Iron in PDB 8w6u: Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min

Protein crystallography data

The structure of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min, PDB code: 8w6u was solved by W.M.Wang, H.F.Xi, W.J.Gong, D.Y.Ma, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.13 / 2.10
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.521, 180.521, 180.521, 90, 90, 90
R / Rfree (%) 18.4 / 23.4

Other elements in 8w6u:

The structure of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iron atom in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min (pdb code 8w6u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min, PDB code: 8w6u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 13 in 8w6u

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Iron binding site 1 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:38.2
occ:1.00
 OD2 A:ASP60 1.9 39.2 1.0
O A:HOH332 2.1 44.4 1.0
OD2 A:ASP138 2.1 37.0 1.0
OD2 A:ASP142 2.1 41.0 1.0
NE2 A:HIS65 2.2 30.9 1.0
CG A:ASP142 3.0 41.1 1.0
CG A:ASP60 3.0 42.5 1.0
CE1 A:HIS65 3.1 30.1 1.0
CG A:ASP138 3.1 41.3 1.0
OD1 A:ASP142 3.1 40.5 1.0
CD2 A:HIS65 3.2 29.7 1.0
OD1 A:ASP60 3.4 41.0 1.0
OD1 A:ASP138 3.5 38.4 1.0
O A:HOH378 4.0 49.9 1.0
O A:HOH371 4.1 32.4 1.0
NZ A:LYS61 4.2 36.5 1.0
ND1 A:HIS65 4.2 34.7 1.0
CB A:ASP60 4.3 35.6 1.0
CB A:ASP142 4.3 34.7 1.0
CG A:HIS65 4.3 31.9 1.0
CB A:ASP138 4.4 33.4 1.0
CH2 A:TRP134 4.6 34.9 1.0
O A:ASP138 4.9 35.0 1.0

Iron binding site 2 out of 13 in 8w6u

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Iron binding site 2 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:110.5
occ:1.00
 NE2 A:HIS56 2.6 44.2 1.0
O A:HOH378 2.9 49.9 1.0
OE2 A:GLU174 2.9 114.4 1.0
CD2 A:HIS56 3.3 48.5 1.0
OE1 A:GLU174 3.5 108.1 1.0
CD A:GLU174 3.5 115.9 1.0
CE1 A:HIS56 3.7 41.6 1.0
OE1 A:GLU145 4.2 54.0 1.0
NZ A:LYS141 4.4 81.8 1.0
CG A:HIS56 4.6 37.7 1.0
OE2 A:GLU145 4.6 72.1 1.0
ND1 A:HIS56 4.7 44.7 1.0
CD A:GLU145 4.9 60.8 1.0
CG A:GLU174 4.9 101.0 1.0

Iron binding site 3 out of 13 in 8w6u

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Iron binding site 3 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:125.9
occ:0.25
 OE1 A:GLU164 1.8 30.0 1.0
FE A:FE212 2.7 132.5 0.2
CD A:GLU164 3.1 30.0 1.0
OE2 A:GLU164 3.8 30.0 1.0
CG A:GLU164 4.2 30.0 1.0

Iron binding site 4 out of 13 in 8w6u

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Iron binding site 4 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:104.5
occ:1.00
 O A:HOH321 2.2 51.4 1.0
OD2 A:ASP94 2.6 50.2 1.0
CG A:ASP94 3.5 40.2 1.0
OD1 A:ASP94 3.8 35.6 1.0
O A:HOH335 4.5 54.4 1.0
OG A:SER93 4.6 48.3 1.0
CB A:ASP94 4.9 33.2 1.0

Iron binding site 5 out of 13 in 8w6u

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Iron binding site 5 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:83.7
occ:1.00
 OD2 A:ASP43 1.8 47.4 1.0
NE2 A:HIS39 2.6 40.5 1.0
CG A:ASP43 2.7 46.8 1.0
O A:HOH301 2.9 52.3 1.0
OD1 A:ASP43 3.4 41.8 1.0
O A:HOH406 3.4 59.3 1.0
CD2 A:HIS39 3.5 37.3 1.0
CB A:ASP43 3.5 38.7 1.0
CE1 A:HIS39 3.6 43.3 1.0
CG A:HIS39 4.7 37.5 1.0
ND1 A:HIS39 4.7 42.6 1.0
CA A:ASP43 4.9 41.7 1.0

Iron binding site 6 out of 13 in 8w6u

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Iron binding site 6 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:45.1
occ:0.58
 NZ A:LYS159 3.3 37.8 1.0
N A:ALA95 3.4 35.1 1.0
O A:HOH394 3.7 39.1 1.0
CB A:ASP94 3.7 33.2 1.0
CD1 A:PHE45 3.7 36.3 1.0
CA A:ASP94 3.9 35.2 1.0
CG A:PHE45 3.9 42.8 1.0
CB A:ALA95 3.9 31.5 1.0
CB A:PHE45 3.9 34.4 1.0
C A:ASP94 4.1 35.7 1.0
CD A:LYS159 4.2 62.1 1.0
CE A:LYS159 4.3 37.0 1.0
CA A:ALA95 4.3 37.0 1.0
CE1 A:PHE45 4.4 43.2 1.0
CA A:PHE45 4.5 32.3 1.0
O A:PHE45 4.5 39.3 1.0
O A:HOH356 4.6 50.8 1.0
CD2 A:PHE45 4.7 34.9 1.0
CG A:ASP94 4.9 40.2 1.0

Iron binding site 7 out of 13 in 8w6u

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Iron binding site 7 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:49.2
occ:0.52
 NZ A:LYS89 3.4 42.4 1.0
CE A:LYS89 3.7 47.8 1.0
CD A:LYS89 3.9 39.3 1.0
CB A:ALA87 4.5 41.5 1.0
CG A:LYS89 4.9 42.1 1.0
O A:HOH318 5.0 50.2 1.0

Iron binding site 8 out of 13 in 8w6u

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Iron binding site 8 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:37.5
occ:0.52
 O A:HOH333 2.9 39.1 1.0
O A:HOH422 3.5 57.9 1.0
CA A:LEU119 3.7 36.1 1.0
N A:LEU119 3.8 37.4 1.0
CG A:LYS118 4.0 35.6 1.0
C A:LYS118 4.0 37.2 1.0
CD A:LYS118 4.1 27.4 1.0
O A:LYS118 4.1 34.1 1.0
CB A:LEU119 4.1 35.7 1.0
CD1 A:LEU119 4.1 38.3 1.0
CB A:ALA122 4.2 38.3 1.0
CE A:LYS118 4.5 44.8 1.0
CB A:LYS118 4.5 33.0 1.0
O A:HOH413 4.8 41.0 1.0
CG A:LEU119 4.8 33.2 1.0
O A:HOH428 4.8 51.8 1.0
O A:HOH323 4.9 47.2 1.0
O A:HOH421 4.9 37.5 1.0
CA A:LYS118 4.9 35.4 1.0
C A:LEU119 4.9 39.1 1.0

Iron binding site 9 out of 13 in 8w6u

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Iron binding site 9 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:38.7
occ:0.46
 N A:LYS89 3.0 39.2 1.0
N A:SER90 3.4 35.6 1.0
O A:ALA87 3.5 42.6 1.0
CA A:LYS89 3.8 32.9 1.0
CB A:LYS89 3.8 35.9 1.0
C A:VAL88 3.9 43.0 1.0
CA A:VAL88 3.9 34.2 1.0
O A:SER90 3.9 46.2 1.0
OG A:SER90 4.0 48.7 1.0
C A:LYS89 4.0 42.8 1.0
CA A:SER90 4.4 44.5 1.0
CG A:LYS89 4.5 42.1 1.0
C A:ALA87 4.5 40.8 1.0
C A:SER90 4.6 47.6 1.0
CB A:SER90 4.6 41.5 1.0
N A:VAL88 4.7 34.1 1.0
CG1 A:VAL88 4.8 38.0 1.0
CB A:VAL88 5.0 36.7 1.0
O A:HOH381 5.0 50.7 1.0

Iron binding site 10 out of 13 in 8w6u

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Iron binding site 10 out of 13 in the Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Ferritin From Ureaplasma Diversum Soaking in FE2+ Solution For 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:107.1
occ:1.00
 OD2 A:ASP42 3.0 50.6 1.0
OD1 A:ASP42 3.7 45.3 1.0
CG A:ASP42 3.7 41.2 1.0
CB A:PRO48 4.0 40.1 1.0
O A:HOH352 4.7 56.4 1.0
CG A:PRO48 4.8 39.4 1.0
O A:HOH314 5.0 46.2 1.0

Reference:

W.Wang, H.Xi, D.Fu, D.Ma, W.Gong, Y.Zhao, X.Li, L.Wu, Y.Guo, G.Zhao, H.Wang. Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized By Protein Nanocages. J.Am.Chem.Soc. V. 146 11657 2024.
ISSN: ESSN 1520-5126
PubMed: 38641862
DOI: 10.1021/JACS.3C13830
Page generated: Sat Aug 10 18:51:20 2024

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