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Cadmium in PDB 1xz3: Complex of Apoferritin with Isoflurane

Protein crystallography data

The structure of Complex of Apoferritin with Isoflurane, PDB code: 1xz3 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 (°) 181.510, 181.510, 181.510, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21

Other elements in 1xz3:

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

Fluorine (F) 5 atoms
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Complex of Apoferritin with Isoflurane (pdb code 1xz3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Complex of Apoferritin with Isoflurane, PDB code: 1xz3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1xz3

Go back to Cadmium Binding Sites List in 1xz3
Cadmium binding site 1 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:21.4
occ:0.50
OD2 A:ASP80 2.1 18.4 1.0
OD1 A:ASP80 2.4 15.8 1.0
O A:HOH1067 2.5 38.3 1.0
CG A:ASP80 2.7 19.4 1.0
CB A:ASP80 4.2 18.0 1.0
O A:HOH1042 4.4 22.2 1.0
O A:HOH1053 4.5 30.3 1.0

Cadmium binding site 2 out of 7 in 1xz3

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Cadmium binding site 2 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:79.7
occ:0.33
OE1 A:GLU130 2.3 41.6 1.0
CD A:CD1007 2.7 46.1 0.3
CD A:GLU130 3.3 41.1 1.0
OE2 A:GLU130 3.5 42.1 1.0
O A:HOH1108 3.9 30.3 0.3
O A:HOH1197 4.3 69.5 1.0
CG A:GLU130 4.7 38.2 1.0
CD A:CD1004 5.0 64.9 0.3

Cadmium binding site 3 out of 7 in 1xz3

Go back to Cadmium Binding Sites List in 1xz3
Cadmium binding site 3 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:98.9
occ:1.00
OE2 A:GLU60 2.4 33.5 1.0
CD A:GLU60 3.1 29.8 1.0
OE1 A:GLU60 3.1 36.8 1.0
O A:HOH1132 3.2 41.8 1.0
OE2 A:GLU56 3.2 37.8 1.0
O A:HOH1140 3.2 44.5 1.0
O A:HOH1135 3.9 41.5 1.0
CD A:GLU56 4.1 32.4 1.0
CG A:GLU56 4.2 25.0 1.0
CG A:GLU60 4.6 23.7 1.0
CG A:GLU57 4.7 26.8 1.0
O A:HOH1190 5.0 49.8 1.0
CA A:GLU57 5.0 18.8 1.0

Cadmium binding site 4 out of 7 in 1xz3

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Cadmium binding site 4 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:64.9
occ:0.33
CD A:CD1007 4.6 46.1 0.3
CD A:CD1002 5.0 79.7 0.3

Cadmium binding site 5 out of 7 in 1xz3

Go back to Cadmium Binding Sites List in 1xz3
Cadmium binding site 5 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:0.9
occ:1.00
SG A:CYS48 2.0 23.1 1.0
CB A:CYS48 3.0 16.0 1.0
C A:CYS48 3.5 15.9 1.0
N A:HIS49 3.6 16.2 1.0
CD A:ARG52 3.7 28.8 1.0
CA A:CYS48 3.9 15.8 1.0
O A:CYS48 3.9 14.8 1.0
CA A:HIS49 4.0 17.7 1.0
NH1 A:ARG52 4.1 38.7 1.0
O A:GLU45 4.3 16.5 1.0
CG A:ARG52 4.4 23.6 1.0
CB A:HIS49 4.6 20.0 1.0
O A:HOH1088 4.7 45.4 1.0
NE A:ARG52 4.7 33.0 1.0
O A:HOH1095 4.7 60.7 1.0
ND1 A:HIS49 4.8 34.4 1.0
CZ A:ARG52 4.9 36.6 1.0
N A:CYS48 5.0 14.6 1.0

Cadmium binding site 6 out of 7 in 1xz3

Go back to Cadmium Binding Sites List in 1xz3
Cadmium binding site 6 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

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

b:1.0
occ:1.00
OE1 A:GLU53 2.6 39.8 1.0
OE1 A:GLU56 2.8 38.1 1.0
OE2 A:GLU53 3.0 41.7 1.0
OE2 A:GLU56 3.1 37.8 1.0
CD A:GLU53 3.2 34.0 1.0
CD A:GLU56 3.2 32.4 1.0
O A:HOH1135 3.9 41.5 1.0
CG A:GLU56 4.6 25.0 1.0
CG A:GLU53 4.7 25.4 1.0
O A:HOH1196 4.8 50.2 1.0
CB A:GLU56 4.9 19.3 1.0

Cadmium binding site 7 out of 7 in 1xz3

Go back to Cadmium Binding Sites List in 1xz3
Cadmium binding site 7 out of 7 in the Complex of Apoferritin with Isoflurane


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Complex of Apoferritin with Isoflurane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1007

b:46.1
occ:0.33
O A:HOH1197 2.2 69.5 1.0
OE2 A:GLU130 2.7 42.1 1.0
CD A:CD1002 2.7 79.7 0.3
OE1 A:GLU130 3.3 41.6 1.0
CD A:GLU130 3.3 41.1 1.0
NE2 A:HIS114 4.4 30.5 1.0
CD A:CD1004 4.6 64.9 0.3
CG A:GLU130 4.7 38.2 1.0
CE1 A:HIS114 4.8 32.0 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: Sat Dec 12 08:15:35 2020

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