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Iron in PDB 6l56: Fe(II) Loaded Tegillarca Granosa Ferritin

Enzymatic activity of Fe(II) Loaded Tegillarca Granosa Ferritin

All present enzymatic activity of Fe(II) Loaded Tegillarca Granosa Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Fe(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6l56 was solved by Q.Q.Jiang, X.R.Su, T.H.Ming, H.S.Huan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.12 / 1.85
Space group P 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 181.900, 182.000, 182.030, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.6

Other elements in 6l56:

The structure of Fe(II) Loaded Tegillarca Granosa Ferritin also contains other interesting chemical elements:

Sodium (Na) 36 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 72;

Binding sites:

The binding sites of Iron atom in the Fe(II) Loaded Tegillarca Granosa Ferritin (pdb code 6l56). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 72 binding sites of Iron where determined in the Fe(II) Loaded Tegillarca Granosa Ferritin, PDB code: 6l56:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 72 in 6l56

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Iron binding site 1 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:66.8
occ:1.00
 OE2 A:GLU168 3.0 29.3 1.0
FE E:FE201 3.0 70.0 1.0
FE D:FE201 3.0 77.1 1.0
OE2 E:GLU168 3.0 38.4 1.0
OE1 A:GLU168 3.0 38.0 1.0
CD A:GLU168 3.4 28.3 1.0
CD E:GLU168 3.7 30.4 1.0
O E:HOH326 3.8 28.3 1.0
OE1 E:GLU168 3.9 27.9 1.0
FE M:FE201 4.1 72.6 1.0
O E:LYS167 4.8 17.7 1.0
CG A:GLU168 4.9 17.1 1.0
CG E:GLU168 4.9 18.1 1.0
OE2 D:GLU168 4.9 34.0 1.0
OE2 M:GLU168 5.0 33.2 1.0

Iron binding site 2 out of 72 in 6l56

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Iron binding site 2 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:17.2
occ:1.00
 OE1 A:GLU25 2.2 16.5 1.0
OE1 A:GLU60 2.2 16.9 1.0
O A:HOH303 2.2 13.4 1.0
O A:HOH302 2.3 20.0 1.0
ND1 A:HIS63 2.3 17.8 1.0
CD A:GLU25 3.1 16.0 1.0
CD A:GLU60 3.1 15.8 1.0
OE2 A:GLU25 3.3 10.9 1.0
CG A:HIS63 3.3 21.0 1.0
OE2 A:GLU60 3.3 20.2 1.0
CE1 A:HIS63 3.3 22.6 1.0
CB A:HIS63 3.5 15.1 1.0
HA A:GLU60 3.6 12.1 1.0
OE1 A:GLN139 4.1 18.6 1.0
O A:HOH387 4.1 17.7 1.0
CG1 A:VAL108 4.2 11.8 1.0
CG A:GLU25 4.4 10.1 1.0
NE2 A:HIS63 4.4 22.1 1.0
CG A:GLU60 4.4 8.4 1.0
CD2 A:HIS63 4.5 18.5 1.0
HB3 A:GLU60 4.5 9.1 1.0
CA A:GLU60 4.5 10.1 1.0
HD2 A:TYR135 4.6 15.3 1.0
HE2 A:TYR135 4.7 17.4 1.0
CB A:GLU60 4.7 7.6 1.0
CB A:GLU25 4.7 8.8 1.0
HG2 A:GLU60 4.9 10.1 1.0
CD A:GLN139 4.9 17.8 1.0
CA A:GLU25 5.0 8.4 1.0

Iron binding site 3 out of 72 in 6l56

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Iron binding site 3 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:55.1
occ:1.00
 O F:HOH309 2.4 19.1 1.0
O J:HOH319 2.5 20.9 1.0
O A:HOH335 2.5 22.0 1.0
O J:HOH337 3.9 18.3 1.0
OE2 A:GLU132 4.0 14.4 1.0
OE2 J:GLU132 4.0 12.9 1.0
O A:HOH347 4.0 18.8 1.0
OE2 F:GLU132 4.1 13.3 1.0
FE A:FE2205 4.2 53.1 1.0
O J:HOH388 4.6 19.6 1.0
OE1 J:GLU132 4.6 22.5 1.0
OE1 F:GLU132 4.7 21.0 1.0
OE1 A:GLU132 4.7 19.8 1.0
CD J:GLU132 4.7 17.5 1.0
CD A:GLU132 4.8 15.7 1.0
O A:HOH338 4.8 17.5 1.0
CD F:GLU132 4.8 19.5 1.0
O F:HOH311 4.9 20.8 1.0
O J:HOH331 5.0 16.7 1.0

Iron binding site 4 out of 72 in 6l56

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Iron binding site 4 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:61.7
occ:1.00
 O J:HOH357 2.4 30.5 1.0
O F:HOH311 2.4 20.8 1.0
O J:HOH331 2.4 16.7 1.0
O A:HOH338 2.5 17.5 1.0
OD1 F:ASP120 4.2 16.1 1.0
OD2 F:ASP120 4.3 14.0 1.0
OD1 J:ASP120 4.3 15.2 1.0
OD1 A:ASP120 4.4 15.7 1.0
OD2 J:ASP120 4.5 17.1 1.0
O J:HOH388 4.5 19.6 1.0
OD2 A:ASP120 4.5 13.7 1.0
CG F:ASP120 4.7 17.6 1.0
CG J:ASP120 4.9 18.1 1.0
CG A:ASP120 4.9 18.1 1.0

Iron binding site 5 out of 72 in 6l56

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Iron binding site 5 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:53.1
occ:1.00
 OE1 A:GLU132 2.6 19.8 1.0
OE1 J:GLU132 2.6 22.5 1.0
OE1 F:GLU132 2.7 21.0 1.0
O A:HOH335 2.9 22.0 1.0
O J:HOH319 3.0 20.9 1.0
O F:HOH309 3.2 19.1 1.0
OD1 A:ASP129 3.4 17.1 1.0
OD1 F:ASP129 3.5 15.1 1.0
OD1 J:ASP129 3.6 17.5 1.0
CD A:GLU132 3.7 15.7 1.0
CD J:GLU132 3.8 17.5 1.0
CD F:GLU132 3.9 19.5 1.0
OE2 A:GLU132 4.2 14.4 1.0
FE A:FE2203 4.2 55.1 1.0
OE2 J:GLU132 4.3 12.9 1.0
OE2 F:GLU132 4.3 13.3 1.0
CG A:ASP129 4.4 17.5 1.0
O A:HOH330 4.4 28.0 1.0
CG F:ASP129 4.5 17.2 1.0
CG J:ASP129 4.5 16.2 1.0
CB A:ASP129 4.5 11.1 1.0
O J:HOH368 4.6 18.2 1.0
CA A:ASP129 4.6 8.6 1.0
O J:HOH345 4.6 21.9 1.0
CB F:ASP129 4.7 9.4 1.0
CB J:ASP129 4.7 8.5 1.0
CA F:ASP129 4.8 10.6 1.0
CA J:ASP129 4.8 10.6 1.0
O J:HOH337 4.9 18.3 1.0
O A:HOH347 5.0 18.8 1.0

Iron binding site 6 out of 72 in 6l56

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Iron binding site 6 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:71.5
occ:1.00
 OE2 H:GLU168 2.9 38.9 1.0
FE H:FE201 3.1 70.0 1.0
FE J:FE201 3.1 75.3 1.0
OE2 B:GLU168 3.2 36.1 1.0
OE1 B:GLU168 3.3 26.7 1.0
CD B:GLU168 3.6 29.1 1.0
CD H:GLU168 3.7 30.3 1.0
O T:HOH311 4.1 29.0 1.0
OE1 H:GLU168 4.1 31.5 1.0
FE T:FE201 4.5 70.3 1.0
O H:LYS167 4.8 19.5 1.0
CG H:GLU168 4.9 18.6 1.0

Iron binding site 7 out of 72 in 6l56

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Iron binding site 7 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:13.4
occ:1.00
 OE1 B:GLU25 2.1 13.7 1.0
O B:HOH304 2.2 16.7 1.0
OE1 B:GLU60 2.2 13.6 1.0
ND1 B:HIS63 2.3 14.2 1.0
O B:HOH330 2.3 15.1 1.0
CD B:GLU60 3.1 15.9 1.0
CD B:GLU25 3.1 15.3 1.0
CE1 B:HIS63 3.2 20.2 1.0
CG B:HIS63 3.2 12.4 1.0
OE2 B:GLU60 3.4 22.0 1.0
OE2 B:GLU25 3.5 16.0 1.0
CB B:HIS63 3.5 9.1 1.0
OE1 B:GLN139 4.0 21.5 1.0
O B:HOH378 4.1 19.8 1.0
CG1 B:VAL108 4.2 12.9 1.0
NE2 B:HIS63 4.3 18.9 1.0
CD2 B:HIS63 4.4 13.2 1.0
CG B:GLU25 4.4 9.8 1.0
CG B:GLU60 4.4 11.9 1.0
CA B:GLU60 4.4 7.2 1.0
CB B:GLU60 4.7 8.1 1.0
CB B:GLU25 4.7 8.1 1.0
CD B:GLN139 4.9 14.6 1.0
CA B:GLU25 5.0 9.4 1.0
O B:GLU60 5.0 8.4 1.0

Iron binding site 8 out of 72 in 6l56

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Iron binding site 8 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe203

b:54.5
occ:1.00
 O G:HOH318 2.4 16.3 1.0
O B:HOH316 2.4 16.6 1.0
O D:HOH317 2.4 17.1 1.0
OD1 G:ASP120 4.2 13.9 1.0
OD1 D:ASP120 4.2 15.3 1.0
OD1 B:ASP120 4.3 14.9 1.0
O D:HOH355 4.3 20.7 1.0
O B:HOH363 4.3 18.3 1.0
O G:HOH353 4.3 19.8 1.0
OD2 G:ASP120 4.4 15.4 1.0
OD2 D:ASP120 4.4 15.5 1.0
OD2 B:ASP120 4.4 15.1 1.0
CG G:ASP120 4.8 17.7 1.0
CG D:ASP120 4.8 15.8 1.0
CG B:ASP120 4.8 17.1 1.0

Iron binding site 9 out of 72 in 6l56

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Iron binding site 9 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe204

b:52.4
occ:1.00
 O B:HOH348 2.4 21.6 1.0
O G:HOH322 2.5 21.0 1.0
O D:HOH331 2.5 21.7 1.0
OE2 B:GLU132 4.0 12.8 1.0
OE2 G:GLU132 4.0 13.1 1.0
OE2 D:GLU132 4.1 15.2 1.0
FE B:FE2207 4.4 54.0 1.0
O B:HOH363 4.7 18.3 1.0
OE1 G:GLU132 4.7 20.2 1.0
OE1 B:GLU132 4.7 22.1 1.0
OE1 D:GLU132 4.7 20.2 1.0
O B:HOH316 4.8 16.6 1.0
CD B:GLU132 4.8 20.0 1.0
CD G:GLU132 4.8 19.0 1.0
O D:HOH355 4.8 20.7 1.0
CD D:GLU132 4.8 18.1 1.0
O G:HOH353 4.8 19.8 1.0
O G:HOH318 4.9 16.3 1.0
O D:HOH317 4.9 17.1 1.0

Iron binding site 10 out of 72 in 6l56

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Iron binding site 10 out of 72 in the Fe(II) Loaded Tegillarca Granosa Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fe(II) Loaded Tegillarca Granosa Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe207

b:54.0
occ:1.00
 OE1 G:GLU132 2.7 20.2 1.0
OE1 D:GLU132 2.7 20.2 1.0
OE1 B:GLU132 2.7 22.1 1.0
O D:HOH331 3.2 21.7 1.0
O G:HOH322 3.2 21.0 1.0
O B:HOH348 3.2 21.6 1.0
OD1 G:ASP129 3.4 13.9 1.0
OD1 D:ASP129 3.4 15.2 1.0
OD1 B:ASP129 3.5 15.2 1.0
CD G:GLU132 3.8 19.0 1.0
CD D:GLU132 3.9 18.1 1.0
CD B:GLU132 3.9 20.0 1.0
OE2 G:GLU132 4.3 13.1 1.0
OE2 D:GLU132 4.3 15.2 1.0
O B:HOH307 4.3 22.8 1.0
OE2 B:GLU132 4.4 12.8 1.0
CG G:ASP129 4.4 18.4 1.0
O D:HOH327 4.4 22.4 1.0
O G:HOH345 4.4 22.4 1.0
CG D:ASP129 4.4 18.6 1.0
FE B:FE2204 4.4 52.4 1.0
CG B:ASP129 4.5 17.8 1.0
CB G:ASP129 4.6 9.6 1.0
CB D:ASP129 4.6 9.4 1.0
CB B:ASP129 4.6 10.1 1.0
CA G:ASP129 4.7 10.8 1.0
CA D:ASP129 4.7 11.6 1.0
CA B:ASP129 4.7 8.9 1.0

Reference:

Q.Q.Jiang, X.R.Su, T.H.Ming, H.S.Huan. Crystal Structure Analysis Unravels How CU2+ in CU2+-Ferritin Nanocage Perturb the Functions of Tegillarca Granosa Ferritin To Be Published.
Page generated: Wed Aug 7 00:39:59 2024

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