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Cadmium in PDB 4de6: Horse Spleen Apo-Ferritin Complex with Arachidonic Acid

Protein crystallography data

The structure of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid, PDB code: 4de6 was solved by W.Bu, R.Liu, I.J.Dmochowski, P.J.Loll, R.G.Eckenhoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.32 / 2.18
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.830, 180.830, 180.830, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid (pdb code 4de6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid, PDB code: 4de6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14;

Cadmium binding site 1 out of 14 in 4de6

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Cadmium binding site 1 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:22.8
occ:0.53
OD2 A:ASP80 2.4 21.1 1.0
O A:HOH312 2.4 24.3 1.0
OD1 A:ASP80 2.5 17.4 1.0
CG A:ASP80 2.8 20.3 1.0
CB A:ASP80 4.3 19.5 1.0
O A:HOH352 4.6 21.9 1.0

Cadmium binding site 2 out of 14 in 4de6

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Cadmium binding site 2 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:47.2
occ:0.54
CD A:CD203 0.0 47.2 0.5
CD A:CD203 2.1 45.6 0.5
SG A:CYS126 2.8 36.5 1.0
CD A:CD209 3.3 32.7 0.6
CB A:CYS126 3.5 29.7 1.0
OE2 A:GLU130 4.3 37.2 1.0
OE1 A:GLU130 4.5 39.0 1.0
CD A:GLU130 4.7 37.2 1.0
O A:PRO123 4.8 23.2 1.0
CA A:CYS126 4.9 27.0 1.0
N A:ASP127 4.9 26.7 1.0
C A:CYS126 4.9 29.0 1.0

Cadmium binding site 3 out of 14 in 4de6

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Cadmium binding site 3 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:45.6
occ:0.46
CD A:CD203 0.0 45.6 0.5
CD A:CD203 2.1 47.2 0.5
OE1 A:GLU130 2.6 39.0 1.0
SG A:CYS126 2.6 36.5 1.0
CD A:GLU130 3.0 37.2 1.0
OE2 A:GLU130 3.1 37.2 1.0
CB A:CYS126 3.8 29.7 1.0
N A:ASP127 3.9 26.7 1.0
C A:CYS126 4.0 29.0 1.0
CG A:GLU130 4.2 31.6 1.0
CA A:ASP127 4.2 29.1 1.0
CD A:CD209 4.2 32.7 0.6
O A:CYS126 4.3 27.7 1.0
CA A:CYS126 4.6 27.0 1.0
CB A:ASP127 4.8 29.4 1.0
O A:PRO123 4.9 23.2 1.0
CB A:GLU130 5.0 32.9 1.0

Cadmium binding site 4 out of 14 in 4de6

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Cadmium binding site 4 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:61.3
occ:0.56
CD A:CD204 0.0 61.3 0.6
CD A:CD204 2.3 49.8 0.4
OE2 A:GLU57 2.6 40.8 1.0
O A:HOH310 2.6 48.0 1.0
OE2 A:GLU60 2.7 37.2 1.0
OE1 A:GLU57 2.9 40.3 1.0
CD A:GLU57 3.1 37.0 1.0
CD A:GLU60 3.7 38.5 1.0
OE1 A:GLU60 4.0 41.7 1.0
CG A:GLU57 4.6 30.5 1.0
OE2 A:GLU53 4.7 39.4 1.0
OE2 A:GLU56 4.8 43.8 1.0

Cadmium binding site 5 out of 14 in 4de6

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Cadmium binding site 5 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:49.8
occ:0.44
CD A:CD204 0.0 49.8 0.4
CD A:CD204 2.3 61.3 0.6
OE1 A:GLU60 2.5 41.7 1.0
OE2 A:GLU56 2.6 43.8 1.0
OE2 A:GLU60 2.7 37.2 1.0
CD A:GLU60 2.9 38.5 1.0
OE2 A:GLU57 3.2 40.8 1.0
CD A:GLU56 3.4 39.8 1.0
CG A:GLU56 3.6 32.6 1.0
OE2 A:GLU53 4.2 39.4 1.0
CD A:GLU57 4.2 37.0 1.0
CG A:GLU60 4.4 32.1 1.0
OE1 A:GLU56 4.5 39.5 1.0
O A:HOH391 4.5 44.9 1.0
OE1 A:GLU57 4.6 40.3 1.0
O A:HOH310 4.7 48.0 1.0
CB A:GLU56 4.9 26.2 1.0

Cadmium binding site 6 out of 14 in 4de6

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Cadmium binding site 6 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:40.8
occ:0.39
OE2 A:GLU11 2.6 24.6 1.0
O A:HOH358 2.7 33.0 1.0
OE1 A:GLU11 2.8 35.2 1.0
CD A:GLU11 3.0 28.4 1.0
CG2 A:THR10 3.6 24.2 1.0
N A:THR10 4.5 22.8 1.0
CB A:SER9 4.5 19.5 1.0
CG A:GLU11 4.5 27.7 1.0
OE1 A:GLN120 4.7 29.9 1.0
CB A:THR10 4.8 27.1 1.0
N A:GLU11 4.9 21.9 1.0
NE2 A:GLN120 4.9 27.9 1.0

Cadmium binding site 7 out of 14 in 4de6

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Cadmium binding site 7 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:57.1
occ:0.48
O A:HOH391 2.5 44.9 1.0
OE1 A:GLU56 2.7 39.5 1.0
OE1 A:GLU53 2.7 46.8 1.0
O A:HOH412 3.2 46.7 1.0
CD A:GLU56 3.5 39.8 1.0
CD A:GLU53 3.6 43.4 1.0
OE2 A:GLU56 3.7 43.8 1.0
OE2 A:GLU53 3.9 39.4 1.0
CG A:GLU56 4.8 32.6 1.0
CG A:GLU53 4.9 36.0 1.0

Cadmium binding site 8 out of 14 in 4de6

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Cadmium binding site 8 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:43.8
occ:0.48
OE1 A:GLU88 2.5 33.9 1.0
OE2 A:GLU88 2.6 34.1 1.0
CD A:GLU88 2.9 31.3 1.0
O A:HOH403 3.1 36.4 1.0
NH2 A:ARG39 4.2 25.6 1.0
CG A:GLU88 4.4 26.8 1.0
NH1 A:ARG39 4.7 24.3 1.0
CZ A:ARG39 5.0 25.0 1.0

Cadmium binding site 9 out of 14 in 4de6

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Cadmium binding site 9 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:38.5
occ:0.42
CD A:CD208 0.0 38.5 0.4
CD A:CD208 1.7 60.5 0.6
OD1 A:ASP38 2.8 23.7 1.0
SG A:CYS48 2.9 31.7 1.0
O A:HOH401 3.2 28.5 1.0
CB A:ASP38 3.3 22.2 1.0
CG A:ASP38 3.4 24.4 1.0
CB A:CYS48 3.4 22.0 1.0
CA A:ASP38 3.9 18.6 1.0
O A:HOH324 4.0 39.1 1.0
CG A:GLU45 4.4 33.3 1.0
OD2 A:ASP38 4.5 23.8 1.0
N A:ASP38 4.6 19.2 1.0
CA A:GLU45 4.7 21.9 1.0
CA A:CYS48 4.9 20.8 1.0
O A:GLU45 4.9 21.3 1.0
O A:HOH377 5.0 39.9 1.0
CB A:GLU45 5.0 22.9 1.0

Cadmium binding site 10 out of 14 in 4de6

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Cadmium binding site 10 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:60.5
occ:0.58
CD A:CD208 0.0 60.5 0.6
CD A:CD208 1.7 38.5 0.4
O A:HOH324 2.4 39.1 1.0
SG A:CYS48 2.7 31.7 1.0
CB A:CYS48 3.5 22.0 1.0
O A:HOH377 3.9 39.9 1.0
OD1 A:ASP38 4.2 23.7 1.0
CG A:GLU45 4.3 33.3 1.0
O A:GLU45 4.5 21.3 1.0
O A:HOH401 4.5 28.5 1.0
NH1 A:ARG52 4.6 42.9 1.0
N A:HIS49 4.6 22.9 1.0
C A:CYS48 4.6 23.3 1.0
CB A:ASP38 4.7 22.2 1.0
CD A:ARG52 4.7 33.1 1.0
CA A:CYS48 4.7 20.8 1.0
CG A:ASP38 4.7 24.4 1.0
CA A:GLU45 5.0 21.9 1.0

Cadmium binding site 11 out of 14 in 4de6

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Cadmium binding site 11 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:32.7
occ:0.62
NE2 A:HIS114 2.2 27.1 1.0
SG A:CYS126 2.6 36.5 1.0
CE1 A:HIS114 2.8 30.3 1.0
CD A:CD203 3.3 47.2 0.5
CD2 A:HIS114 3.3 26.9 1.0
CB A:CYS126 3.4 29.7 1.0
OG A:SER118 3.8 37.7 1.0
ND1 A:HIS114 4.0 25.6 1.0
OE2 A:GLU130 4.1 37.2 1.0
CD A:CD203 4.2 45.6 0.5
CG A:HIS114 4.3 27.3 1.0
CA A:CYS126 4.7 27.0 1.0
CD A:GLU130 5.0 37.2 1.0

Cadmium binding site 12 out of 14 in 4de6

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Cadmium binding site 12 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:60.6
occ:0.63
NE2 A:HIS132 2.4 46.4 1.0
O A:HOH335 2.6 39.0 1.0
CD2 A:HIS132 3.3 41.2 1.0
CE1 A:HIS132 3.4 47.3 1.0
ND1 A:HIS132 4.5 44.5 1.0
CG A:HIS132 4.5 43.3 1.0
NH1 A:ARG64 4.7 49.1 1.0
CD1 A:PHE128 4.8 27.1 1.0

Cadmium binding site 13 out of 14 in 4de6

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Cadmium binding site 13 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:64.9
occ:0.37
O A:HOH330 2.5 35.8 1.0
OD2 A:ASP127 2.8 34.9 1.0
OG A:SER131 2.8 42.9 1.0
OD1 A:ASP127 3.3 38.5 1.0
CG A:ASP127 3.4 35.5 1.0
CB A:SER131 4.0 38.8 1.0
O A:HOH335 4.1 39.0 1.0
O A:ASP127 4.7 28.9 1.0
CB A:ASP127 4.9 29.4 1.0

Cadmium binding site 14 out of 14 in 4de6

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Cadmium binding site 14 out of 14 in the Horse Spleen Apo-Ferritin Complex with Arachidonic Acid


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Horse Spleen Apo-Ferritin Complex with Arachidonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:73.9
occ:0.28
O A:HOH388 2.6 47.6 1.0
OE1 A:GLU53 4.2 46.8 1.0
CG A:GLU53 4.5 36.0 1.0
CD A:GLU53 4.6 43.4 1.0

Reference:

W.Bu, R.Liu, J.C.Cheung-Lau, I.J.Dmochowski, P.J.Loll, R.G.Eckenhoff. Ferritin Couples Iron and Fatty Acid Metabolism. Faseb J. V. 26 2394 2012.
ISSN: ISSN 0892-6638
PubMed: 22362897
DOI: 10.1096/FJ.11-198853
Page generated: Fri Aug 28 14:23:45 2020
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