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Cadmium in PDB 3f35: Apoferritin: Complex with 2,6-Diethylphenol

Protein crystallography data

The structure of Apoferritin: Complex with 2,6-Diethylphenol, PDB code: 3f35 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) 28.92 / 1.92
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.929, 182.929, 182.929, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with 2,6-Diethylphenol (pdb code 3f35). 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 2,6-Diethylphenol, PDB code: 3f35:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11;

Cadmium binding site 1 out of 11 in 3f35

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Cadmium binding site 1 out of 11 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:22.5
occ:0.25
OD2 A:ASP80 1.7 38.5 1.0
CG A:ASP80 2.5 32.6 1.0
OD1 A:ASP80 2.6 29.2 1.0
CB A:ASP80 3.9 28.9 1.0
O A:HOH210 4.3 37.3 1.0

Cadmium binding site 2 out of 11 in 3f35

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Cadmium binding site 2 out of 11 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:27.5
occ:0.25
OE1 A:GLN82 2.9 38.9 1.0
CD A:GLN82 4.1 0.2 1.0
NE2 A:GLN82 4.7 37.6 1.0
CG A:LYS83 4.7 27.2 1.0
CD A:LYS83 4.9 33.5 1.0

Cadmium binding site 3 out of 11 in 3f35

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Cadmium binding site 3 out of 11 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:51.1
occ:0.11
CD A:CD1002 0.0 51.1 0.1
CD A:CD1002 2.0 47.6 0.2
OE1 A:GLU130 2.5 49.4 1.0
CD A:GLU130 3.6 39.2 1.0
OE2 A:GLU130 3.9 47.6 1.0
CD A:CD1003 4.0 48.9 0.2
OD2 A:ASP127 4.6 55.9 1.0
CG A:GLU130 4.9 36.5 1.0

Cadmium binding site 4 out of 11 in 3f35

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Cadmium binding site 4 out of 11 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:47.6
occ:0.22
CD A:CD1002 0.0 47.6 0.2
CD A:CD1002 2.0 51.1 0.1
OE1 A:GLU130 2.6 49.4 1.0
OE2 A:GLU130 2.8 47.6 1.0
CD A:GLU130 3.0 39.2 1.0
O A:HOH231 4.2 51.4 1.0
CG A:GLU130 4.5 36.5 1.0
NE2 A:HIS114 4.9 37.4 1.0

Cadmium binding site 5 out of 11 in 3f35

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Cadmium binding site 5 out of 11 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:48.9
occ:0.16
OD2 A:ASP127 3.1 55.9 1.0
CD A:CD1002 4.0 51.1 0.1
CG A:ASP127 4.4 88.9 1.0
OE1 A:GLU130 4.4 49.4 1.0
OG A:SER131 4.6 70.3 1.0

Cadmium binding site 6 out of 11 in 3f35

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Cadmium binding site 6 out of 11 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:58.1
occ:0.33
OE1 A:GLU11 2.6 43.2 1.0
OE2 A:GLU11 2.7 35.2 1.0
CD A:GLU11 3.0 40.7 1.0
O A:HOH257 3.4 42.7 1.0
OG1 A:THR10 4.2 33.6 1.0
CG A:GLU11 4.5 31.6 1.0
OE1 A:GLN120 4.8 49.8 1.0
NE2 A:GLN120 4.8 35.5 1.0
CB A:SER9 4.9 28.0 1.0

Cadmium binding site 7 out of 11 in 3f35

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Cadmium binding site 7 out of 11 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:0.5
occ:0.75
CD A:CD1005 0.0 0.5 0.8
OE2 A:GLU56 2.5 52.3 1.0
OE2 A:GLU53 3.0 94.7 1.0
CD A:CD1005 3.2 97.1 0.2
CD A:GLU56 3.5 0.1 1.0
OE1 A:GLU56 3.7 51.4 1.0
CD A:GLU53 3.8 0.3 1.0
OE1 A:GLU53 3.9 64.5 1.0
CG A:GLU56 4.8 36.1 1.0

Cadmium binding site 8 out of 11 in 3f35

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Cadmium binding site 8 out of 11 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 8 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:97.1
occ:0.25
CD A:CD1005 0.0 97.1 0.2
OE1 A:GLU56 2.8 51.4 1.0
CD A:CD1005 3.2 0.5 0.8
CD A:GLU56 3.5 0.1 1.0
OE2 A:GLU56 3.6 52.3 1.0
CG A:GLU56 4.9 36.1 1.0

Cadmium binding site 9 out of 11 in 3f35

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Cadmium binding site 9 out of 11 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 9 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:64.9
occ:0.50
CD A:CD1006 0.0 64.9 0.5
CD A:CD1006 2.3 51.6 0.2
OE1 A:GLU60 2.5 55.5 1.0
OE2 A:GLU60 2.8 49.7 1.0
OE1 A:GLU56 2.9 51.4 1.0
CD A:GLU60 3.0 57.0 1.0
CD A:GLU56 3.2 0.1 1.0
OE2 A:GLU57 3.3 66.3 1.0
CG A:GLU56 3.7 36.1 1.0
OE2 A:GLU56 3.9 52.3 1.0
CD A:GLU57 4.4 0.4 1.0
CG A:GLU60 4.5 34.4 1.0
O A:HOH270 4.6 55.4 1.0
OE1 A:GLU53 4.7 64.5 1.0
OE1 A:GLU57 4.8 68.2 1.0

Cadmium binding site 10 out of 11 in 3f35

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Cadmium binding site 10 out of 11 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 10 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:51.6
occ:0.25
CD A:CD1006 0.0 51.6 0.2
CD A:CD1006 2.3 64.9 0.5
OE2 A:GLU57 2.4 66.3 1.0
OE2 A:GLU60 2.5 49.7 1.0
O A:HOH270 2.8 55.4 1.0
OE1 A:GLU57 2.9 68.2 1.0
CD A:GLU57 3.0 0.4 1.0
CD A:GLU60 3.5 57.0 1.0
OE1 A:GLU60 3.8 55.5 1.0
CG A:GLU57 4.5 36.5 1.0
OE1 A:GLU53 4.7 64.5 1.0
CG A:GLU60 4.9 34.4 1.0
CD A:GLU56 4.9 0.1 1.0
OE1 A:GLU56 4.9 51.4 1.0
CA A:GLU57 5.0 23.9 1.0
CG A:GLU56 5.0 36.1 1.0

Cadmium binding site 11 out of 11 in 3f35

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Cadmium binding site 11 out of 11 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 11 of Apoferritin: Complex with 2,6-Diethylphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1007

b:0.7
occ:0.50
OE1 A:GLU88 2.4 71.4 1.0
OE2 A:GLU88 2.5 64.3 1.0
CD A:GLU88 2.8 0.1 1.0
O A:HOH261 3.8 52.1 1.0
CG A:GLU88 4.2 45.2 1.0
NH2 A:ARG39 4.8 35.2 1.0
NH1 A:ARG39 4.8 29.9 1.0

Reference:

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
Page generated: Fri Aug 28 13:35:03 2020
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