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Iron in PDB 8ykr: Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering

Enzymatic activity of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering

All present enzymatic activity of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering:
1.16.3.1;

Protein crystallography data

The structure of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering, PDB code: 8ykr was solved by C.K.Gu, S.J.Wang, G.H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 2.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 125.08, 125.08, 175.917, 90, 90, 90
R / Rfree (%) 18.5 / 23

Iron Binding Sites:

The binding sites of Iron atom in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering (pdb code 8ykr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering, PDB code: 8ykr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8ykr

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Iron binding site 1 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:102.5
occ:1.00
 OE1 B:GLU59 2.7 54.0 1.0
OE1 B:GLU24 2.8 53.4 1.0
CD2 B:HIS62 3.1 66.0 1.0
OE2 B:GLU59 3.3 60.4 1.0
OE2 B:GLU24 3.4 67.4 1.0
CD B:GLU59 3.4 56.2 1.0
CD B:GLU24 3.4 57.4 1.0
NE2 B:GLN138 3.7 91.5 1.0
CG1 B:VAL107 3.7 43.5 1.0
CG B:HIS62 3.7 62.8 1.0
NE2 B:HIS62 3.8 68.0 1.0
CE1 B:TYR134 3.8 84.4 1.0
CD B:GLN138 4.1 92.5 1.0
CB B:HIS62 4.2 52.8 1.0
FE B:FE202 4.2 110.1 1.0
OE1 B:GLN138 4.3 90.3 1.0
CD1 B:TYR134 4.5 86.2 1.0
ND1 B:HIS62 4.7 72.4 1.0
CE1 B:HIS62 4.7 75.7 1.0
CG B:GLN138 4.8 90.7 1.0
CZ B:TYR134 4.8 80.0 1.0
CG B:GLU59 4.8 42.3 1.0
CB B:VAL107 4.9 50.5 1.0
OH B:TYR134 4.9 75.8 1.0
CG B:GLU24 4.9 47.2 1.0

Iron binding site 2 out of 10 in 8ykr

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Iron binding site 2 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:110.1
occ:1.00
 OE1 B:GLN138 2.9 90.3 1.0
NE2 B:GLN138 3.0 91.5 1.0
OE2 B:GLU59 3.2 60.4 1.0
CD B:GLN138 3.3 92.5 1.0
OE1 B:GLU58 3.3 78.3 1.0
OG B:SER141 3.4 67.4 0.7
OG B:SER141 3.5 76.4 0.3
OE2 B:GLU104 3.7 73.5 1.0
CB B:SER141 3.8 73.6 0.3
CB B:SER141 3.8 73.7 0.7
NE2 B:HIS62 3.9 68.0 1.0
OE1 B:GLU104 3.9 53.5 1.0
CD B:GLU104 4.2 65.7 1.0
CD B:GLU58 4.2 78.8 1.0
CD2 B:HIS62 4.2 66.0 1.0
FE B:FE201 4.2 102.5 1.0
CD B:GLU59 4.3 56.2 1.0
CG B:GLU58 4.6 62.6 1.0
OE2 B:GLU137 4.8 86.6 1.0
CG B:GLN138 4.9 90.7 1.0
OE1 B:GLU59 4.9 54.0 1.0

Iron binding site 3 out of 10 in 8ykr

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Iron binding site 3 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:105.8
occ:1.00
 OE2 A:GLU59 2.6 58.4 1.0
OE2 A:GLU24 2.8 55.7 1.0
ND1 A:HIS62 2.8 64.8 1.0
OE1 A:GLU59 3.0 63.6 1.0
CD A:GLU59 3.1 53.6 1.0
CE1 A:HIS62 3.4 60.8 1.0
OE2 A:GLU137 3.5 83.0 1.0
CD A:GLU24 3.6 56.8 1.0
OE1 A:GLU24 3.7 60.0 1.0
CD A:GLU137 4.0 86.8 1.0
CG A:HIS62 4.1 64.5 1.0
CG1 A:VAL107 4.1 46.2 1.0
OE1 A:GLU137 4.3 87.5 1.0
OE2 A:GLU104 4.4 71.5 1.0
CB A:HIS62 4.5 48.6 1.0
CG A:GLU59 4.6 42.7 1.0
NE2 A:HIS62 4.7 69.8 1.0
CG A:GLU137 4.8 83.5 1.0
OE1 A:GLU104 4.9 60.2 1.0

Iron binding site 4 out of 10 in 8ykr

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Iron binding site 4 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:113.2
occ:1.00
 OE1 C:GLU59 2.8 53.4 1.0
OE2 C:GLU59 3.0 61.6 1.0
CD C:GLU59 3.3 54.5 1.0
OE1 C:GLU24 3.4 55.9 1.0
ND1 C:HIS62 3.6 67.7 1.0
NE2 C:GLN138 3.6 88.0 1.0
CG1 C:VAL107 3.9 56.8 1.0
CE1 C:HIS62 3.9 72.8 1.0
OE2 C:GLU104 4.0 80.3 1.0
CD C:GLN138 4.0 91.1 1.0
OE1 C:GLN138 4.1 90.7 1.0
OE2 C:GLU24 4.2 62.1 1.0
CD C:GLU24 4.2 54.8 1.0
OE1 C:GLU104 4.2 60.5 1.0
CG C:HIS62 4.5 64.0 1.0
CD C:GLU104 4.5 68.4 1.0
ND2 C:ASN108 4.6 78.1 1.0
CG C:GLU59 4.8 42.8 1.0
CB C:VAL107 4.8 59.9 1.0
NE2 C:HIS62 4.9 78.5 1.0
CB C:HIS62 5.0 53.0 1.0

Iron binding site 5 out of 10 in 8ykr

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Iron binding site 5 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:107.9
occ:1.00
 OE1 D:GLU59 2.5 55.8 1.0
OE2 D:GLU24 2.9 61.6 1.0
OE2 D:GLU59 2.9 62.1 1.0
CD D:GLU59 3.0 48.5 1.0
ND1 D:HIS62 3.2 67.9 1.0
CD D:GLU24 3.7 60.4 1.0
FE D:FE202 3.8 114.5 1.0
CG1 D:VAL107 3.9 45.7 1.0
OE1 D:GLU24 3.9 66.5 1.0
CE1 D:HIS62 4.0 71.2 1.0
CG D:HIS62 4.1 65.6 1.0
CB D:HIS62 4.3 50.9 1.0
NE2 D:GLN138 4.3 90.8 1.0
CD D:GLN138 4.4 94.0 1.0
CG D:GLU59 4.5 40.4 1.0
CE1 D:TYR134 4.6 81.8 1.0
CD1 D:TYR134 4.7 87.8 1.0
OE1 D:GLN138 4.7 93.6 1.0
CG D:GLN138 4.8 85.7 1.0
CA D:GLU59 4.9 43.5 1.0
OE2 D:GLU104 4.9 59.3 1.0
CB D:VAL107 4.9 47.8 1.0

Iron binding site 6 out of 10 in 8ykr

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Iron binding site 6 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:114.5
occ:1.00
 NE2 D:GLN138 2.4 90.8 1.0
OE2 D:GLU59 3.0 62.1 1.0
OG D:SER141 3.1 69.9 0.7
OG D:SER141 3.2 75.5 0.3
OE1 D:GLU104 3.3 76.0 1.0
CD D:GLN138 3.6 94.0 1.0
CB D:SER141 3.6 72.8 0.3
CB D:SER141 3.6 74.0 0.7
FE D:FE201 3.8 107.9 1.0
OE2 D:GLU104 3.9 59.3 1.0
OE2 D:GLU58 4.0 81.4 1.0
CD D:GLU104 4.0 58.4 1.0
CE1 D:HIS62 4.2 71.2 1.0
CD D:GLU59 4.2 48.5 1.0
OE1 D:GLN138 4.3 93.6 1.0
CG D:GLN138 4.5 85.7 1.0
ND1 D:HIS62 4.5 67.9 1.0
CD D:GLU58 4.7 75.0 1.0
OE2 D:GLU137 4.8 101.6 1.0
OE1 D:GLU59 4.8 55.8 1.0
CG D:GLU58 4.8 62.5 1.0

Iron binding site 7 out of 10 in 8ykr

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Iron binding site 7 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:100.8
occ:1.00
 OE1 E:GLU24 2.4 50.4 1.0
OE1 E:GLU59 2.4 51.8 1.0
CD2 E:HIS62 3.0 59.9 1.0
CD E:GLU59 3.2 52.0 1.0
CD E:GLU24 3.2 54.0 1.0
OE2 E:GLU59 3.2 58.0 1.0
OE2 E:GLU24 3.3 59.8 1.0
CG E:HIS62 3.4 58.9 1.0
FE E:FE202 3.7 106.5 1.0
CB E:HIS62 3.8 48.4 1.0
NE2 E:HIS62 3.8 61.4 1.0
CG1 E:VAL107 4.3 46.7 1.0
ND1 E:HIS62 4.4 71.4 1.0
NE2 E:GLN138 4.5 84.3 1.0
CG E:GLU24 4.5 41.6 1.0
CE1 E:HIS62 4.5 72.0 1.0
CG E:GLU59 4.6 39.8 1.0
CA E:GLU59 4.7 43.4 1.0
CB E:GLU24 5.0 41.1 1.0
CB E:GLU59 5.0 35.9 1.0

Iron binding site 8 out of 10 in 8ykr

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Iron binding site 8 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:106.5
occ:1.00
 OE2 E:GLU59 2.7 58.0 1.0
NE2 E:GLN138 2.9 84.3 1.0
OE1 E:GLU104 3.0 73.0 1.0
OE2 E:GLU104 3.5 55.7 1.0
OE1 E:GLN138 3.5 78.2 1.0
CD E:GLU104 3.6 62.3 1.0
OG E:SER141 3.6 73.8 0.1
OG E:SER141 3.6 74.2 0.9
CD E:GLN138 3.6 88.2 1.0
FE E:FE201 3.7 100.8 1.0
CD E:GLU59 3.9 52.0 1.0
CB E:SER141 3.9 75.8 0.9
CB E:SER141 3.9 75.5 0.1
NE2 E:HIS62 4.3 61.4 1.0
OE1 E:GLU59 4.3 51.8 1.0
CD2 E:HIS62 4.4 59.9 1.0

Iron binding site 9 out of 10 in 8ykr

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Iron binding site 9 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:113.0
occ:1.00
 OE1 F:GLU24 2.2 59.2 1.0
OE1 F:GLU59 2.7 60.0 1.0
ND1 F:HIS62 2.9 69.6 1.0
CD F:GLU24 3.1 63.9 1.0
OE2 F:GLU59 3.3 58.1 1.0
OE2 F:GLU24 3.3 72.3 1.0
CD F:GLU59 3.4 58.1 1.0
CG F:HIS62 3.7 66.5 1.0
CB F:HIS62 3.7 50.5 1.0
CG1 F:VAL107 3.8 45.5 1.0
CE1 F:HIS62 3.9 63.7 1.0
CG F:GLU24 4.4 55.4 1.0
CE2 F:TYR134 4.4 84.8 1.0
CD2 F:TYR134 4.4 83.9 1.0
FE F:FE202 4.5 113.5 1.0
CB F:GLU24 4.7 48.1 1.0
CG F:GLU59 4.9 44.4 1.0
CD2 F:HIS62 4.9 66.8 1.0
NE2 F:HIS62 5.0 63.1 1.0

Iron binding site 10 out of 10 in 8ykr

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Iron binding site 10 out of 10 in the Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:113.5
occ:1.00
 OG F:SER141 3.2 67.4 0.9
OG F:SER141 3.4 77.0 0.1
OE2 F:GLU104 3.4 79.1 1.0
OE2 F:GLU59 3.5 58.1 1.0
CB F:SER141 3.6 71.3 0.1
CB F:SER141 3.6 71.1 0.9
OE1 F:GLU104 3.7 68.1 1.0
CD F:GLU104 3.9 64.0 1.0
CE1 F:HIS62 4.0 63.7 1.0
ND1 F:HIS62 4.5 69.6 1.0
FE F:FE201 4.5 113.0 1.0
O F:GLU137 4.6 93.2 1.0
CD F:GLU59 4.7 58.1 1.0

Reference:

C.K.Gu, S.J.Wang, G.H.Zhao. Enhancing the Gastric Stability of Ferritin Nanocage Via Computational-Assisted Disulfide Bond Engineering To Be Published.
Page generated: Fri Aug 8 01:43:05 2025

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