Zinc in PDB 7cpi: His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding

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

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

Protein crystallography data

The structure of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding, PDB code: 7cpi 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) 34.11 / 2.60
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 126.374, 126.374, 177.109, 90, 90, 90
R / Rfree (%) 19.4 / 27.2

Other elements in 7cpi:

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

Iron (Fe) 12 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 7cpi

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Zinc binding site 1 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn203

b:97.6
occ:1.00
 O E:HOH301 2.8 61.9 1.0
O C:HOH302 3.9 61.8 1.0
HE2 E:HIS159 4.9 107.7 1.0
NE2 E:HIS159 4.9 89.9 1.0

Zinc binding site 2 out of 7 in 7cpi

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Zinc binding site 2 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:59.2
occ:0.25
 HE1 A:HIS161 1.4 62.8 1.0
CE1 A:HIS161 2.3 52.4 1.0
NE2 A:HIS161 3.0 54.2 1.0
HE2 A:HIS161 3.1 64.9 1.0
ND1 A:HIS161 3.3 56.1 1.0
CD2 A:HIS161 4.3 55.5 1.0
CG A:HIS161 4.4 54.9 1.0
HG3 A:MET165 4.5 84.9 1.0

Zinc binding site 3 out of 7 in 7cpi

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Zinc binding site 3 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:92.4
occ:0.25
 O A:HOH301 3.4 56.7 1.0
HE2 A:HIS159 4.8 100.7 1.0

Zinc binding site 4 out of 7 in 7cpi

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Zinc binding site 4 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:60.6
occ:1.00
 NE2 E:HIS161 2.0 65.8 1.0
O E:HOH302 2.3 47.8 1.0
NE2 C:HIS161 2.4 58.5 1.0
O E:HOH303 2.7 40.2 1.0
CD2 E:HIS161 3.0 68.0 1.0
CE1 E:HIS161 3.0 64.0 1.0
HD2 E:HIS161 3.1 81.4 1.0
CE1 C:HIS161 3.2 49.4 1.0
HE1 C:HIS161 3.2 59.2 1.0
HE1 E:HIS161 3.3 76.7 1.0
CD2 C:HIS161 3.5 56.0 1.0
HD2 C:HIS161 3.7 67.1 1.0
ND1 E:HIS161 4.1 71.7 1.0
CG E:HIS161 4.1 63.1 1.0
HG3 C:MET165 4.3 76.9 1.0
ND1 C:HIS161 4.4 56.3 1.0
HG3 E:MET165 4.5 86.1 1.0
CG C:HIS161 4.5 55.0 1.0
HD1 E:HIS161 4.9 85.9 1.0
HG2 C:MET165 4.9 76.9 1.0

Zinc binding site 5 out of 7 in 7cpi

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Zinc binding site 5 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:67.2
occ:0.25
 HE2 D:HIS161 1.5 87.3 1.0
NE2 D:HIS161 2.3 72.8 1.0
O D:HOH301 2.9 40.9 0.2
CE1 D:HIS161 3.2 67.5 1.0
HE1 D:HIS161 3.3 80.8 1.0
CD2 D:HIS161 3.3 64.1 1.0
HD2 D:HIS161 3.5 76.7 1.0
ND1 D:HIS161 4.3 64.6 1.0
CG D:HIS161 4.4 57.9 1.0
HG3 D:MET165 4.5 82.7 1.0

Zinc binding site 6 out of 7 in 7cpi

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Zinc binding site 6 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn204

b:102.4
occ:0.25
 HE2 D:HIS159 4.0 105.9 1.0
O D:HOH302 4.0 48.2 1.0
NE2 D:HIS159 4.7 88.4 1.0
HD2 D:HIS159 5.0 98.8 1.0

Zinc binding site 7 out of 7 in 7cpi

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Zinc binding site 7 out of 7 in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Zn Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn203

b:115.2
occ:1.00
 OD1 F:ASP133 3.1 61.1 1.0
CG F:ASP133 3.8 61.7 1.0
OD2 F:ASP133 3.9 65.4 1.0
HG2 F:LYS129 4.5 59.4 1.0
HG3 F:LYS129 4.5 59.4 1.0
HE2 F:LYS129 4.6 74.0 1.0
CG F:LYS129 5.0 49.6 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: Mon Jul 12 16:59:50 2021

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