Cadmium in PDB 3u90: Apoferritin: Complex with Sds

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

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 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 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 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 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 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 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 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 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 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 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

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