Cadmium in PDB 3f39: Apoferritin: Complex with Phenol

The structure of Apoferritin: Complex with Phenol, PDB code: 3f39 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)	20.97 / 1.85
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.532, 181.532, 181.532, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with Phenol (pdb code 3f39). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the Apoferritin: Complex with Phenol, PDB code: 3f39:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:27.0 occ:0.35 CD A:CD1001 0.0 27.0 0.3 CD A:CD1001 1.6 12.5 0.1 OD2 A:ASP80 2.1 37.2 1.0 OD1 A:ASP80 2.7 27.6 1.0 CG A:ASP80 2.8 27.3 1.0 O A:HOH290 3.9 39.6 1.0 CB A:ASP80 4.2 25.4 1.0 O A:HOH230 4.7 39.5 1.0

Cadmium binding site 2 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:12.5 occ:0.15 CD A:CD1001 0.0 12.5 0.1 CD A:CD1001 1.6 27.0 0.3 OD1 A:ASP80 2.9 27.6 1.0 OD2 A:ASP80 2.9 37.2 1.0 CG A:ASP80 3.3 27.3 1.0 O A:HOH230 4.1 39.5 1.0 O A:HOH290 4.5 39.6 1.0 CB A:ASP80 4.7 25.4 1.0

Cadmium binding site 3 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:58.3 occ:0.16 CD A:CD1003 1.8 37.6 0.2 OE2 A:GLU130 2.7 40.0 1.0 CD A:GLU130 3.5 36.0 1.0 OE1 A:GLU130 3.6 34.8 1.0 CD A:CD1004 4.6 36.9 0.2 O A:HOH263 4.8 54.7 1.0 CG A:GLU130 5.0 35.5 1.0

Cadmium binding site 4 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:37.6 occ:0.16 CD A:CD1002 1.8 58.3 0.2 OE1 A:GLU130 2.7 34.8 1.0 OE2 A:GLU130 2.7 40.0 1.0 CD A:GLU130 3.0 36.0 1.0 O A:HOH263 3.7 54.7 1.0 CG A:GLU130 4.5 35.5 1.0 NE2 A:HIS114 4.7 27.6 1.0 O A:HOH272 4.8 52.7 1.0

Cadmium binding site 5 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1004 b:36.9 occ:0.16 OD2 A:ASP127 3.3 42.5 1.0 OG A:SER131 4.1 45.0 1.0 OE2 A:GLU130 4.5 40.0 1.0 CG A:ASP127 4.6 36.2 1.0 CD A:CD1002 4.6 58.3 0.2

Cadmium binding site 6 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:24.4 occ:0.15 CD A:CD1005 0.0 24.4 0.1 CD A:CD1005 1.8 29.7 0.1 OE2 A:GLU60 2.4 38.1 1.0 CD A:GLU60 3.2 36.8 1.0 OE1 A:GLU60 3.2 43.0 1.0 O A:HOH313 3.2 60.5 1.0 OE2 A:GLU56 3.7 43.0 1.0 O A:HOH280 4.2 50.4 1.0 CG A:GLU57 4.4 31.6 1.0 CD A:GLU56 4.6 38.7 1.0 CG A:GLU60 4.6 29.1 1.0 CG A:GLU56 4.9 29.7 1.0

Cadmium binding site 7 out of 11 in the Apoferritin: Complex with Phenol


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 Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:29.7 occ:0.15 CD A:CD1005 0.0 29.7 0.1 CD A:CD1005 1.8 24.4 0.1 OE2 A:GLU56 2.1 43.0 1.0 OE1 A:GLU60 2.2 43.0 1.0 OE2 A:GLU60 2.9 38.1 1.0 CD A:GLU60 2.9 36.8 1.0 CD A:GLU56 3.2 38.7 1.0 CG A:GLU56 3.8 29.7 1.0 OE1 A:GLU56 4.3 42.8 1.0 O A:HOH280 4.3 50.4 1.0 CG A:GLU60 4.4 29.1 1.0 O A:HOH313 4.7 60.5 1.0 CD A:CD1007 4.8 73.9 0.3

Cadmium binding site 8 out of 11 in the Apoferritin: Complex with Phenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Apoferritin: Complex with Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1006 b:56.2 occ:0.50 OE1 A:GLU11 2.5 26.7 1.0 OE2 A:GLU11 2.5 35.2 1.0 CD A:GLU11 2.9 31.4 1.0 O A:HOH256 3.2 35.8 1.0 OG1 A:THR10 4.0 29.9 1.0 CG A:GLU11 4.4 26.4 1.0 CB A:SER9 4.6 25.3 1.0 OE1 A:GLN120 4.7 39.9 1.0 NE2 A:GLN120 4.7 37.4 1.0 N A:THR10 4.8 24.8 1.0

Cadmium binding site 9 out of 11 in the Apoferritin: Complex with Phenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Apoferritin: Complex with Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1007 b:70.4 occ:0.30 CD A:CD1007 0.0 70.4 0.3 CD A:CD1007 2.3 73.9 0.3 OE2 A:GLU53 2.6 44.9 1.0 OE1 A:GLU56 2.6 42.8 1.0 OE1 A:GLU53 2.7 45.9 1.0 CD A:GLU53 3.0 42.7 1.0 CD A:GLU56 3.5 38.7 1.0 OE2 A:GLU56 3.6 43.0 1.0 O A:HOH280 4.3 50.4 1.0 CG A:GLU53 4.5 33.5 1.0 CG A:GLU56 4.8 29.7 1.0

Cadmium binding site 10 out of 11 in the Apoferritin: Complex with Phenol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Apoferritin: Complex with Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1007 b:73.9 occ:0.30 CD A:CD1007 0.0 73.9 0.3 CD A:CD1007 2.3 70.4 0.3 OE1 A:GLU56 2.6 42.8 1.0 OE2 A:GLU56 3.0 43.0 1.0 CD A:GLU56 3.1 38.7 1.0 CG A:GLU56 4.6 29.7 1.0 CD A:CD1005 4.8 29.7 0.1 OE2 A:GLU53 4.8 44.9 1.0 OE1 A:GLU53 4.9 45.9 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