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Iron in PDB 8j9m: Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3

Enzymatic activity of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3

All present enzymatic activity of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3, PDB code: 8j9m was solved by X.Chen, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 2.90
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.331, 143.331, 166.663, 90, 90, 90
R / Rfree (%) 20.3 / 24.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 (pdb code 8j9m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3, PDB code: 8j9m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8j9m

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Iron binding site 1 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:65.9
occ:1.00
 OE2 A:GLU62 2.3 49.0 1.0
OE2 A:GLU27 2.3 56.4 1.0
ND1 A:HIS65 2.5 58.1 1.0
OE1 A:GLU62 2.9 57.9 1.0
CD A:GLU62 3.0 55.6 1.0
CE1 A:HIS65 3.2 61.6 1.0
CD A:GLU27 3.3 50.5 1.0
OE1 A:GLU27 3.5 44.7 1.0
OE1 A:GLN141 3.5 50.9 1.0
CG A:HIS65 3.5 60.8 1.0
O A:HOH302 3.7 50.9 1.0
CG1 A:VAL110 4.0 48.1 1.0
CB A:HIS65 4.0 50.0 1.0
OE1 A:GLU107 4.3 55.9 1.0
NE2 A:HIS65 4.3 64.8 1.0
CG A:GLU62 4.4 46.8 1.0
CD A:GLN141 4.5 49.4 1.0
CD2 A:HIS65 4.5 59.9 1.0
CG A:GLU27 4.7 38.5 1.0
CA A:GLU62 4.9 50.4 1.0
CB A:GLU62 5.0 44.0 1.0

Iron binding site 2 out of 8 in 8j9m

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Iron binding site 2 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:90.9
occ:0.50
 CE1 A:HIS173 3.0 45.7 1.0
ND1 A:HIS173 3.9 45.1 1.0
NE2 A:HIS173 3.9 44.7 1.0
CD2 A:LEU169 4.1 42.6 1.0
CD1 A:LEU169 5.0 48.0 1.0

Iron binding site 3 out of 8 in 8j9m

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Iron binding site 3 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:103.3
occ:1.00
 OE1 A:GLN58 2.6 71.1 1.0
O A:HOH302 2.8 50.9 1.0
OE2 A:GLU107 2.8 59.3 1.0
OE1 A:GLU62 3.1 57.9 1.0
OE1 A:GLU61 3.5 75.3 1.0
CD A:GLN58 3.7 65.5 1.0
CD A:GLU107 3.7 58.4 1.0
CB A:ALA144 3.8 37.8 1.0
NE2 A:GLN58 4.2 67.0 1.0
OE1 A:GLU107 4.2 55.9 1.0
CD A:GLU62 4.3 55.6 1.0
CE1 A:HIS65 4.4 61.6 1.0
OE1 A:GLU140 4.5 75.7 1.0
CD A:GLU61 4.7 80.0 1.0
CG A:GLU107 4.8 42.0 1.0
OH A:TYR34 4.8 44.1 1.0
CG A:GLU62 4.8 46.8 1.0
CE2 A:TYR34 5.0 43.0 1.0
CG A:GLN58 5.0 48.5 1.0
CB A:GLU61 5.0 50.0 1.0

Iron binding site 4 out of 8 in 8j9m

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Iron binding site 4 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:60.6
occ:1.00
 OE2 B:GLU27 2.5 61.0 1.0
OE1 B:GLU62 2.6 55.2 1.0
ND1 B:HIS65 2.7 52.5 1.0
OE2 B:GLU62 2.9 71.1 1.0
CD B:GLU62 3.1 63.0 1.0
OE1 B:GLN141 3.1 57.7 1.0
OE1 B:GLU27 3.1 46.3 1.0
CD B:GLU27 3.2 51.6 1.0
CE1 B:HIS65 3.4 59.4 1.0
CG B:HIS65 3.6 56.4 1.0
CG1 B:VAL110 3.9 46.2 1.0
CB B:HIS65 4.0 49.6 1.0
CD B:GLN141 4.1 50.0 1.0
NE2 B:HIS65 4.4 65.0 1.0
OE1 B:GLU107 4.5 63.9 1.0
CD2 B:HIS65 4.5 56.8 1.0
CG B:GLU62 4.6 54.8 1.0
NE2 B:GLN141 4.6 48.6 1.0
CG B:GLU27 4.7 40.2 1.0
CB B:VAL110 4.9 48.1 1.0
CD2 B:TYR137 5.0 49.0 1.0

Iron binding site 5 out of 8 in 8j9m

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Iron binding site 5 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:98.7
occ:1.00
 NE2 B:GLN58 2.5 63.0 1.0
OE2 B:GLU107 3.1 59.6 1.0
OE2 B:GLU62 3.6 71.1 1.0
OE1 B:GLU61 3.7 65.1 1.0
CD B:GLN58 3.8 59.9 1.0
CB B:GLN58 4.2 46.8 1.0
CD B:GLU107 4.2 66.2 1.0
CD B:GLU62 4.4 63.0 1.0
CG B:GLU62 4.4 54.8 1.0
CA B:GLN58 4.5 43.8 1.0
O B:GLN58 4.5 46.0 1.0
CG B:GLN58 4.6 54.0 1.0
CE2 B:TYR34 4.6 51.9 1.0
OE1 B:GLU107 4.6 63.9 1.0
OE1 B:GLN58 4.7 61.9 1.0
CB B:ALA144 4.7 34.5 1.0
CB B:GLU61 4.7 50.8 1.0
OH B:TYR34 4.7 52.9 1.0
CD B:GLU61 4.8 73.9 1.0
CZ B:TYR34 4.9 56.5 1.0
C B:GLN58 5.0 45.6 1.0
CE1 B:HIS65 5.0 59.4 1.0

Iron binding site 6 out of 8 in 8j9m

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Iron binding site 6 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:61.9
occ:1.00
 OE2 C:GLU27 2.4 55.6 1.0
OE1 C:GLU62 2.4 52.4 1.0
OE2 C:GLU62 2.6 71.0 1.0
ND1 C:HIS65 2.7 59.8 1.0
CD C:GLU62 2.9 59.7 1.0
NE2 C:GLN141 2.9 60.9 1.0
CD C:GLU27 3.1 49.9 1.0
OE1 C:GLU27 3.1 51.6 1.0
CE1 C:HIS65 3.4 64.7 1.0
CG C:HIS65 3.6 55.9 1.0
CB C:HIS65 3.9 50.8 1.0
CD C:GLN141 4.1 54.9 1.0
CG1 C:VAL110 4.1 47.4 1.0
O C:HOH307 4.2 55.1 1.0
CG C:GLU62 4.4 52.1 1.0
NE2 C:HIS65 4.4 65.2 1.0
OE1 C:GLN141 4.5 58.4 1.0
CD2 C:HIS65 4.5 57.4 1.0
CG C:GLU27 4.6 41.6 1.0
OE2 C:GLU107 4.6 65.5 1.0
CD2 C:TYR137 4.9 51.9 1.0
CB C:VAL110 5.0 50.8 1.0
CA C:GLU62 5.0 50.6 1.0

Iron binding site 7 out of 8 in 8j9m

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Iron binding site 7 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:107.5
occ:1.00
 OE2 C:GLU61 2.4 76.5 1.0
O C:HOH307 2.9 55.1 1.0
OE1 C:GLU107 3.1 66.2 1.0
OE1 C:GLN58 3.1 65.1 1.0
CD C:GLU61 3.3 77.9 1.0
OE2 C:GLU62 3.4 71.0 1.0
CG C:GLU61 3.9 68.4 1.0
CD C:GLU107 4.0 61.4 1.0
CB C:ALA144 4.0 37.3 1.0
OE2 C:GLU107 4.2 65.5 1.0
CD C:GLN58 4.3 56.9 1.0
OE1 C:GLU61 4.3 82.8 1.0
CD C:GLU62 4.3 59.7 1.0
CG C:GLU62 4.6 52.1 1.0
CE1 C:HIS65 4.7 64.7 1.0
OH C:TYR34 4.9 45.4 1.0
CE2 C:TYR34 4.9 43.5 1.0
CB C:GLN58 4.9 47.6 1.0
O C:GLN58 4.9 46.8 1.0

Iron binding site 8 out of 8 in 8j9m

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Iron binding site 8 out of 8 in the Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Human H-Ferritin Variant 123F Assembling in SOLUTION3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe203

b:100.5
occ:0.25
 NE2 C:HIS173 3.1 42.1 1.0
CE1 C:HIS173 4.0 50.3 1.0
CD2 C:HIS173 4.0 46.9 1.0
CD2 C:LEU169 4.5 43.5 1.0

Reference:

X.Chen, T.Zhang, H.Liu, J.Zang, C.Lv, M.Du, G.Zhao. Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks By Designed Intermolecular Pi-Pi Interactions. Adv Sci V. 10 05398 2023.
ISSN: ESSN 2198-3844
PubMed: 37870198
DOI: 10.1002/ADVS.202305398
Page generated: Sat Aug 10 06:37:28 2024

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