Cadmium in PDB 3f34: Apoferritin: Complex with 2,6-Diethylphenol

The structure of Apoferritin: Complex with 2,6-Diethylphenol, PDB code: 3f34 was solved by L.S.Vedula, N.J.Economou, M.J.Rossi, R.G.Eckenhoff, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.67 / 1.68
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.456, 181.456, 181.456, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The binding sites of Cadmium atom in the Apoferritin: Complex with 2,6-Diethylphenol (pdb code 3f34). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Apoferritin: Complex with 2,6-Diethylphenol, PDB code: 3f34:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:20.4 occ:0.25 CD A:CD1001 0.0 20.4 0.2 CD A:CD1001 1.6 21.2 0.2 OD1 A:ASP80 2.8 27.0 1.0 OD2 A:ASP80 3.0 48.3 1.0 CG A:ASP80 3.2 31.3 1.0 O A:HOH226 4.3 33.7 1.0 CB A:ASP80 4.7 29.3 1.0

Cadmium binding site 2 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:21.2 occ:0.25 CD A:CD1001 0.0 21.2 0.2 CD A:CD1001 1.6 20.4 0.2 OD2 A:ASP80 2.2 48.3 1.0 OD1 A:ASP80 2.8 27.0 1.0 CG A:ASP80 2.8 31.3 1.0 CB A:ASP80 4.2 29.3 1.0 O A:HOH226 5.0 33.7 1.0

Cadmium binding site 3 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:35.1 occ:0.16 CD A:CD1002 0.0 35.1 0.2 CD A:CD1002 1.4 36.3 0.2 OE1 A:GLU130 2.3 40.2 1.0 O A:HOH186 3.1 46.1 0.3 CD A:GLU130 3.3 38.0 1.0 OE2 A:GLU130 3.5 37.4 1.0 O A:HOH187 4.2 53.1 1.0 CD A:CD1005 4.5 38.3 0.2 CG A:GLU130 4.6 25.7 1.0 CB A:GLU130 5.0 31.4 1.0

Cadmium binding site 4 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:36.3 occ:0.16 CD A:CD1002 0.0 36.3 0.2 CD A:CD1002 1.4 35.1 0.2 O A:HOH186 1.9 46.1 0.3 OE1 A:GLU130 2.6 40.2 1.0 OE2 A:GLU130 2.8 37.4 1.0 O A:HOH187 2.8 53.1 1.0 CD A:GLU130 3.0 38.0 1.0 O A:HOH188 4.1 45.8 1.0 CG A:GLU130 4.5 25.7 1.0 NE2 A:HIS114 4.9 27.4 1.0

Cadmium binding site 5 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:0.4 occ:1.00 OE2 A:GLU60 2.5 36.7 1.0 OE2 A:GLU57 2.7 43.0 0.5 OE1 A:GLU60 3.0 57.1 1.0 CD A:GLU60 3.1 45.2 1.0 OE2 A:GLU56 3.4 54.8 1.0 OE1 A:GLU57 3.4 31.8 0.5 CD A:GLU57 3.5 0.0 0.5 CD A:GLU56 4.1 0.0 1.0 CG A:GLU56 4.2 33.5 1.0 CG A:GLU60 4.6 29.2 1.0 O A:HOH310 4.7 47.9 1.0 CG A:GLU57 4.7 45.9 0.5 CG A:GLU57 4.9 23.6 0.5

Cadmium binding site 6 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1004 b:57.4 occ:0.30 OE1 A:GLU56 2.6 54.4 1.0 OE1 A:GLU53 2.7 57.9 1.0 OE2 A:GLU53 2.9 71.7 1.0 CD A:GLU53 3.2 0.0 1.0 CD A:GLU56 3.3 0.0 1.0 OE2 A:GLU56 3.4 54.8 1.0 CG A:GLU53 4.7 49.9 1.0 CG A:GLU56 4.7 33.5 1.0 O A:HOH310 4.9 47.9 1.0

Cadmium binding site 7 out of 7 in the Apoferritin: Complex with 2,6-Diethylphenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:38.3 occ:0.16 OD2 A:ASP127 3.6 43.3 1.0 OG A:SER131 4.1 34.8 0.5 CD A:CD1002 4.5 35.1 0.2 OE1 A:GLU130 4.7 40.2 1.0 CG A:ASP127 4.8 60.2 1.0

L.S.Vedula, G.Brannigan, N.J.Economou, J.Xi, M.A.Hall, R.Liu, M.J.Rossi, W.P.Dailey, K.C.Grasty, M.L.Klein, R.G.Eckenhoff, P.J.Loll. A Unitary Anesthetic Binding Site at High Resolution. J.Biol.Chem. V. 284 24176 2009.
ISSN: ISSN 0021-9258
PubMed: 19605349
DOI: 10.1074/JBC.M109.017814