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Nickel 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:

Iron (Fe) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 6 binding sites of Nickel where determined in the His-Mediated Reversible Self-Assembly of Ferritin Nanocage with Ni Binding, PDB code: 7cpc:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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:Ni201

b:33.7
occ:1.00
 NE2 B:HIS161 2.1 32.8 1.0
NE2 D:HIS161 2.1 35.1 1.0
CE1 D:HIS161 2.9 28.0 1.0
CE1 B:HIS161 3.0 26.3 1.0
CD2 D:HIS161 3.2 33.2 1.0
CD2 B:HIS161 3.2 34.2 1.0
ND1 D:HIS161 4.0 26.2 1.0
ND1 B:HIS161 4.1 28.9 1.0
CG D:HIS161 4.2 34.0 1.0
CG B:HIS161 4.3 28.6 1.0
SD D:MET165 4.5 75.8 1.0
CE D:MET165 4.6 48.5 1.0

Nickel binding site 2 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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:Ni201

b:31.1
occ:0.25
 NE2 A:HIS161 2.2 38.3 1.0
CE1 A:HIS161 3.1 38.3 1.0
CD2 A:HIS161 3.2 33.5 1.0
ND1 A:HIS161 4.2 28.3 1.0
CG A:HIS161 4.3 31.8 1.0
SD A:MET165 4.9 68.7 1.0

Nickel binding site 3 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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
A:Ni202

b:59.7
occ:0.25
 O A:HOH301 3.2 37.1 1.0
NE2 A:HIS159 4.6 45.6 1.0

Nickel binding site 4 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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
C:Ni201

b:52.1
occ:1.00
 O F:HOH301 2.4 26.0 1.0
O C:HOH301 3.2 25.8 1.0
NE2 F:HIS159 4.2 46.5 1.0
NE2 C:HIS159 4.6 61.6 1.0
CD2 F:HIS159 4.8 50.5 1.0
CE1 C:HIS159 5.0 70.9 1.0

Nickel binding site 5 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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:Ni201

b:37.3
occ:0.25
 NE2 E:HIS161 2.2 38.7 1.0
O E:HOH301 2.3 33.8 0.2
CE1 E:HIS161 3.1 37.5 1.0
CD2 E:HIS161 3.2 35.2 1.0
O E:HOH303 3.5 25.9 0.2
ND1 E:HIS161 4.3 29.4 1.0
CG E:HIS161 4.4 27.7 1.0

Nickel binding site 6 out of 6 in 7cpc

Go back to Nickel Binding Sites List in 7cpc
Nickel 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 Nickel with other atoms in the Ni 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
E:Ni202

b:57.3
occ:0.25
 O E:HOH302 3.5 22.4 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 Oct 10 09:08:13 2024

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