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Cadmium in PDB 2v2o: Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions

Protein crystallography data

The structure of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions, PDB code: 2v2o 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) 106.00 / 1.87
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.801, 183.801, 183.801, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions (pdb code 2v2o). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions, PDB code: 2v2o:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 2v2o

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Cadmium binding site 1 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1170

b:80.7
occ:0.33
 OD1 A:ASP127 3.6 40.2 1.0
OE1 A:GLU130 4.3 36.7 1.0
OG A:SER131 4.6 36.7 1.0
CG A:ASP127 4.6 30.6 1.0

Cadmium binding site 2 out of 9 in 2v2o

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Cadmium binding site 2 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1171

b:44.5
occ:0.33
 CD A:CD1173 3.9 48.6 0.3

Cadmium binding site 3 out of 9 in 2v2o

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Cadmium binding site 3 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1172

b:20.9
occ:0.50
 OD2 A:ASP80 2.1 20.0 1.0
CG A:ASP80 3.0 20.4 1.0
OD1 A:ASP80 3.1 18.6 1.0
CB A:ASP80 4.4 18.8 1.0
O A:HOH2088 4.4 18.7 1.0
O A:HOH2090 4.7 42.8 0.5

Cadmium binding site 4 out of 9 in 2v2o

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Cadmium binding site 4 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1173

b:48.6
occ:0.33
 OE1 A:GLU130 3.1 36.7 1.0
OE2 A:GLU130 3.5 24.3 1.0
CD A:GLU130 3.7 30.4 1.0
CD A:CD1171 3.9 44.5 0.3
CB A:CYS126 4.4 26.0 1.0
N A:ASP127 4.5 26.2 1.0
C A:CYS126 4.6 24.9 1.0
CA A:ASP127 4.7 25.9 1.0
O A:CYS126 4.9 25.8 1.0

Cadmium binding site 5 out of 9 in 2v2o

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Cadmium binding site 5 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1174

b:90.1
occ:1.00
 SG A:CYS48 2.8 19.7 1.0
OD1 A:ASP38 3.1 14.8 1.0
CB A:CYS48 3.5 17.4 1.0
CG A:ASP38 3.9 16.7 1.0
CB A:ASP38 4.0 16.3 1.0
CG A:GLU45 4.1 23.1 1.0
CA A:ASP38 4.5 15.2 1.0
CA A:GLU45 4.7 17.2 1.0
O A:GLU45 4.7 15.6 1.0
OE2 A:GLU45 4.7 36.2 1.0
CB A:GLU45 4.9 18.1 1.0
OD2 A:ASP38 4.9 15.9 1.0
CD A:GLU45 4.9 25.5 1.0
CA A:CYS48 4.9 16.7 1.0

Cadmium binding site 6 out of 9 in 2v2o

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Cadmium binding site 6 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1175

b:0.4
occ:1.00
 OE1 A:GLU57 2.5 35.5 1.0
OE1 A:GLU60 2.6 38.5 1.0
OE2 A:GLU57 3.1 40.5 1.0
CD A:GLU57 3.2 33.4 1.0
CD A:GLU60 3.7 27.0 1.0
OE2 A:GLU60 4.2 37.6 1.0
OE2 A:GLU136 4.5 39.0 1.0
CG A:GLU57 4.6 27.1 1.0
CB A:GLU60 4.9 20.5 1.0
CG A:GLU60 4.9 25.0 1.0

Cadmium binding site 7 out of 9 in 2v2o

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Cadmium binding site 7 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1176

b:74.6
occ:1.00
 OE1 A:GLU11 2.6 20.4 1.0
OE2 A:GLU11 2.6 29.0 1.0
CD A:GLU11 3.0 22.6 1.0
O A:HOH2022 3.4 26.0 1.0
OG1 A:THR10 4.1 18.7 1.0
OE1 A:GLN120 4.4 26.9 1.0
CG A:GLU11 4.5 20.3 1.0
CB A:SER9 4.7 17.5 1.0
NE2 A:GLN120 4.7 28.1 1.0
O A:HOH2026 4.9 42.5 1.0
CD A:GLN120 5.0 28.5 1.0

Cadmium binding site 8 out of 9 in 2v2o

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Cadmium binding site 8 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1177

b:79.3
occ:1.00
 OE1 A:GLU56 2.3 32.2 1.0
OE1 A:GLU53 2.7 34.8 1.0
OE2 A:GLU53 2.8 34.6 1.0
CD A:GLU56 3.1 26.6 1.0
CD A:GLU53 3.1 29.3 1.0
OE2 A:GLU56 3.2 34.1 1.0
O A:HOH2074 3.8 48.4 1.0
O A:HOH2076 4.0 37.3 1.0
CG A:GLU56 4.5 24.9 1.0
CG A:GLU53 4.5 24.1 1.0
CB A:GLU56 5.0 20.1 1.0

Cadmium binding site 9 out of 9 in 2v2o

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Cadmium binding site 9 out of 9 in the Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Mutant R59M Recombinant Horse Spleen Apoferritin Cocrystallized with Haemin in Basic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1178

b:0.6
occ:1.00
 OE2 A:GLU45 2.5 36.2 1.0
OE1 A:GLU45 2.8 31.7 1.0
CD A:GLU45 2.9 25.5 1.0
CG A:GLU45 4.4 23.1 1.0

Reference:

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
Page generated: Fri Jul 19 15:14:15 2024

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