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Cadmium in PDB 3u90: Apoferritin: Complex with Sds

Protein crystallography data

The structure of Apoferritin: Complex with Sds, PDB code: 3u90 was solved by R.Liu, W.Bu, J.Xi, S.R.Mortazavi, J.C.Cheung-Lau, I.J.Dmochowski, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.90
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.830, 181.830, 181.830, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with Sds (pdb code 3u90). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Apoferritin: Complex with Sds, PDB code: 3u90:
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 3u90

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Cadmium binding site 1 out of 14 in the Apoferritin: Complex with Sds


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd176

b:22.4
occ:0.56
OD2 A:ASP80 2.3 20.9 1.0
O A:HOH199 2.4 20.9 1.0
OD1 A:ASP80 2.5 16.5 1.0
CG A:ASP80 2.7 19.1 1.0
CB A:ASP80 4.2 18.9 1.0
O A:HOH230 4.5 21.9 1.0
O A:HOH235 4.6 23.5 1.0

Cadmium binding site 2 out of 14 in 3u90

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Cadmium binding site 2 out of 14 in the Apoferritin: Complex with Sds


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd177

b:44.0
occ:0.55
CD A:CD177 0.0 44.0 0.6
CD A:CD177 1.9 40.7 0.5
SG A:CYS126 2.7 33.7 1.0
CD A:CD183 3.4 32.2 0.7
CB A:CYS126 3.4 28.2 1.0
O A:HOH308 3.8 35.6 0.6
OE2 A:GLU130 4.5 35.2 1.0
OE1 A:GLU130 4.6 37.9 1.0
CD A:GLU130 4.8 35.7 1.0
CA A:CYS126 4.8 23.9 1.0
O A:PRO123 4.8 21.9 1.0
N A:ASP127 4.9 25.3 1.0
C A:CYS126 4.9 26.7 1.0
CA A:PRO123 5.0 22.4 1.0

Cadmium binding site 3 out of 14 in 3u90

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Cadmium binding site 3 out of 14 in the Apoferritin: Complex with Sds


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd177

b:40.7
occ:0.45
CD A:CD177 0.0 40.7 0.5
CD A:CD177 1.9 44.0 0.6
O A:HOH308 2.3 35.6 0.6
SG A:CYS126 2.5 33.7 1.0
OE1 A:GLU130 2.7 37.9 1.0
CD A:GLU130 3.1 35.7 1.0
OE2 A:GLU130 3.2 35.2 1.0
CB A:CYS126 3.6 28.2 1.0
N A:ASP127 3.9 25.3 1.0
C A:CYS126 4.0 26.7 1.0
CD A:CD183 4.1 32.2 0.7
CA A:ASP127 4.2 26.8 1.0
O A:CYS126 4.2 23.8 1.0
CG A:GLU130 4.4 28.1 1.0
CA A:CYS126 4.4 23.9 1.0
O A:PRO123 4.8 21.9 1.0
CB A:ASP127 4.9 27.8 1.0

Cadmium binding site 4 out of 14 in 3u90

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Cadmium binding site 4 out of 14 in the Apoferritin: Complex with Sds


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd178

b:53.2
occ:0.53
CD A:CD178 0.0 53.2 0.5
CD A:CD178 2.1 50.2 0.5
OE2 A:GLU57 2.5 37.4 1.0
OE2 A:GLU60 2.6 35.1 1.0
OE1 A:GLU57 2.7 36.7 1.0
CD A:GLU57 2.9 34.4 1.0
CD A:GLU60 3.5 35.0 1.0
OE1 A:GLU60 3.8 41.9 1.0
CG A:GLU57 4.4 27.8 1.0
OE2 A:GLU53 4.6 36.9 1.0
OE2 A:GLU56 4.7 43.8 1.0
CG A:GLU60 4.9 28.0 1.0

Cadmium binding site 5 out of 14 in 3u90

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Cadmium binding site 5 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd178

b:50.2
occ:0.47
CD A:CD178 0.0 50.2 0.5
CD A:CD178 2.1 53.2 0.5
OE1 A:GLU60 2.5 41.9 1.0
OE2 A:GLU60 2.6 35.1 1.0
OE2 A:GLU56 2.7 43.8 1.0
OE2 A:GLU57 2.9 37.4 1.0
CD A:GLU60 2.9 35.0 1.0
CD A:GLU56 3.5 38.2 1.0
CG A:GLU56 3.7 30.5 1.0
CD A:GLU57 3.9 34.4 1.0
OE2 A:GLU53 4.1 36.9 1.0
OE1 A:GLU57 4.3 36.7 1.0
CG A:GLU60 4.4 28.0 1.0
OE1 A:GLU56 4.6 36.6 1.0

Cadmium binding site 6 out of 14 in 3u90

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Cadmium binding site 6 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd179

b:35.8
occ:0.39
OE2 A:GLU11 2.5 24.1 1.0
O A:HOH275 2.6 42.0 1.0
OE1 A:GLU11 2.7 30.1 1.0
O A:HOH242 2.7 29.8 1.0
CD A:GLU11 3.0 29.3 1.0
OG1 A:THR10 3.7 27.5 1.0
CB A:SER9 4.4 19.1 1.0
N A:THR10 4.4 21.6 1.0
CG A:GLU11 4.5 25.6 1.0
OE1 A:GLN120 4.7 31.1 1.0
N A:GLU11 4.8 20.7 1.0
CB A:THR10 4.8 25.7 1.0
NE2 A:GLN120 4.9 25.6 1.0
CA A:SER9 5.0 21.2 1.0

Cadmium binding site 7 out of 14 in 3u90

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Cadmium binding site 7 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd180

b:57.1
occ:0.45
OE1 A:GLU53 2.5 41.2 1.0
OE1 A:GLU56 2.7 36.6 1.0
CD A:GLU56 3.4 38.2 1.0
OE2 A:GLU56 3.5 43.8 1.0
CD A:GLU53 3.6 39.1 1.0
OE2 A:GLU53 3.9 36.9 1.0
CG A:GLU56 4.7 30.5 1.0
CG A:GLU53 4.9 33.0 1.0

Cadmium binding site 8 out of 14 in 3u90

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Cadmium binding site 8 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd181

b:36.3
occ:0.42
OE1 A:GLU88 2.4 33.9 1.0
OE2 A:GLU88 2.6 32.2 1.0
CD A:GLU88 2.9 32.7 1.0
NH2 A:ARG39 4.3 25.2 1.0
CG A:GLU88 4.4 22.7 1.0
NH1 A:ARG39 4.7 21.8 1.0
CZ A:ARG39 5.0 23.6 1.0

Cadmium binding site 9 out of 14 in 3u90

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Cadmium binding site 9 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd182

b:37.4
occ:0.46
CD A:CD182 0.0 37.4 0.5
CD A:CD182 1.7 59.3 0.5
OD1 A:ASP38 2.9 24.3 1.0
SG A:CYS48 2.9 29.7 1.0
CB A:CYS48 3.4 19.4 1.0
CG A:ASP38 3.5 23.4 1.0
CB A:ASP38 3.6 20.8 1.0
CA A:ASP38 4.1 17.9 1.0
CG A:GLU45 4.5 30.8 1.0
OD2 A:ASP38 4.6 22.0 1.0
CA A:GLU45 4.7 20.6 1.0
N A:ASP38 4.8 18.2 1.0
O A:GLU45 4.9 20.2 1.0
CA A:CYS48 4.9 18.7 1.0

Cadmium binding site 10 out of 14 in 3u90

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Cadmium binding site 10 out of 14 in the Apoferritin: Complex with Sds


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd182

b:59.3
occ:0.54
CD A:CD182 0.0 59.3 0.5
CD A:CD182 1.7 37.4 0.5
SG A:CYS48 2.7 29.7 1.0
CB A:CYS48 3.5 19.4 1.0
CG A:GLU45 4.3 30.8 1.0
O A:GLU45 4.3 20.2 1.0
OD1 A:ASP38 4.4 24.3 1.0
NH1 A:ARG52 4.4 39.5 1.0
N A:HIS49 4.5 19.4 1.0
C A:CYS48 4.6 20.6 1.0
CD A:ARG52 4.6 32.4 1.0
CA A:CYS48 4.7 18.7 1.0
OE2 A:GLU45 4.8 47.0 1.0
CA A:GLU45 4.9 20.6 1.0
CB A:ASP38 5.0 20.8 1.0
CA A:HIS49 5.0 21.7 1.0
CG A:ASP38 5.0 23.4 1.0

Cadmium binding site 11 out of 14 in 3u90

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Cadmium binding site 11 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd183

b:32.2
occ:0.65
NE2 A:HIS114 2.2 27.9 1.0
SG A:CYS126 2.5 33.7 1.0
CE1 A:HIS114 2.9 28.3 1.0
CD2 A:HIS114 3.3 28.0 1.0
CD A:CD177 3.4 44.0 0.6
CB A:CYS126 3.5 28.2 1.0
ND1 A:HIS114 4.1 26.9 1.0
CD A:CD177 4.1 40.7 0.5
CG A:HIS114 4.3 27.5 1.0
OE2 A:GLU130 4.5 35.2 1.0
CA A:CYS126 4.7 23.9 1.0
CB A:SER118 4.7 27.7 1.0
OG A:SER118 5.0 31.9 1.0

Cadmium binding site 12 out of 14 in 3u90

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Cadmium binding site 12 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd184

b:52.8
occ:0.53
CD A:CD184 0.0 52.8 0.5
NE2 A:HIS132 2.4 45.5 1.0
CD A:CD184 2.7 57.4 0.5
CE1 A:HIS132 3.1 44.5 1.0
CD2 A:HIS132 3.4 38.8 1.0
ND1 A:HIS132 4.2 43.8 1.0
CG A:HIS132 4.4 39.9 1.0
O A:HOH302 4.8 32.4 1.0
CD1 A:PHE128 4.9 26.1 1.0
O A:HOH283 4.9 33.6 1.0

Cadmium binding site 13 out of 14 in 3u90

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Cadmium binding site 13 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd184

b:57.4
occ:0.47
CD A:CD184 0.0 57.4 0.5
CD A:CD184 2.7 52.8 0.5
NE2 A:HIS132 2.9 45.5 1.0
CE1 A:HIS132 3.4 44.5 1.0
CD2 A:HIS132 4.0 38.8 1.0
CB A:SER131 4.1 37.0 1.0
OG A:SER131 4.2 40.6 1.0
OD1 A:ASP127 4.3 38.1 1.0
O A:HOH300 4.6 28.3 1.0
ND1 A:HIS132 4.6 43.8 1.0
CG A:HIS132 4.9 39.9 1.0

Cadmium binding site 14 out of 14 in 3u90

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Cadmium binding site 14 out of 14 in the Apoferritin: Complex with Sds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Apoferritin: Complex with Sds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd185

b:70.0
occ:0.49
NE2 A:HIS49 2.7 44.4 1.0
CD2 A:HIS49 3.1 36.8 1.0
CE1 A:HIS49 3.9 43.5 1.0
CG A:HIS49 4.4 34.8 1.0
ND1 A:HIS49 4.8 39.5 1.0
OE1 A:GLU53 4.9 41.2 1.0

Reference:

R.Liu, W.Bu, J.Xi, S.R.Mortazavi, J.C.Cheung-Lau, I.J.Dmochowski, P.J.Loll. Beyond the Detergent Effect: A Binding Site For Sodium Dodecyl Sulfate (Sds) in Mammalian Apoferritin. Acta Crystallogr.,Sect.D V. 68 497 2012.
ISSN: ISSN 0907-4449
PubMed: 22525747
DOI: 10.1107/S0907444912002740
Page generated: Fri Aug 28 14:02:35 2020
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