.8 1.0
CA L:ASP131 4.4 25.4 1.0
OD2 L:ASP131 4.5 27.4 1.0
CB L:GLU134 4.5 26.0 1.0
OD2 J:ASP131 4.6 29.3 1.0
CB C:GLU134 4.6 24.1 1.0
CG L:GLU134 4.7 24.4 1.0
CG C:GLU134 4.7 26.9 1.0
CA J:ASP131 4.7 24.1 1.0
CB C:ASP131 4.8 25.7 1.0
CA C:ASP131 4.9 23.9 1.0

Iron binding site 6 out of 20 in 7ke3

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Iron binding site 6 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe303

b:27.9
occ:0.85
 OE2 C:GLU62 2.0 31.1 1.0
OE2 C:GLU27 2.0 29.3 1.0
ND1 C:HIS65 2.1 25.8 1.0
CD C:GLU62 2.9 29.4 1.0
CE1 C:HIS65 3.0 32.9 1.0
CG C:HIS65 3.1 27.6 1.0
CD C:GLU27 3.1 24.7 1.0
OE1 C:GLU62 3.2 34.2 1.0
CB C:HIS65 3.5 24.1 1.0
OE1 C:GLU27 3.6 24.9 1.0
OE1 C:GLN141 3.8 30.5 1.0
NE2 C:HIS65 4.1 36.8 1.0
CG1 C:VAL110 4.1 18.9 1.0
CD2 C:HIS65 4.2 32.5 1.0
CG C:GLU62 4.2 27.9 1.0
O C:HOH429 4.3 32.0 1.0
CA C:GLU62 4.3 27.1 1.0
O C:HOH427 4.4 32.1 1.0
CG C:GLU27 4.4 26.2 1.0
CB C:GLU62 4.5 25.4 1.0
CB C:GLU27 4.7 21.4 1.0
CD C:GLN141 4.8 26.9 1.0
O C:GLU62 4.9 20.5 1.0
CA C:HIS65 5.0 24.8 1.0

Iron binding site 7 out of 20 in 7ke3

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Iron binding site 7 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe304

b:31.9
occ:0.41
 NE2 C:HIS173 2.1 29.0 1.0
O C:HOH450 2.2 16.0 0.5
NE2 K:HIS173 2.3 33.7 1.0
CE1 C:HIS173 2.5 27.4 1.0
CE1 K:HIS173 2.5 28.8 1.0
CD2 C:HIS173 3.4 28.4 1.0
CD2 K:HIS173 3.6 27.8 1.0
ND1 C:HIS173 3.8 28.9 1.0
ND1 K:HIS173 3.8 33.4 1.0
CG C:HIS173 4.2 30.2 1.0
CG K:HIS173 4.4 29.2 1.0

Iron binding site 8 out of 20 in 7ke3

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Iron binding site 8 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:36.7
occ:0.76
 OD1 D:ASP131 2.4 29.5 1.0
OE1 G:GLU134 2.4 35.2 1.0
OE1 D:GLU134 2.5 36.0 1.0
OD1 G:ASP131 2.9 30.4 1.0
CG D:ASP131 3.6 29.9 1.0
CD G:GLU134 3.7 28.9 1.0
CD D:GLU134 3.8 31.4 1.0
CG G:ASP131 4.0 33.1 1.0
CB D:ASP131 4.2 27.5 1.0
OE2 G:GLU134 4.3 29.7 1.0
CB G:ASP131 4.4 25.9 1.0
OE2 D:GLU134 4.5 29.4 1.0
CA D:ASP131 4.5 26.4 1.0
OD2 D:ASP131 4.6 28.6 1.0
CA G:ASP131 4.7 24.6 1.0
CB G:GLU134 4.7 26.5 1.0
CB D:GLU134 4.8 28.5 1.0
CG G:GLU134 4.8 28.9 1.0
CG D:GLU134 4.9 27.3 1.0

Iron binding site 9 out of 20 in 7ke3

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Iron binding site 9 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:31.5
occ:1.00
 OE2 D:GLU27 1.9 27.5 1.0
OE2 D:GLU62 2.0 22.7 1.0
ND1 D:HIS65 2.1 27.4 1.0
CD D:GLU62 2.9 25.5 1.0
CD D:GLU27 3.0 23.7 1.0
CE1 D:HIS65 3.0 30.8 1.0
CG D:HIS65 3.1 28.3 1.0
OE1 D:GLU62 3.2 29.5 1.0
OE1 D:GLU27 3.3 23.6 1.0
CB D:HIS65 3.4 21.9 1.0
OE1 D:GLN141 3.8 29.7 1.0
O D:HOH409 4.0 32.6 1.0
CG1 D:VAL110 4.1 21.7 1.0
NE2 D:HIS65 4.2 34.5 1.0
CD2 D:HIS65 4.2 28.6 1.0
CG D:GLU62 4.3 24.3 1.0
CG D:GLU27 4.3 24.2 1.0
CA D:GLU62 4.4 26.8 1.0
CB D:GLU62 4.6 26.7 1.0
CB D:GLU27 4.6 21.0 1.0
CD D:GLN141 4.7 28.1 1.0
O D:GLU62 4.9 21.4 1.0
CA D:HIS65 5.0 23.7 1.0

Iron binding site 10 out of 20 in 7ke3

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Iron binding site 10 out of 20 in the Heavy Chain Ferritin with C-Terminal EBNA1 Epitope


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Heavy Chain Ferritin with C-Terminal EBNA1 Epitope within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:25.9
occ:0.36
 NE2 E:HIS173 2.2 31.1 1.0
NE2 A:HIS173 2.2 29.8 1.0
O E:HOH455 2.3 17.1 0.5
CE1 A:HIS173 2.6 29.4 1.0
CE1 E:HIS173 2.6 26.9 1.0
CD2 E:HIS173 3.5 25.2 1.0
CD2 A:HIS173 3.5 24.6 1.0
ND1 A:HIS173 3.9 30.2 1.0
ND1 E:HIS173 3.9 29.2 1.0
CG E:HIS173 4.3 25.4 1.0
CG A:HIS173 4.4 25.0 1.0

Reference:

Y.Qu, B.Zhang, Y.Wang, S.Yin, J.L.Pederick, J.B.Bruning, Y.Sun, A.Middelberg, J.Bi. Immunogenicity Study of Engineered Ferritins with C- and N-Terminus Insertion of Epstein-Barr Nuclear Antigen 1 Epitope. Vaccine V. 39 4830 2021.
ISSN: ESSN 1873-2518
PubMed: 34284876
DOI: 10.1016/J.VACCINE.2021.07.021
Page generated: Fri Sep 24 14:08:35 2021

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