Cadmium in PDB 1xz3: Complex of Apoferritin with Isoflurane

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

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

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

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 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 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 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 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 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 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 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

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