Cadmium in PDB 2v2i: Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions

The structure of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions, PDB code: 2v2i was solved by N.De Val, J.P.Declercq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.334, 182.334, 182.334, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.7

The binding sites of Cadmium atom in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions (pdb code 2v2i). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions, PDB code: 2v2i:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:60.1 occ:0.33 OD1 A:ASP127 3.3 52.9 1.0 OG A:SER131 4.5 52.1 1.0 OE1 A:GLU130 4.5 44.8 1.0 CG A:ASP127 4.5 36.7 1.0

Cadmium binding site 2 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1172 b:32.9 occ:0.50 OD2 A:ASP80 2.0 25.1 1.0 OD1 A:ASP80 2.7 23.0 1.0 CG A:ASP80 2.8 23.1 1.0 CB A:ASP80 4.3 29.6 1.0 O A:HOH2097 4.6 28.3 1.0

Cadmium binding site 3 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1173 b:35.4 occ:0.33 OE1 A:GLU130 2.4 44.8 1.0 OE2 A:GLU130 3.0 32.2 1.0 CD A:GLU130 3.0 37.8 1.0 CG A:GLU130 4.5 30.1 1.0 CD A:CD1174 4.6 31.2 0.3

Cadmium binding site 4 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1174 b:31.2 occ:0.33 CE1 A:HIS114 2.6 30.9 1.0 NE2 A:HIS114 2.7 31.6 1.0 CB A:CYS126 3.4 38.9 1.0 OE2 A:GLU130 3.5 32.2 1.0 SG A:CYS126 3.7 38.7 1.0 ND1 A:HIS114 3.8 25.8 1.0 CD2 A:HIS114 4.0 27.9 1.0 CG A:HIS114 4.5 26.4 1.0 CD A:CD1173 4.6 35.4 0.3 CD A:GLU130 4.6 37.8 1.0 CB A:SER118 4.6 28.0 1.0 CA A:CYS126 4.7 27.7 1.0 OG A:SER118 4.9 34.7 1.0

Cadmium binding site 5 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1175 b:49.4 occ:1.00 O A:HOH2068 2.3 49.7 1.0 OD1 A:ASP38 2.7 22.7 1.0 SG A:CYS48 2.7 26.3 1.0 O A:HOH2070 2.8 40.4 1.0 O A:HOH2055 3.1 40.9 1.0 CG A:ASP38 3.4 22.3 1.0 CB A:CYS48 3.5 19.6 1.0 CB A:ASP38 3.5 20.7 1.0 CA A:ASP38 4.1 20.1 1.0 OE2 A:GLU45 4.5 31.9 1.0 OD2 A:ASP38 4.5 26.7 1.0 CD2 A:HIS49 4.5 53.6 1.0 CG A:GLU45 4.6 31.4 1.0 NE2 A:HIS49 4.6 44.8 1.0 CD A:GLU45 4.8 43.9 1.0 CA A:GLU45 4.8 20.6 1.0 N A:ASP38 4.9 20.6 1.0 CA A:CYS48 4.9 19.2 1.0 CB A:GLU45 5.0 18.2 1.0

Cadmium binding site 6 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1176 b:64.0 occ:1.00 OE2 A:GLU60 2.5 40.6 1.0 OE1 A:GLU60 2.6 31.1 1.0 OE2 A:GLU57 2.7 37.9 1.0 OE2 A:GLU56 2.9 52.1 1.0 CD A:GLU60 2.9 31.2 1.0 CD A:GLU57 3.7 35.4 1.0 CD A:GLU56 3.7 36.9 1.0 CG A:GLU56 3.8 23.2 1.0 OE1 A:GLU57 3.9 32.0 1.0 O A:HOH2081 3.9 59.7 1.0 O A:HOH2075 4.0 42.7 1.0 CG A:GLU60 4.4 20.4 1.0 OE1 A:GLU56 4.9 41.4 1.0

Cadmium binding site 7 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1177 b:86.3 occ:1.00 OE1 A:GLU11 2.6 22.3 1.0 OE2 A:GLU11 2.6 35.7 1.0 O A:HOH2155 2.7 44.9 1.0 CD A:GLU11 2.9 31.1 1.0 O A:HOH2020 3.2 32.2 1.0 O A:HOH2011 3.9 47.8 1.0 OG1 A:THR10 4.1 27.9 1.0 CG A:GLU11 4.4 24.0 1.0 OE1 A:GLN120 4.6 30.8 1.0 NE2 A:GLN120 4.6 32.5 1.0 CB A:SER9 4.7 24.5 1.0 CD A:GLN120 4.9 35.9 1.0 N A:THR10 4.9 22.4 1.0

Cadmium binding site 8 out of 8 in the Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Wild Type Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Acidic Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1178 b:90.7 occ:1.00 OE1 A:GLU56 2.7 41.4 1.0 OE2 A:GLU53 2.9 39.9 1.0 OE1 A:GLU53 2.9 49.8 1.0 OE2 A:GLU56 3.1 52.1 1.0 CD A:GLU53 3.3 37.0 1.0 CD A:GLU56 3.3 36.9 1.0 O A:HOH2075 4.1 42.7 1.0 CG A:GLU56 4.7 23.2 1.0 CG A:GLU53 4.8 29.1 1.0

N.De Val, J.P.Declercq, C.K.Lim, R.R.Crichton. Structural Analysis of Haemin Demetallation By L-Chain Apoferritins J.Inorg.Biochem. V. 112 77 2012.
ISSN: ISSN 0162-0134
PubMed: 22561545
DOI: 10.1016/J.JINORGBIO.2012.02.031