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Iron in PDB 33bf: Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment

Enzymatic activity of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment

All present enzymatic activity of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment:
1.16.3.1;

Iron Binding Sites:

The binding sites of Iron atom in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment (pdb code 33bf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment, PDB code: 33bf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 33bf

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Iron binding site 1 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe901

b:172.6
occ:1.00
 OE2 F:GLU62 2.0 149.9 1.0
OE2 A:GLU32 2.0 143.1 1.0
OE1 A:GLU62 2.0 148.5 1.0
ND1 A:HIS65 2.0 133.0 1.0
CD A:GLU32 2.7 142.2 1.0
CE1 A:HIS65 2.8 134.2 1.0
OE1 A:GLU32 2.8 144.4 1.0
CD A:GLU62 2.9 144.6 1.0
CD F:GLU62 3.1 143.2 1.0
CG A:HIS65 3.2 124.1 1.0
OE2 A:GLU62 3.2 151.8 1.0
CB A:HIS65 3.7 122.0 1.0
OE1 F:GLU62 3.8 146.6 1.0
NE2 A:HIS65 4.0 132.3 1.0
FE F:FE901 4.0 170.1 1.0
CG F:GLU62 4.1 129.0 1.0
CG A:GLU62 4.1 129.2 1.0
CG A:GLU32 4.2 137.6 1.0
CD2 A:HIS65 4.2 125.9 1.0
CA A:GLU62 4.4 121.3 1.0
CB A:GLU62 4.5 121.2 1.0
OH F:TYR39 4.9 125.8 1.0
CB A:GLU32 5.0 127.7 1.0
CE1 F:HIS65 5.0 130.6 1.0

Iron binding site 2 out of 10 in 33bf

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Iron binding site 2 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe901

b:168.0
occ:1.00
 OE1 B:GLU32 1.9 142.4 1.0
OE2 J:GLU62 1.9 148.6 1.0
OE1 B:GLU62 2.0 149.4 1.0
ND1 B:HIS65 2.0 130.3 1.0
CD B:GLU32 2.6 139.5 1.0
OE2 B:GLU32 2.7 139.5 1.0
CE1 B:HIS65 2.9 129.5 1.0
CD B:GLU62 3.0 145.7 1.0
CD J:GLU62 3.1 143.0 1.0
CG B:HIS65 3.1 123.3 1.0
OE2 B:GLU62 3.4 151.6 1.0
CB B:HIS65 3.6 120.0 1.0
OE1 J:GLU62 3.8 145.9 1.0
NE2 B:HIS65 4.0 128.8 1.0
CG B:GLU32 4.1 133.3 1.0
FE J:FE901 4.1 169.1 1.0
CG J:GLU62 4.1 131.7 1.0
CD2 B:HIS65 4.2 124.0 1.0
CG B:GLU62 4.2 133.6 1.0
CA B:GLU62 4.3 124.7 1.0
CB B:GLU62 4.5 126.2 1.0
OH J:TYR39 4.8 128.1 1.0
CB B:GLU32 4.8 121.6 1.0

Iron binding site 3 out of 10 in 33bf

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Iron binding site 3 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe901

b:170.2
occ:1.00
 OE2 I:GLU62 2.0 151.9 1.0
OE1 C:GLU32 2.0 140.2 1.0
OE1 C:GLU62 2.0 145.8 1.0
ND1 C:HIS65 2.0 130.4 1.0
CD C:GLU32 2.7 140.8 1.0
CE1 C:HIS65 2.8 131.8 1.0
OE2 C:GLU32 2.9 142.2 1.0
CD C:GLU62 2.9 144.3 1.0
CD I:GLU62 3.0 146.0 1.0
OE2 C:GLU62 3.2 151.6 1.0
CG C:HIS65 3.2 122.1 1.0
CB C:HIS65 3.7 120.7 1.0
OE1 I:GLU62 3.7 149.0 1.0
FE I:FE901 4.0 168.7 1.0
NE2 C:HIS65 4.0 130.2 1.0
CG I:GLU62 4.0 133.8 1.0
CG C:GLU32 4.2 135.7 1.0
CG C:GLU62 4.2 131.9 1.0
CD2 C:HIS65 4.2 124.2 1.0
CA C:GLU62 4.4 123.0 1.0
CB C:GLU62 4.5 124.2 1.0
CE1 I:HIS65 4.9 132.2 1.0
OH I:TYR39 5.0 126.0 1.0
CB C:GLU32 5.0 124.2 1.0

Iron binding site 4 out of 10 in 33bf

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Iron binding site 4 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe901

b:168.3
occ:1.00
 OE2 H:GLU62 2.0 149.1 1.0
OE1 D:GLU62 2.0 145.2 1.0
ND1 D:HIS65 2.1 130.1 1.0
OE1 D:GLU32 2.1 136.7 1.0
CD D:GLU32 2.3 137.2 1.0
OE2 D:GLU32 2.3 139.2 1.0
CE1 D:HIS65 2.9 130.9 1.0
CD D:GLU62 3.1 141.2 1.0
CG D:HIS65 3.2 121.3 1.0
CD H:GLU62 3.2 142.9 1.0
CG D:GLU32 3.4 127.8 1.0
OE2 D:GLU62 3.5 148.5 1.0
CB D:HIS65 3.6 119.2 1.0
OE1 H:GLU62 4.0 147.8 1.0
NE2 D:HIS65 4.1 126.7 1.0
CG H:GLU62 4.1 128.0 1.0
CD2 D:HIS65 4.2 120.0 1.0
FE H:FE901 4.2 172.0 1.0
CG D:GLU62 4.3 128.4 1.0
CA D:GLU62 4.4 120.0 1.0
CB D:GLU62 4.5 121.0 1.0
CB D:GLU32 4.7 121.2 1.0
OH H:TYR39 4.7 124.0 1.0
CE2 H:TYR39 4.9 122.4 1.0

Iron binding site 5 out of 10 in 33bf

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Iron binding site 5 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe901

b:174.9
occ:1.00
 OE1 E:GLU62 1.9 148.9 1.0
OE2 G:GLU62 2.0 148.7 1.0
OE2 E:GLU32 2.0 141.2 1.0
ND1 E:HIS65 2.0 132.3 1.0
CD E:GLU32 2.7 139.3 1.0
OE1 E:GLU32 2.7 140.4 1.0
CE1 E:HIS65 2.8 132.8 1.0
CD E:GLU62 2.9 144.0 1.0
CD G:GLU62 3.1 142.2 1.0
CG E:HIS65 3.2 122.3 1.0
OE2 E:GLU62 3.2 149.6 1.0
CB E:HIS65 3.7 121.0 1.0
OE1 G:GLU62 3.8 145.3 1.0
NE2 E:HIS65 4.0 129.4 1.0
CG G:GLU62 4.1 129.5 1.0
CG E:GLU32 4.1 132.6 1.0
FE G:FE901 4.1 169.0 1.0
CG E:GLU62 4.2 130.4 1.0
CD2 E:HIS65 4.2 121.4 1.0
CA E:GLU62 4.4 121.4 1.0
CB E:GLU62 4.5 122.1 1.0
OH G:TYR39 4.9 124.0 1.0
CB E:GLU32 4.9 121.4 1.0
CE1 G:HIS65 5.0 132.5 1.0

Iron binding site 6 out of 10 in 33bf

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Iron binding site 6 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe901

b:170.1
occ:1.00
 OE1 F:GLU32 2.0 136.9 1.0
OE2 A:GLU62 2.0 151.8 1.0
OE1 F:GLU62 2.0 146.6 1.0
ND1 F:HIS65 2.0 129.8 1.0
CD F:GLU32 2.6 135.7 1.0
OE2 F:GLU32 2.7 137.3 1.0
CE1 F:HIS65 2.9 130.6 1.0
CD F:GLU62 2.9 143.2 1.0
CD A:GLU62 3.1 144.6 1.0
CG F:HIS65 3.2 120.7 1.0
OE2 F:GLU62 3.3 149.9 1.0
CB F:HIS65 3.7 119.2 1.0
OE1 A:GLU62 3.9 148.5 1.0
FE A:FE901 4.0 172.6 1.0
NE2 F:HIS65 4.0 126.6 1.0
CG A:GLU62 4.1 129.2 1.0
CG F:GLU32 4.1 131.7 1.0
CG F:GLU62 4.2 129.0 1.0
CD2 F:HIS65 4.2 120.3 1.0
CA F:GLU62 4.4 120.5 1.0
CB F:GLU62 4.5 121.7 1.0
CB F:GLU32 4.9 122.1 1.0
OH A:TYR39 4.9 124.0 1.0

Iron binding site 7 out of 10 in 33bf

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Iron binding site 7 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe901

b:169.0
occ:1.00
 OE1 G:GLU62 2.0 145.3 1.0
OE2 G:GLU32 2.0 141.2 1.0
OE2 E:GLU62 2.0 149.6 1.0
ND1 G:HIS65 2.1 131.2 1.0
OE1 G:GLU32 2.5 139.3 1.0
CD G:GLU32 2.6 139.1 1.0
CE1 G:HIS65 2.9 132.5 1.0
CD G:GLU62 3.0 142.2 1.0
CD E:GLU62 3.2 144.0 1.0
CG G:HIS65 3.2 121.9 1.0
OE2 G:GLU62 3.4 148.7 1.0
CB G:HIS65 3.6 120.4 1.0
OE1 E:GLU62 3.9 148.9 1.0
CG G:GLU32 4.0 134.5 1.0
NE2 G:HIS65 4.1 129.3 1.0
CG E:GLU62 4.1 130.4 1.0
FE E:FE901 4.1 174.9 1.0
CD2 G:HIS65 4.2 121.5 1.0
CG G:GLU62 4.3 129.5 1.0
CA G:GLU62 4.4 119.2 1.0
CB G:GLU62 4.5 120.7 1.0
OH E:TYR39 4.7 126.5 1.0
CB G:GLU32 4.8 122.5 1.0
CE2 E:TYR39 4.9 128.2 1.0

Iron binding site 8 out of 10 in 33bf

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Iron binding site 8 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe901

b:172.0
occ:1.00
 OE2 D:GLU62 2.0 148.5 1.0
OE2 H:GLU32 2.0 142.4 1.0
OE1 H:GLU62 2.0 147.8 1.0
ND1 H:HIS65 2.0 133.4 1.0
CD H:GLU32 2.7 141.8 1.0
OE1 H:GLU32 2.8 144.5 1.0
CE1 H:HIS65 2.8 133.7 1.0
CD H:GLU62 2.9 142.9 1.0
CD D:GLU62 3.1 141.2 1.0
CG H:HIS65 3.2 124.5 1.0
OE2 H:GLU62 3.2 149.1 1.0
CB H:HIS65 3.6 122.6 1.0
OE1 D:GLU62 3.7 145.2 1.0
NE2 H:HIS65 4.0 131.9 1.0
CG H:GLU32 4.1 138.2 1.0
CG D:GLU62 4.1 128.4 1.0
CG H:GLU62 4.2 128.0 1.0
CD2 H:HIS65 4.2 125.4 1.0
FE D:FE901 4.2 168.3 1.0
CA H:GLU62 4.4 119.5 1.0
CB H:GLU62 4.5 120.2 1.0
OH D:TYR39 4.9 124.8 1.0
CB H:GLU32 4.9 127.8 1.0
CE1 D:HIS65 5.0 130.9 1.0

Iron binding site 9 out of 10 in 33bf

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Iron binding site 9 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe901

b:168.7
occ:1.00
 OE2 I:GLU32 2.0 143.2 1.0
OE2 C:GLU62 2.0 151.6 1.0
OE1 I:GLU62 2.0 149.0 1.0
ND1 I:HIS65 2.0 131.1 1.0
CD I:GLU32 2.6 139.5 1.0
OE1 I:GLU32 2.7 139.8 1.0
CE1 I:HIS65 2.8 132.2 1.0
CD I:GLU62 2.9 146.0 1.0
CD C:GLU62 3.1 144.3 1.0
CG I:HIS65 3.2 124.2 1.0
OE2 I:GLU62 3.3 151.9 1.0
CB I:HIS65 3.7 122.3 1.0
OE1 C:GLU62 3.8 145.8 1.0
FE C:FE901 4.0 170.2 1.0
NE2 I:HIS65 4.0 131.1 1.0
CG I:GLU32 4.1 132.7 1.0
CG C:GLU62 4.1 131.9 1.0
CD2 I:HIS65 4.2 124.5 1.0
CG I:GLU62 4.2 133.8 1.0
CA I:GLU62 4.4 123.9 1.0
CB I:GLU62 4.5 125.7 1.0
CB I:GLU32 4.8 122.0 1.0
OH C:TYR39 4.8 126.2 1.0

Iron binding site 10 out of 10 in 33bf

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Iron binding site 10 out of 10 in the Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Single Particle Reconstruction of Rhodospirillum Rubrum Encapsulated Ferritin in Encapsulin Nano Compartment within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe901

b:169.1
occ:1.00
 OE1 J:GLU32 1.9 140.9 1.0
OE2 B:GLU62 1.9 151.6 1.0
OE1 J:GLU62 2.0 145.9 1.0
ND1 J:HIS65 2.0 129.2 1.0
CD J:GLU32 2.7 141.5 1.0
OE2 J:GLU32 2.8 144.0 1.0
CE1 J:HIS65 2.8 129.6 1.0
CD J:GLU62 2.9 143.0 1.0
CD B:GLU62 3.1 145.7 1.0
CG J:HIS65 3.2 120.1 1.0
OE2 J:GLU62 3.3 148.6 1.0
CB J:HIS65 3.7 119.9 1.0
OE1 B:GLU62 3.7 149.4 1.0
NE2 J:HIS65 4.0 126.6 1.0
FE B:FE901 4.1 168.0 1.0
CG J:GLU32 4.1 133.9 1.0
CG B:GLU62 4.1 133.6 1.0
CG J:GLU62 4.2 131.7 1.0
CD2 J:HIS65 4.2 119.8 1.0
CA J:GLU62 4.4 122.7 1.0
CB J:GLU62 4.5 123.6 1.0
CB J:GLU32 4.8 122.4 1.0
OH B:TYR39 4.8 125.5 1.0
CE2 B:TYR39 5.0 125.5 1.0

Reference:

Z.Mciver, D.He, J.Ross, M.Cozzaglio, C.Piergentili, A.Dornau, N.Sumpner, F.Brady, K.Bialik, T.Mccorvie, C.Sissi, A.Basle, D.J.Clarke, J.Marles-Wright. Single Particle Cryo-Em Analysis of the Rhodospirillum Rubrum Encapsulin Nanocompartment Shows Variable Loading of Encapsulated Ferritin Cargo Proteins and Differences in the Fivefold Pore. J.Struct.Biol. V. 218 08357 2026.
ISSN: ESSN 1095-8657
PubMed: 42603627
DOI: 10.1016/J.JSB.2026.108357
Page generated: Sun Oct 4 10:38:49 2026

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