Iron in PDB 8wpv: Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN

Protein crystallography data

The structure of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN, PDB code: 8wpv 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) 31.93 / 2.06
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.599, 180.599, 180.599, 90, 90, 90
R / Rfree (%) 21.7 / 24.9

Other elements in 8wpv:

The structure of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN (pdb code 8wpv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN, PDB code: 8wpv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8wpv

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Iron binding site 1 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:56.9
occ:1.00
 OD2 A:ASP138 1.9 63.3 1.0
NE2 A:HIS65 2.1 56.5 1.0
OD2 A:ASP60 2.1 63.8 1.0
OD2 A:ASP142 2.2 63.9 1.0
CE1 A:HIS65 2.9 61.3 1.0
CG A:ASP142 3.0 56.9 1.0
CG A:ASP138 3.0 51.7 1.0
FE A:FE202 3.1 97.3 1.0
CD2 A:HIS65 3.1 51.4 1.0
OD1 A:ASP142 3.1 57.0 1.0
CG A:ASP60 3.2 49.8 1.0
FE A:FE207 3.5 101.0 1.0
OD1 A:ASP138 3.6 63.6 1.0
OD1 A:ASP60 3.9 59.3 1.0
ND1 A:HIS65 4.1 58.7 1.0
CG A:HIS65 4.2 48.4 1.0
CB A:ASP138 4.2 52.2 1.0
O A:HOH347 4.2 53.3 1.0
CB A:ASP60 4.3 49.0 1.0
CB A:ASP142 4.4 51.6 1.0
CH2 A:TRP134 4.4 55.4 1.0
NZ A:LYS61 4.6 59.8 1.0
O A:ASP138 4.6 49.0 1.0
CE A:LYS61 4.8 50.6 1.0
O A:HOH363 4.9 78.2 1.0
CZ2 A:TRP134 5.0 52.2 1.0

Iron binding site 2 out of 10 in 8wpv

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Iron binding site 2 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:97.3
occ:1.00
 O A:HOH363 2.0 78.2 1.0
FE A:FE207 2.5 101.0 1.0
OD1 A:ASP138 2.6 63.6 1.0
O A:HOH360 2.7 75.5 1.0
OD1 A:ASP142 2.8 57.0 1.0
OD2 A:ASP138 3.0 63.3 1.0
FE A:FE201 3.1 56.9 1.0
CG A:ASP138 3.1 51.7 1.0
O A:HOH377 3.6 62.5 1.0
OD2 A:ASP60 3.6 63.8 1.0
CG A:ASP142 3.7 56.9 1.0
O A:HOH372 3.8 70.3 1.0
OD2 A:ASP142 4.0 63.9 1.0
CG A:ASP60 4.5 49.8 1.0
CB A:ASP138 4.6 52.2 1.0
OD1 A:ASP60 4.7 59.3 1.0
OE1 A:GLU145 4.7 69.0 1.0
OE2 A:GLU145 4.8 84.8 1.0
O A:ASP138 4.9 49.0 1.0
NE2 A:HIS65 4.9 56.5 1.0
N A:ASP142 5.0 43.4 1.0
CB A:ASP142 5.0 51.6 1.0

Iron binding site 3 out of 10 in 8wpv

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Iron binding site 3 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:95.2
occ:0.25
 FE A:FE204 2.4 89.1 0.2
OE2 A:GLU164 2.6 71.0 1.0
CD A:GLU164 3.4 82.6 1.0
OE1 A:GLU164 3.5 96.8 1.0
CD1 A:ILE161 4.7 43.4 1.0
CG A:GLU164 4.8 62.6 1.0

Iron binding site 4 out of 10 in 8wpv

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Iron binding site 4 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:89.1
occ:0.25
 OE1 A:GLU164 2.1 96.8 1.0
FE A:FE203 2.4 95.2 0.2
CD A:GLU164 2.9 82.6 1.0
OE2 A:GLU164 3.1 71.0 1.0
FE A:FE205 3.2 118.5 1.0
O A:HOH380 3.4 81.7 0.2
CG A:GLU164 4.4 62.6 1.0

Iron binding site 5 out of 10 in 8wpv

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Iron binding site 5 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:118.5
occ:1.00
 OE1 A:GLU164 2.3 96.8 1.0
O A:HOH380 2.8 81.7 0.2
FE A:FE206 3.0 133.7 1.0
OE1 A:GLU168 3.1 85.2 1.0
FE A:FE204 3.2 89.1 0.2
CD A:GLU164 3.3 82.6 1.0
OE2 A:GLU168 3.5 88.4 1.0
CD A:GLU168 3.6 91.0 1.0
CG A:GLU164 3.9 62.6 1.0
OE2 A:GLU164 4.1 71.0 1.0
CG A:GLU168 4.9 77.8 1.0

Iron binding site 6 out of 10 in 8wpv

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Iron binding site 6 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:133.7
occ:1.00
 O A:HOH380 2.8 81.7 0.2
FE A:FE205 3.0 118.5 1.0
O A:HOH402 3.6 67.5 0.2
OE2 A:GLU168 4.1 88.4 1.0
CD A:GLU168 4.3 91.0 1.0
OE1 A:GLU168 4.4 85.2 1.0
CG A:GLU168 4.9 77.8 1.0

Iron binding site 7 out of 10 in 8wpv

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Iron binding site 7 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:101.0
occ:1.00
 O A:HOH360 2.5 75.5 1.0
FE A:FE202 2.5 97.3 1.0
OD1 A:ASP60 2.9 59.3 1.0
O A:HOH377 2.9 62.5 1.0
OD2 A:ASP60 3.1 63.8 1.0
CG A:ASP60 3.3 49.8 1.0
OD1 A:ASP138 3.5 63.6 1.0
FE A:FE201 3.5 56.9 1.0
OD2 A:ASP138 4.0 63.3 1.0
O A:HOH363 4.1 78.2 1.0
CG A:ASP138 4.2 51.7 1.0
CZ2 A:TRP134 4.3 52.2 1.0
O A:HOH372 4.3 70.3 1.0
CH2 A:TRP134 4.6 55.4 1.0
NE2 A:HIS65 4.6 56.5 1.0
OD1 A:ASP142 4.8 57.0 1.0
CB A:ASP60 4.8 49.0 1.0
CG2 A:VAL64 4.8 48.6 1.0
CD2 A:HIS65 5.0 51.4 1.0

Iron binding site 8 out of 10 in 8wpv

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Iron binding site 8 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:116.9
occ:1.00
 OD2 A:ASP94 2.7 57.9 1.0
OD1 A:ASP94 3.0 40.2 1.0
CG A:ASP94 3.2 45.1 1.0
O A:HOH301 3.5 48.9 1.0
O A:HOH392 3.8 58.9 1.0
CE A:LYS96 4.5 68.4 1.0
N A:ALA97 4.6 39.1 1.0
CB A:LYS96 4.6 40.9 1.0
CB A:ALA97 4.6 41.3 1.0
CD A:LYS96 4.7 52.7 1.0
CB A:ASP94 4.7 37.3 1.0

Iron binding site 9 out of 10 in 8wpv

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Iron binding site 9 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:117.2
occ:1.00
 O A:HOH365 3.3 54.4 1.0
OD2 A:ASP42 3.4 46.8 1.0
OD1 A:ASP42 3.9 47.1 1.0
CG A:ASP42 4.0 46.1 1.0
CB A:PRO48 4.3 37.8 1.0
CG A:PRO48 5.0 34.9 1.0

Iron binding site 10 out of 10 in 8wpv

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Iron binding site 10 out of 10 in the Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Truncated Mutant (1-171) of Ferritin From Ureaplasma Diversum Soaked in FE2+ Solution For 30MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe210

b:112.6
occ:1.00
 O A:HOH332 2.9 60.8 1.0
O A:SER85 3.6 41.8 1.0
CL A:CL212 3.7 55.3 1.0
OE2 A:GLU29 3.8 39.3 1.0
O A:HOH340 4.0 48.3 1.0
CD A:GLU29 4.5 42.2 1.0
C A:SER85 4.8 35.7 1.0
OE1 A:GLU29 4.8 38.1 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 19:34:36 2024

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