Iron in PDB 8y6f: The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin

Protein crystallography data

The structure of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin, PDB code: 8y6f was solved by C.Yuan, M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.52 / 2.01
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 219.66, 219.66, 148.31, 90, 90, 90
R / Rfree (%) 24.5 / 28.7

Other elements in 8y6f:

The structure of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iron atom in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin (pdb code 8y6f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 17 binding sites of Iron where determined in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin, PDB code: 8y6f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 17 in 8y6f

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Iron binding site 1 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:32.3
occ:1.00
 OE1 A:GLU28 2.1 18.1 1.0
OE1 A:GLU63 2.2 21.9 1.0
ND1 A:HIS66 2.4 23.6 1.0
O A:HOH327 2.5 19.4 1.0
CD A:GLU63 2.9 23.5 1.0
OE2 A:GLU63 3.0 18.9 1.0
CD A:GLU28 3.1 17.0 1.0
CE1 A:HIS66 3.4 25.5 1.0
CG A:HIS66 3.4 21.7 1.0
OE2 A:GLU28 3.4 18.5 1.0
CB A:HIS66 3.7 18.1 1.0
NE2 A:GLN142 4.0 23.0 1.0
CG1 A:VAL111 4.2 19.8 1.0
CG A:GLU63 4.3 15.7 1.0
CG A:GLU28 4.4 16.1 1.0
O A:HOH451 4.5 24.5 1.0
NE2 A:HIS66 4.5 25.9 1.0
CA A:GLU63 4.5 16.1 1.0
CD2 A:HIS66 4.5 23.0 1.0
CB A:GLU28 4.7 14.9 1.0
CB A:GLU63 4.7 14.0 1.0
OE1 A:GLU108 4.8 18.4 1.0
O A:HOH313 4.8 21.4 1.0
CD A:GLN142 5.0 18.7 1.0
O A:GLU63 5.0 14.4 1.0

Iron binding site 2 out of 17 in 8y6f

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Iron binding site 2 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:31.4
occ:1.00
 OE1 B:GLU135 2.3 15.8 1.0
O L:HOH311 2.4 28.9 1.0
OE2 L:GLU135 2.4 22.3 1.0
OD1 G:ASP132 2.6 18.8 1.0
OE1 G:GLU135 2.6 21.8 1.0
OD1 L:ASP132 2.6 25.5 1.0
OD2 B:ASP132 2.8 20.2 1.0
CD B:GLU135 3.5 18.4 1.0
CD L:GLU135 3.7 20.8 1.0
CG G:ASP132 3.8 20.7 1.0
CG L:ASP132 3.8 24.6 1.0
CD G:GLU135 3.8 20.4 1.0
CG B:ASP132 4.0 24.7 1.0
OE2 B:GLU135 4.1 19.4 1.0
O L:HOH322 4.2 25.8 1.0
CB L:ASP132 4.4 19.0 1.0
OE1 L:GLU135 4.4 23.2 1.0
CB G:ASP132 4.4 17.8 1.0
CB B:GLU135 4.5 13.3 1.0
OE2 G:GLU135 4.5 22.1 1.0
CG B:GLU135 4.5 16.3 1.0
CB L:GLU135 4.6 16.8 1.0
O G:HOH452 4.6 23.6 1.0
CB B:ASP132 4.6 18.8 1.0
CG L:GLU135 4.7 21.9 1.0
CA G:ASP132 4.7 17.0 1.0
OD2 G:ASP132 4.7 20.0 1.0
CA L:ASP132 4.7 19.5 1.0
CB G:GLU135 4.8 21.6 1.0
OD2 L:ASP132 4.8 23.0 1.0
O L:HOH416 4.8 24.4 1.0
CA B:ASP132 4.9 16.1 1.0
CG G:GLU135 4.9 16.2 1.0
OD1 B:ASP132 5.0 23.4 1.0

Iron binding site 3 out of 17 in 8y6f

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Iron binding site 3 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:37.2
occ:1.00
 OE1 B:GLU28 2.1 18.7 1.0
OE1 B:GLU63 2.2 22.0 1.0
ND1 B:HIS66 2.3 23.3 1.0
O B:HOH361 2.5 22.0 1.0
CD B:GLU63 3.1 20.9 1.0
CD B:GLU28 3.1 19.8 1.0
CE1 B:HIS66 3.2 27.9 1.0
OE2 B:GLU63 3.3 26.1 1.0
CG B:HIS66 3.3 23.8 1.0
OE2 B:GLU28 3.5 14.8 1.0
CB B:HIS66 3.7 20.7 1.0
OE1 B:GLN142 4.1 19.5 1.0
CG1 B:VAL111 4.2 20.1 1.0
O B:HOH419 4.2 31.9 1.0
NE2 B:HIS66 4.4 31.2 1.0
CG B:GLU63 4.4 16.9 1.0
CA B:GLU63 4.4 18.4 1.0
CD2 B:HIS66 4.4 25.2 1.0
CG B:GLU28 4.5 15.2 1.0
CB B:GLU63 4.7 15.3 1.0
OE1 B:GLU108 4.7 16.4 1.0
CB B:GLU28 4.7 12.4 1.0
CD B:GLN142 5.0 16.6 1.0

Iron binding site 4 out of 17 in 8y6f

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Iron binding site 4 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:30.8
occ:1.00
 O C:HOH364 2.2 25.3 1.0
OE1 C:GLU28 2.2 20.4 1.0
OE1 C:GLU63 2.2 22.5 1.0
O C:HOH310 2.2 21.5 1.0
ND1 C:HIS66 2.4 25.8 1.0
CD C:GLU63 3.0 25.1 1.0
OE2 C:GLU63 3.2 21.9 1.0
CD C:GLU28 3.2 17.7 1.0
CE1 C:HIS66 3.3 27.7 1.0
CG C:HIS66 3.5 23.7 1.0
OE2 C:GLU28 3.5 18.1 1.0
CB C:HIS66 3.8 19.1 1.0
OE1 C:GLN142 4.0 27.0 1.0
O C:HOH386 4.1 25.1 1.0
CG1 C:VAL111 4.1 17.6 1.0
CG C:GLU63 4.4 18.7 1.0
O C:HOH458 4.5 30.5 1.0
NE2 C:HIS66 4.5 28.2 1.0
CG C:GLU28 4.5 16.3 1.0
CA C:GLU63 4.5 18.0 1.0
CD2 C:HIS66 4.6 24.7 1.0
CB C:GLU63 4.7 15.6 1.0
CD C:GLN142 4.8 25.1 1.0
CB C:GLU28 4.9 15.4 1.0
OE1 C:GLU108 5.0 18.7 1.0

Iron binding site 5 out of 17 in 8y6f

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Iron binding site 5 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:39.4
occ:1.00
 OE1 D:GLU135 2.7 19.1 1.0
OD1 D:ASP132 3.5 27.6 1.0
CD D:GLU135 3.9 20.8 1.0
O D:HOH352 4.5 24.2 1.0
OE2 D:GLU135 4.5 24.4 1.0
CG D:ASP132 4.6 21.7 1.0
CB D:GLU135 4.7 18.7 1.0
CG D:GLU135 4.8 16.4 1.0

Iron binding site 6 out of 17 in 8y6f

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Iron binding site 6 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe203

b:36.0
occ:1.00
 O D:HOH304 2.0 22.5 1.0
OE1 D:GLU28 2.2 19.1 1.0
OE1 D:GLU63 2.4 25.3 1.0
ND1 D:HIS66 2.5 22.7 1.0
CD D:GLU28 3.1 21.9 1.0
CD D:GLU63 3.1 19.9 1.0
OE2 D:GLU63 3.2 27.5 1.0
CE1 D:HIS66 3.4 26.0 1.0
OE2 D:GLU28 3.4 20.6 1.0
CG D:HIS66 3.6 23.9 1.0
OE1 D:GLN142 3.8 18.1 1.0
CB D:HIS66 3.9 21.5 1.0
CG1 D:VAL111 4.0 17.1 1.0
O D:HOH330 4.1 23.5 1.0
O D:HOH423 4.3 27.4 1.0
OE2 D:GLU108 4.5 21.2 1.0
CG D:GLU63 4.5 16.7 1.0
CG D:GLU28 4.5 16.0 1.0
NE2 D:HIS66 4.5 28.8 1.0
CD2 D:HIS66 4.7 27.0 1.0
CD D:GLN142 4.7 21.4 1.0
CA D:GLU63 4.7 21.1 1.0
CB D:GLU63 4.9 17.1 1.0
CB D:GLU28 4.9 14.3 1.0

Iron binding site 7 out of 17 in 8y6f

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Iron binding site 7 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe202

b:32.8
occ:1.00
 OE1 E:GLU28 2.0 21.0 1.0
O E:HOH312 2.2 15.9 1.0
OE1 E:GLU63 2.2 17.6 1.0
ND1 E:HIS66 2.4 21.8 1.0
O E:HOH314 2.5 21.1 1.0
CD E:GLU28 3.0 20.9 1.0
CD E:GLU63 3.1 19.1 1.0
CE1 E:HIS66 3.2 23.1 1.0
OE2 E:GLU63 3.3 22.4 1.0
CG E:HIS66 3.4 21.4 1.0
OE2 E:GLU28 3.4 19.0 1.0
CB E:HIS66 3.7 17.1 1.0
OE1 E:GLN142 4.0 24.3 1.0
CG1 E:VAL111 4.2 19.5 1.0
O E:HOH344 4.3 25.6 1.0
NE2 E:HIS66 4.3 24.9 1.0
CG E:GLU28 4.4 15.2 1.0
CG E:GLU63 4.4 14.8 1.0
CD2 E:HIS66 4.4 20.4 1.0
CA E:GLU63 4.5 17.0 1.0
CB E:GLU28 4.7 15.0 1.0
CB E:GLU63 4.7 17.2 1.0
CD E:GLN142 4.8 20.7 1.0
OE1 E:GLU108 5.0 21.6 1.0

Iron binding site 8 out of 17 in 8y6f

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Iron binding site 8 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:34.7
occ:1.00
 OE1 F:GLU28 2.0 21.9 1.0
OE2 F:GLU63 2.2 22.6 1.0
O F:HOH307 2.2 23.8 1.0
O F:HOH325 2.3 23.2 1.0
ND1 F:HIS66 2.4 21.6 1.0
CD F:GLU63 3.0 21.6 1.0
CD F:GLU28 3.0 22.5 1.0
OE1 F:GLU63 3.2 23.1 1.0
CE1 F:HIS66 3.3 26.2 1.0
OE2 F:GLU28 3.4 23.6 1.0
CG F:HIS66 3.4 21.8 1.0
CB F:HIS66 3.7 18.9 1.0
OE1 F:GLN142 4.1 25.6 1.0
CG1 F:VAL111 4.1 20.8 1.0
O F:HOH354 4.3 20.9 1.0
CG F:GLU63 4.4 17.4 1.0
CG F:GLU28 4.4 18.5 1.0
NE2 F:HIS66 4.5 26.8 1.0
CA F:GLU63 4.5 17.2 1.0
O F:HOH428 4.5 23.0 1.0
CD2 F:HIS66 4.6 22.2 1.0
CB F:GLU63 4.6 16.0 1.0
CB F:GLU28 4.7 16.3 1.0
CD F:GLN142 4.8 22.1 1.0
OE1 F:GLU108 4.9 21.2 1.0

Iron binding site 9 out of 17 in 8y6f

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Iron binding site 9 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:33.5
occ:1.00
 OE1 G:GLU28 2.1 20.8 1.0
OE1 G:GLU63 2.2 18.0 1.0
ND1 G:HIS66 2.3 23.8 1.0
O G:HOH325 2.3 20.0 1.0
O G:HOH305 2.3 23.8 1.0
CD G:GLU63 3.0 21.5 1.0
CD G:GLU28 3.1 18.5 1.0
CE1 G:HIS66 3.2 23.8 1.0
OE2 G:GLU63 3.2 24.9 1.0
CG G:HIS66 3.3 21.0 1.0
OE2 G:GLU28 3.4 19.5 1.0
CB G:HIS66 3.6 15.6 1.0
OE1 G:GLN142 4.1 22.1 1.0
CG1 G:VAL111 4.2 20.9 1.0
NE2 G:HIS66 4.3 26.3 1.0
CG G:GLU63 4.4 17.6 1.0
CD2 G:HIS66 4.4 18.6 1.0
CG G:GLU28 4.4 15.8 1.0
CA G:GLU63 4.5 17.6 1.0
CB G:GLU63 4.7 17.7 1.0
CB G:GLU28 4.7 16.7 1.0
CD G:GLN142 4.9 19.3 1.0
OE1 G:GLU108 4.9 24.7 1.0

Iron binding site 10 out of 17 in 8y6f

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Iron binding site 10 out of 17 in the The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Crystal Structure of Mmps Cleavable Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:69.6
occ:1.00
 OE1 H:GLU135 2.7 23.3 1.0
OD1 J:ASP132 2.8 18.4 1.0
O J:HOH439 3.2 27.4 1.0
OD1 H:ASP132 3.3 24.4 1.0
O H:HOH430 3.6 27.5 1.0
CD H:GLU135 3.9 21.9 1.0
CG J:ASP132 3.9 20.7 1.0
OE1 J:GLU135 4.1 21.8 1.0
CB H:GLU135 4.2 18.8 1.0
CG H:ASP132 4.5 22.0 1.0
CG H:GLU135 4.6 17.5 1.0
OD2 J:ASP132 4.6 24.4 1.0
O J:HOH350 4.7 28.3 1.0
OE2 H:GLU135 4.8 23.5 1.0
CB J:ASP132 4.9 16.8 1.0

Reference:

W.Yan, H.Li, J.Ning, S.Huang, L.Jiang, P.Xu, M.Huang, C.Yuan. Engineered Protein Cages with Enhanced Extracellular Drug Release For Elevated Antitumor Efficacy. Int.J.Biol.Macromol. V. 267 31492 2024.
ISSN: ISSN 0141-8130
PubMed: 38604418
DOI: 10.1016/J.IJBIOMAC.2024.131492
Page generated: Sat Aug 10 20:27:24 2024

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