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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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

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;

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


Mono view


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


Mono view


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


Mono view


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


Mono view


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

Go back to Cadmium Binding Sites List in 3u90
Cadmium binding site 10 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 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

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: Sat Dec 12 08:23:17 2020

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