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Iron in PDB 7cpc: His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding

Enzymatic activity of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding

All present enzymatic activity of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding:
1.16.3.1;

Protein crystallography data

The structure of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding, PDB code: 7cpc was solved by C.Gu, T.Zhang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.28 / 2.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 125.845, 125.845, 176.41, 90, 90, 90
R / Rfree (%) 19.5 / 27

Other elements in 7cpc:

The structure of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding also contains other interesting chemical elements:

Nickel (Ni) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding (pdb code 7cpc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding, PDB code: 7cpc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7cpc

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Iron binding site 1 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:47.2
occ:1.00
 OE1 B:GLU60 1.9 31.1 1.0
OE1 B:GLU24 2.2 41.2 1.0
ND1 B:HIS63 2.6 37.1 1.0
CD B:GLU60 2.8 36.6 1.0
CD B:GLU24 3.1 35.3 1.0
OE2 B:GLU60 3.1 46.1 1.0
OE2 B:GLU24 3.2 33.6 1.0
CG B:HIS63 3.4 37.3 1.0
CE1 B:HIS63 3.4 40.2 1.0
CB B:HIS63 3.7 31.3 1.0
OE1 B:GLN139 3.9 20.9 1.0
CG B:GLU60 4.1 29.3 1.0
CD2 B:HIS63 4.4 38.0 1.0
NE2 B:HIS63 4.4 46.8 1.0
CG1 B:VAL108 4.4 20.2 1.0
CG B:GLU24 4.4 28.5 1.0
CA B:GLU60 4.5 27.7 1.0
CB B:GLU60 4.6 28.3 1.0
CB B:GLU24 4.9 24.7 1.0
CD B:GLN139 4.9 26.2 1.0

Iron binding site 2 out of 6 in 7cpc

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Iron binding site 2 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:47.1
occ:1.00
 OE2 A:GLU60 1.9 44.6 1.0
OE1 A:GLU24 2.2 37.4 1.0
OE1 A:GLU60 2.3 31.7 1.0
CD A:GLU60 2.4 39.3 1.0
CD A:GLU24 3.1 35.9 1.0
ND1 A:HIS63 3.2 36.1 1.0
OE2 A:GLU24 3.4 43.6 1.0
CG A:HIS63 3.5 32.8 1.0
CB A:HIS63 3.6 24.9 1.0
CG A:GLU60 3.9 29.6 1.0
CE1 A:HIS63 4.0 45.2 1.0
OE1 A:GLN139 4.1 24.9 1.0
CG1 A:VAL108 4.3 27.6 1.0
CD2 A:HIS63 4.4 37.3 1.0
CG A:GLU24 4.5 25.4 1.0
CA A:GLU60 4.5 26.4 1.0
NE2 A:HIS63 4.7 44.0 1.0
CB A:GLU60 4.7 26.6 1.0
NE2 A:GLN139 4.7 23.3 1.0
CD A:GLN139 4.8 26.3 1.0
CB A:GLU24 4.8 27.1 1.0
CD1 A:TYR135 4.9 21.7 1.0

Iron binding site 3 out of 6 in 7cpc

Go back to Iron Binding Sites List in 7cpc
Iron binding site 3 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:46.7
occ:1.00
 OE1 C:GLU60 2.0 25.4 1.0
OE1 C:GLU24 2.2 28.6 1.0
ND1 C:HIS63 2.7 35.5 1.0
CD C:GLU24 3.0 24.9 1.0
CD C:GLU60 3.0 28.6 1.0
OE2 C:GLU24 3.1 26.2 1.0
OE2 C:GLU60 3.3 30.8 1.0
CG C:HIS63 3.4 28.9 1.0
CE1 C:HIS63 3.4 40.6 1.0
CB C:HIS63 3.7 25.0 1.0
OE1 C:GLN139 4.0 28.2 1.0
CG1 C:VAL108 4.2 16.2 1.0
NE2 C:HIS63 4.3 41.0 1.0
CG C:GLU60 4.4 22.9 1.0
CD2 C:HIS63 4.4 31.2 1.0
CG C:GLU24 4.4 23.5 1.0
CA C:GLU60 4.5 23.3 1.0
CB C:GLU60 4.7 22.4 1.0
CD C:GLN139 4.8 22.1 1.0
NE2 C:GLN139 4.9 18.7 1.0
CB C:GLU24 5.0 18.7 1.0

Iron binding site 4 out of 6 in 7cpc

Go back to Iron Binding Sites List in 7cpc
Iron binding site 4 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:41.8
occ:1.00
 OE2 D:GLU60 2.0 34.2 1.0
OE1 D:GLU24 2.2 36.5 1.0
OE1 D:GLU60 2.4 43.9 1.0
CD D:GLU60 2.5 35.3 1.0
ND1 D:HIS63 2.9 34.4 1.0
CD D:GLU24 3.2 28.2 1.0
OE2 D:GLU24 3.4 23.6 1.0
NE2 D:GLN139 3.4 21.9 1.0
CG D:HIS63 3.6 36.5 1.0
CE1 D:HIS63 3.7 46.9 1.0
CB D:HIS63 3.8 28.2 1.0
CG D:GLU60 3.9 18.8 1.0
CG1 D:VAL108 4.4 20.0 1.0
CA D:GLU60 4.5 23.4 1.0
CD2 D:HIS63 4.5 38.2 1.0
CG D:GLU24 4.5 28.6 1.0
NE2 D:HIS63 4.6 45.5 1.0
CD D:GLN139 4.6 18.2 1.0
CB D:GLU60 4.6 21.1 1.0
CD1 D:TYR135 4.9 27.6 1.0
CB D:GLU24 4.9 28.9 1.0

Iron binding site 5 out of 6 in 7cpc

Go back to Iron Binding Sites List in 7cpc
Iron binding site 5 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe203

b:49.6
occ:1.00
 OE1 E:GLU60 2.1 20.4 1.0
OE1 E:GLU24 2.1 38.2 1.0
CD E:GLU60 2.8 30.2 1.0
CD E:GLU24 2.9 33.6 1.0
OE2 E:GLU24 3.0 38.5 1.0
ND1 E:HIS63 3.1 43.7 1.0
OE2 E:GLU60 3.1 41.5 1.0
CB E:HIS63 3.8 32.9 1.0
CG E:HIS63 3.9 35.8 1.0
CE1 E:HIS63 4.1 47.1 1.0
OE1 E:GLN139 4.2 29.1 1.0
CG1 E:VAL108 4.2 30.5 1.0
CG E:GLU60 4.2 24.9 1.0
CG E:GLU24 4.3 24.0 1.0
CA E:GLU60 4.4 28.9 1.0
CB E:GLU60 4.5 32.6 1.0
CB E:GLU24 4.8 26.9 1.0
NE2 E:GLN139 5.0 27.5 1.0
CD E:GLN139 5.0 32.4 1.0

Iron binding site 6 out of 6 in 7cpc

Go back to Iron Binding Sites List in 7cpc
Iron binding site 6 out of 6 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:46.5
occ:1.00
 OE1 F:GLU60 1.9 41.5 1.0
OE1 F:GLU24 2.2 40.4 1.0
OE2 F:GLU60 2.5 37.2 1.0
CD F:GLU60 2.5 38.8 1.0
CD F:GLU24 3.1 31.4 1.0
ND1 F:HIS63 3.3 47.8 1.0
OE2 F:GLU24 3.4 31.4 1.0
CB F:HIS63 3.9 38.0 1.0
CG1 F:VAL108 3.9 23.5 1.0
OE1 F:GLN139 3.9 24.5 1.0
CG F:GLU60 4.0 20.6 1.0
CG F:HIS63 4.1 47.3 1.0
CE1 F:HIS63 4.4 46.7 1.0
CG F:GLU24 4.4 28.8 1.0
OE1 F:GLU105 4.7 40.3 1.0
CA F:GLU60 4.7 32.3 1.0
CB F:GLU60 4.7 25.8 1.0
CD F:GLN139 4.7 28.4 1.0
CB F:GLU24 4.8 26.3 1.0
NE2 F:GLN139 4.8 25.2 1.0
CB F:VAL108 5.0 20.9 1.0

Reference:

C.Gu, T.Zhang, C.Lv, Y.Liu, Y.Wang, G.Zhao. His-Mediated Reversible Self-Assembly of Ferritin Nanocages Through Two Different Switches For Encapsulation of Cargo Molecules. Acs Nano 2020.
ISSN: ESSN 1936-086X
PubMed: 33197176
DOI: 10.1021/ACSNANO.0C06670
Page generated: Thu Aug 8 03:17:26 2024

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