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Cadmium in PDB 1xz1: Complex of Halothane with Apoferritin

Protein crystallography data

The structure of Complex of Halothane with Apoferritin, PDB code: 1xz1 was solved by R.Liu, P.J.Loll, R.G.Eckenhoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.610, 181.610, 181.610, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.2

Other elements in 1xz1:

The structure of Complex of Halothane with Apoferritin also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Bromine (Br) 1 atom
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Complex of Halothane with Apoferritin (pdb code 1xz1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Complex of Halothane with Apoferritin, PDB code: 1xz1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1xz1

Go back to Cadmium Binding Sites List in 1xz1
Cadmium binding site 1 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:20.1
occ:0.50
OD2 A:ASP80 2.1 18.7 1.0
O A:HOH2061 2.4 34.2 1.0
OD1 A:ASP80 2.5 16.7 1.0
CG A:ASP80 2.7 18.8 1.0
CB A:ASP80 4.2 17.9 1.0
O A:HOH2019 4.5 20.6 1.0
O A:HOH2048 4.5 28.1 1.0

Cadmium binding site 2 out of 6 in 1xz1

Go back to Cadmium Binding Sites List in 1xz1
Cadmium binding site 2 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:79.4
occ:0.33
OE1 A:GLU130 2.5 37.7 1.0
CD A:CD1006 2.8 53.9 0.3
CD A:GLU130 3.3 37.2 1.0
OE2 A:GLU130 3.5 37.8 1.0
CG A:GLU130 4.7 35.0 1.0

Cadmium binding site 3 out of 6 in 1xz1

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Cadmium binding site 3 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:0.8
occ:1.00
NE2 A:HIS49 2.9 35.0 1.0
CD2 A:HIS49 3.1 32.8 1.0
CD A:GLU53 3.9 33.7 1.0
OE2 A:GLU53 3.9 39.8 1.0
CG A:GLU53 4.0 25.3 1.0
CE1 A:HIS49 4.2 35.7 1.0
OE1 A:GLU53 4.3 40.9 1.0
CG A:HIS49 4.4 27.3 1.0
ND1 A:HIS49 4.9 34.5 1.0

Cadmium binding site 4 out of 6 in 1xz1

Go back to Cadmium Binding Sites List in 1xz1
Cadmium binding site 4 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:0.6
occ:1.00
OE2 A:GLU88 2.6 27.5 1.0
OE1 A:GLU88 2.6 30.4 1.0
CD A:GLU88 2.9 27.1 1.0
NH2 A:ARG39 4.1 19.9 1.0
O A:HOH2167 4.2 42.4 1.0
CG A:GLU88 4.4 21.5 1.0
NH1 A:ARG39 4.7 18.4 1.0
CZ A:ARG39 4.9 19.4 1.0
CB A:GLU88 5.0 17.9 1.0

Cadmium binding site 5 out of 6 in 1xz1

Go back to Cadmium Binding Sites List in 1xz1
Cadmium binding site 5 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:94.0
occ:1.00
OE2 A:GLU60 2.4 31.6 1.0
O A:HOH2148 3.1 39.8 1.0
O A:HOH2152 3.1 46.8 1.0
CD A:GLU60 3.2 29.4 1.0
OE2 A:GLU56 3.2 38.4 1.0
OE1 A:GLU60 3.2 36.5 1.0
O A:HOH2123 3.9 40.4 1.0
CD A:GLU56 4.1 32.3 1.0
CG A:GLU56 4.3 25.1 1.0
CG A:GLU60 4.6 23.1 1.0
CG A:GLU57 4.6 26.6 1.0
O A:HOH2181 4.9 46.3 1.0
CA A:GLU57 5.0 18.8 1.0

Cadmium binding site 6 out of 6 in 1xz1

Go back to Cadmium Binding Sites List in 1xz1
Cadmium binding site 6 out of 6 in the Complex of Halothane with Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Complex of Halothane with Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:53.9
occ:0.33
OE2 A:GLU130 2.6 37.8 1.0
CD A:CD1002 2.8 79.4 0.3
O A:HOH2026 2.9 30.1 0.7
CD A:GLU130 3.3 37.2 1.0
OE1 A:GLU130 3.3 37.7 1.0
NE2 A:HIS114 4.2 33.7 1.0
CE1 A:HIS114 4.4 33.1 1.0
CG A:GLU130 4.7 35.0 1.0

Reference:

R.Liu, P.J.Loll, R.G.Eckenhoff. Structural Basis For High-Affinity Volatile Anesthetic Binding in A Natural 4-Helix Bundle Protein. Faseb J. V. 19 567 2005.
ISSN: ISSN 0892-6638
PubMed: 15791007
DOI: 10.1096/FJ.04-3171COM
Page generated: Wed Oct 28 09:58:00 2020
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