Iron in PDB 8w7q: Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin

Protein crystallography data

The structure of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7q 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) 45.02 / 2.10
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.096, 180.096, 180.096, 90, 90, 90
R / Rfree (%) 16.6 / 21.5

Other elements in 8w7q:

The structure of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin (pdb code 8w7q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin, PDB code: 8w7q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8w7q

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Iron binding site 1 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:44.4
occ:1.00
 OD2 A:ASP138 2.0 43.2 1.0
NE2 A:HIS65 2.1 36.5 1.0
O A:HOH345 2.1 45.7 1.0
OD2 A:ASP60 2.2 43.3 1.0
OD2 A:ASP142 2.2 47.9 1.0
CG A:ASP142 2.9 46.6 1.0
CE1 A:HIS65 2.9 35.2 1.0
OD1 A:ASP142 2.9 40.9 1.0
CG A:ASP138 3.0 44.8 1.0
CG A:ASP60 3.0 48.0 1.0
CD2 A:HIS65 3.2 35.9 1.0
OD1 A:ASP60 3.3 48.3 1.0
OD1 A:ASP138 3.4 42.7 1.0
ND1 A:HIS65 4.1 35.1 1.0
O A:HOH412 4.1 59.2 1.0
O A:HOH382 4.3 44.5 1.0
CG A:HIS65 4.3 40.9 1.0
CB A:ASP138 4.4 37.3 1.0
CB A:ASP142 4.4 39.6 1.0
CB A:ASP60 4.4 35.5 1.0
NZ A:LYS61 4.5 39.0 1.0
CH2 A:TRP134 4.6 40.3 1.0
O A:ASP138 4.8 36.1 1.0

Iron binding site 2 out of 10 in 8w7q

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Iron binding site 2 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:133.3
occ:1.00
 O A:HOH434 2.4 66.2 1.0
O A:HOH412 3.4 59.2 1.0
O A:HOH428 3.6 48.1 1.0
OE1 A:GLU145 4.1 70.3 1.0
OE2 A:GLU145 4.2 72.5 1.0
NZ A:LYS141 4.3 79.7 1.0
CD A:GLU145 4.5 68.9 1.0

Iron binding site 3 out of 10 in 8w7q

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Iron binding site 3 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:106.9
occ:1.00
 OD2 A:ASP94 2.3 56.2 1.0
O A:HOH348 2.3 47.3 1.0
CG A:ASP94 3.3 45.3 1.0
OD1 A:ASP94 3.7 42.9 1.0
CB A:ASP94 4.7 40.5 1.0
O A:HOH335 4.7 49.8 1.0

Iron binding site 4 out of 10 in 8w7q

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Iron binding site 4 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:116.2
occ:1.00
 OD2 A:ASP42 3.6 48.9 1.0
OD1 A:ASP42 4.2 45.8 1.0
CB A:PRO48 4.3 37.3 1.0
CG A:ASP42 4.3 43.0 1.0
O A:HOH381 4.7 59.7 1.0
CG A:PRO48 4.9 43.0 1.0

Iron binding site 5 out of 10 in 8w7q

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Iron binding site 5 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:79.9
occ:0.15
 FE A:FE206 2.2 79.8 0.2
OE1 A:GLU164 2.4 70.4 1.0
CD A:GLU164 3.2 77.3 1.0
OE2 A:GLU164 3.3 95.2 1.0
FE A:FE207 4.5 134.6 1.0
CD1 A:ILE161 4.6 52.6 1.0
CG A:GLU164 4.6 66.7 1.0

Iron binding site 6 out of 10 in 8w7q

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Iron binding site 6 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:79.8
occ:0.19
 FE A:FE205 2.2 79.9 0.1
OE2 A:GLU164 2.5 95.2 1.0
FE A:FE207 2.7 134.6 1.0
O A:HOH436 2.9 106.5 0.2
CD A:GLU164 3.0 77.3 1.0
OE1 A:GLU164 3.0 70.4 1.0
CG A:GLU164 4.2 66.7 1.0

Iron binding site 7 out of 10 in 8w7q

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Iron binding site 7 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:134.6
occ:1.00
 O A:HOH436 2.0 106.5 0.2
OE2 A:GLU164 2.4 95.2 1.0
FE A:FE206 2.7 79.8 0.2
FE A:FE208 3.0 149.5 1.0
CD A:GLU164 3.0 77.3 1.0
CG A:GLU164 3.3 66.7 1.0
OE1 A:GLU164 3.8 70.4 1.0
O A:HOH456 3.9 105.1 0.2
OE1 A:GLU168 4.2 93.0 1.0
FE A:FE205 4.5 79.9 0.1
CB A:GLU164 4.8 43.6 1.0

Iron binding site 8 out of 10 in 8w7q

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Iron binding site 8 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:149.5
occ:1.00
 O A:HOH456 2.3 105.1 0.2
OE1 A:GLU168 2.9 93.0 1.0
FE A:FE210 2.9 126.8 1.0
FE A:FE207 3.0 134.6 1.0
O A:HOH436 3.0 106.5 0.2
FE A:FE209 3.3 125.7 0.2
O A:HOH377 3.7 82.9 1.0
CD A:GLU168 3.8 92.0 1.0
OE2 A:GLU168 4.2 96.0 1.0
O A:HOH457 4.4 89.4 1.0

Iron binding site 9 out of 10 in 8w7q

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Iron binding site 9 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:125.7
occ:0.25
 O A:HOH456 1.9 105.1 0.2
O A:HOH457 3.0 89.4 1.0
FE A:FE210 3.2 126.8 1.0
FE A:FE208 3.3 149.5 1.0
O A:HOH377 4.3 82.9 1.0
O A:HOH436 4.4 106.5 0.2

Iron binding site 10 out of 10 in 8w7q

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Iron binding site 10 out of 10 in the Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Fe-O Nanocluster of Form-VI in the 4-Fold Channel of Ureaplasma Diversum Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:126.8
occ:1.00
 FE A:FE208 2.9 149.5 1.0
O A:HOH377 3.0 82.9 1.0
O A:HOH457 3.0 89.4 1.0
FE A:FE209 3.2 125.7 0.2
OE1 A:GLU168 3.8 93.0 1.0
O A:HOH456 3.8 105.1 0.2
OE2 A:GLU168 4.5 96.0 1.0
CD A:GLU168 4.6 92.0 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 19:17:39 2024

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