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Cadmium in PDB 1ies: Tetragonal Crystal Structure of Native Horse Spleen Ferritin

Protein crystallography data

The structure of Tetragonal Crystal Structure of Native Horse Spleen Ferritin, PDB code: 1ies was solved by T.Granier, B.Gallois, A.Dautant, B.Langlois D'estaintot, G.Precigoux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 147.229, 147.229, 152.576, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin (pdb code 1ies). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin, PDB code: 1ies:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1ies

Go back to Cadmium Binding Sites List in 1ies
Cadmium binding site 1 out of 5 in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Tetragonal Crystal Structure of Native Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:20.0
occ:0.25
OE1 A:GLU130 2.5 50.6 1.0
OE1 C:GLU130 2.6 43.9 1.0
OE1 B:GLU130 2.7 44.8 1.0
OE2 A:GLU130 3.1 49.0 1.0
CD A:GLU130 3.2 47.6 1.0
OE2 C:GLU130 3.3 39.1 1.0
CD C:GLU130 3.4 40.0 1.0
OE2 B:GLU130 3.5 43.4 1.0
CD B:GLU130 3.5 42.0 1.0
CG A:GLU130 4.7 43.9 1.0
CG C:GLU130 4.9 37.3 1.0

Cadmium binding site 2 out of 5 in 1ies

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Cadmium binding site 2 out of 5 in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Tetragonal Crystal Structure of Native Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:20.0
occ:0.35
OD1 B:ASP127 3.4 40.4 1.0
OD1 C:ASP127 3.6 40.2 1.0
OD1 A:ASP127 4.0 43.8 1.0
OE1 A:GLU130 4.4 50.6 1.0
OG A:SER131 4.4 44.1 1.0
OE1 B:GLU130 4.4 44.8 1.0
OE1 C:GLU130 4.5 43.9 1.0
OG C:SER131 4.6 46.2 1.0
CG B:ASP127 4.6 37.4 1.0
OG B:SER131 4.8 40.6 1.0
CG C:ASP127 4.8 38.7 1.0

Cadmium binding site 3 out of 5 in 1ies

Go back to Cadmium Binding Sites List in 1ies
Cadmium binding site 3 out of 5 in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Tetragonal Crystal Structure of Native Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:21.4
occ:1.00
OE2 B:GLU11 2.2 17.7 1.0
OG1 B:THR10 2.5 17.8 1.0
OE1 B:GLU11 2.7 17.6 1.0
CD B:GLU11 2.8 16.4 1.0
CB B:THR10 3.8 14.3 1.0
N B:THR10 4.1 14.0 1.0
CG2 B:THR10 4.3 13.6 1.0
CG B:GLU11 4.3 13.5 1.0
N B:GLU11 4.5 13.7 1.0
CA B:THR10 4.5 14.0 1.0
C B:THR10 4.8 14.1 1.0
CB B:SER9 4.9 11.3 1.0

Cadmium binding site 4 out of 5 in 1ies

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Cadmium binding site 4 out of 5 in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Tetragonal Crystal Structure of Native Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd203

b:20.0
occ:0.25
OE1 F:GLU130 2.4 54.2 1.0
OE1 D:GLU130 2.6 46.2 1.0
OE1 E:GLU130 2.7 52.1 1.0
OE2 F:GLU130 3.2 52.9 1.0
CD F:GLU130 3.2 52.6 1.0
OE2 D:GLU130 3.4 44.7 1.0
CD D:GLU130 3.4 45.0 1.0
OE2 E:GLU130 3.5 50.8 1.0
CD E:GLU130 3.5 49.7 1.0
CG F:GLU130 4.7 49.5 1.0
CG D:GLU130 4.9 42.5 1.0
CG E:GLU130 5.0 47.0 1.0

Cadmium binding site 5 out of 5 in 1ies

Go back to Cadmium Binding Sites List in 1ies
Cadmium binding site 5 out of 5 in the Tetragonal Crystal Structure of Native Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Tetragonal Crystal Structure of Native Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd204

b:20.0
occ:0.35
OD1 F:ASP127 4.0 43.4 1.0
OG D:SER131 4.0 50.3 1.0
OD1 E:ASP127 4.1 46.7 1.0
OD1 D:ASP127 4.1 46.5 1.0
OE1 D:GLU130 4.3 46.2 1.0
OE1 E:GLU130 4.5 52.1 1.0
CB D:GLU130 4.7 40.0 1.0
OE1 F:GLU130 4.7 54.2 1.0
O D:ASP127 4.8 35.3 1.0
OG F:SER131 4.8 49.8 1.0
OG E:SER131 4.9 46.5 1.0
N D:SER131 4.9 42.5 1.0

Reference:

T.Granier, B.Gallois, A.Dautant, B.Langlois D'estaintot, G.Precigoux. Comparison of the Structures of the Cubic and Tetragonal Forms of Horse-Spleen Apoferritin. Acta Crystallogr.,Sect.D V. 53 580 1997.
ISSN: ISSN 0907-4449
PubMed: 15299889
DOI: 10.1107/S0907444997003314
Page generated: Fri Aug 28 11:57:13 2020
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