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Cadmium in PDB 2g4h: Anomalous Substructure of Apoferritin

Protein crystallography data

The structure of Anomalous Substructure of Apoferritin, PDB code: 2g4h was solved by C.Mueller-Dieckmann, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.160, 182.160, 182.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.8

Other elements in 2g4h:

The structure of Anomalous Substructure of Apoferritin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Anomalous Substructure of Apoferritin (pdb code 2g4h). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Anomalous Substructure of Apoferritin, PDB code: 2g4h:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 2g4h

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Cadmium binding site 1 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:36.8
occ:0.50
 OE1 A:GLN86 2.4 38.8 1.0
CD A:GLN86 3.4 38.3 1.0
NE2 A:GLN86 3.9 32.4 1.0
CG A:GLN86 4.7 33.8 1.0
CB A:GLN86 5.0 27.3 1.0
CA A:GLN86 5.0 27.6 1.0
N A:LYS87 5.0 27.8 1.0

Cadmium binding site 2 out of 9 in 2g4h

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Cadmium binding site 2 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:30.3
occ:0.25
 OE2 A:GLU64 2.1 40.3 1.0
OE1 A:GLU60 2.2 44.5 1.0
OE1 A:GLU64 2.7 39.0 1.0
CD A:GLU64 2.8 28.5 1.0
OE2 A:GLU61 2.9 57.3 1.0
CD A:GLU60 3.1 30.8 1.0
CG A:GLU60 3.5 26.8 1.0
CD A:GLU61 4.0 46.3 1.0
CG A:GLU64 4.3 26.6 1.0
OE2 A:GLU60 4.3 46.6 1.0
O A:HOH229 4.3 43.8 1.0
OE1 A:GLU61 4.5 51.6 1.0
CB A:GLU60 4.9 23.9 1.0

Cadmium binding site 3 out of 9 in 2g4h

Go back to Cadmium Binding Sites List in 2g4h
Cadmium binding site 3 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:48.5
occ:0.20
 OD1 A:ASP131 2.9 51.8 1.0
OG A:SER135 3.8 47.0 1.0
OE1 A:GLU134 4.1 48.5 1.0
CG A:ASP131 4.1 35.6 1.0
CD A:CD204 4.5 45.4 0.2
CB A:GLU134 4.8 37.5 1.0
O A:ASP131 4.9 32.0 1.0
CB A:ASP131 4.9 32.5 1.0
CA A:ASP131 4.9 32.1 1.0

Cadmium binding site 4 out of 9 in 2g4h

Go back to Cadmium Binding Sites List in 2g4h
Cadmium binding site 4 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:45.4
occ:0.18
 O A:HOH306 1.4 35.8 1.0
OE1 A:GLU134 2.4 48.5 1.0
CD A:GLU134 3.3 38.6 1.0
OE2 A:GLU134 3.4 34.7 1.0
CD A:CD203 4.5 48.5 0.2
CG A:GLU134 4.7 36.6 1.0
CA A:ASP131 4.7 32.1 1.0
N A:ASP131 4.8 32.4 1.0

Cadmium binding site 5 out of 9 in 2g4h

Go back to Cadmium Binding Sites List in 2g4h
Cadmium binding site 5 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:35.1
occ:0.16
 OE2 A:GLU60 2.6 46.6 1.0
CD A:GLU60 3.4 30.8 1.0
OE1 A:GLU60 3.5 44.5 1.0
O A:HOH229 4.1 43.8 1.0
CG A:GLU57 4.7 31.3 1.0
CG A:GLU60 4.7 26.8 1.0

Cadmium binding site 6 out of 9 in 2g4h

Go back to Cadmium Binding Sites List in 2g4h
Cadmium binding site 6 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:25.1
occ:0.10
 OE1 A:GLU15 2.5 33.1 1.0
OE2 A:GLU15 2.6 39.1 1.0
CD A:GLU15 2.9 39.0 1.0
O A:HOH275 3.3 36.5 1.0
OG1 A:THR14 4.0 30.5 1.0
CG A:GLU15 4.4 28.3 1.0
NE2 A:GLN124 4.5 45.9 1.0
OE1 A:GLN124 4.5 41.7 1.0
CB A:SER13 4.7 27.3 1.0
CD A:GLN124 4.9 43.6 1.0
N A:THR14 5.0 26.1 1.0

Cadmium binding site 7 out of 9 in 2g4h

Go back to Cadmium Binding Sites List in 2g4h
Cadmium binding site 7 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:31.1
occ:0.08
 OE1 A:GLU49 2.3 43.7 1.0
CD A:GLU49 2.9 33.6 1.0
OE2 A:GLU49 2.9 51.7 1.0
O A:HOH233 4.2 41.5 1.0
CG A:GLU49 4.3 28.5 1.0

Cadmium binding site 8 out of 9 in 2g4h

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Cadmium binding site 8 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:26.6
occ:0.07
 OE2 A:GLU92 2.2 43.5 1.0
CD A:GLU92 2.9 35.0 1.0
OE1 A:GLU92 3.0 46.4 1.0
CG A:GLU92 4.4 32.6 1.0
NH2 A:ARG43 4.6 37.2 1.0
NH1 A:ARG43 4.8 34.9 1.0

Cadmium binding site 9 out of 9 in 2g4h

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Cadmium binding site 9 out of 9 in the Anomalous Substructure of Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Anomalous Substructure of Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:19.6
occ:0.05
 OD1 A:ASP42 2.9 29.5 1.0
SG A:CYS52 3.1 30.7 1.0
CG A:ASP42 3.6 24.3 1.0
O A:HOH224 3.6 41.0 1.0
CB A:ASP42 3.7 21.1 1.0
CB A:CYS52 3.8 23.6 1.0
CA A:ASP42 4.3 22.3 1.0
CG A:GLU49 4.5 28.5 1.0
OD2 A:ASP42 4.6 27.5 1.0
CA A:GLU49 4.8 25.0 1.0
O A:GLU49 5.0 23.4 1.0

Reference:

C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss. On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part IV. Efficient Determination of Anomalous Substructures in Biomacromolecules Using Longer X-Ray Wavelengths. Acta Crystallogr.,Sect.D V. 63 366 2007.
ISSN: ISSN 0907-4449
PubMed: 17327674
DOI: 10.1107/S0907444906055624
Page generated: Fri Jul 19 14:55:50 2024

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