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Cadmium in PDB 3f33: Apoferritin: Complex with Propofol

Protein crystallography data

The structure of Apoferritin: Complex with Propofol, PDB code: 3f33 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) 35.11 / 1.70
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.487, 182.487, 182.487, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with Propofol (pdb code 3f33). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Apoferritin: Complex with Propofol, PDB code: 3f33:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 3f33

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Cadmium binding site 1 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:25.5
occ:0.50
 OD2 A:ASP80 1.9 9.2 1.0
CG A:ASP80 2.7 21.2 1.0
O A:HOH304 2.8 37.5 1.0
OD1 A:ASP80 2.8 17.7 1.0
CB A:ASP80 4.1 20.2 1.0
O A:HOH312 4.4 29.6 1.0
O A:HOH243 4.4 25.3 1.0

Cadmium binding site 2 out of 8 in 3f33

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Cadmium binding site 2 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:56.6
occ:0.16
 CD A:CD1002 0.0 56.6 0.2
CD A:CD1002 1.9 29.8 0.2
OE1 A:GLU130 2.5 43.2 1.0
CD A:GLU130 3.4 40.1 1.0
OE2 A:GLU130 3.5 39.6 1.0
O A:HOH383 4.3 67.7 1.0
O A:HOH210 4.3 21.1 0.3
O A:HOH283 4.7 39.9 1.0
CG A:GLU130 4.8 36.7 1.0
CA A:ASP127 5.0 29.8 1.0

Cadmium binding site 3 out of 8 in 3f33

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Cadmium binding site 3 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:29.8
occ:0.16
 CD A:CD1002 0.0 29.8 0.2
CD A:CD1002 1.9 56.6 0.2
O A:HOH383 2.4 67.7 1.0
OE2 A:GLU130 2.5 39.6 1.0
OE1 A:GLU130 2.6 43.2 1.0
CD A:GLU130 2.9 40.1 1.0
O A:HOH283 3.5 39.9 1.0
CG A:GLU130 4.4 36.7 1.0
NE2 A:HIS114 4.7 28.3 1.0

Cadmium binding site 4 out of 8 in 3f33

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Cadmium binding site 4 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:0.0
occ:1.00
 OE1 A:GLU56 2.5 36.2 1.0
OE1 A:GLU53 2.9 37.8 1.0
OE2 A:GLU53 3.1 37.0 1.0
OE2 A:GLU56 3.2 36.5 1.0
CD A:GLU56 3.2 33.6 1.0
CD A:GLU53 3.4 34.5 1.0
O A:HOH370 4.0 39.5 1.0
CG A:GLU56 4.6 24.6 1.0
CG A:GLU53 4.9 27.0 1.0
CD A:CD1005 4.9 29.3 0.2

Cadmium binding site 5 out of 8 in 3f33

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Cadmium binding site 5 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:0.9
occ:1.00
 OE1 A:GLU88 2.6 33.8 1.0
OE2 A:GLU88 2.7 31.5 1.0
CD A:GLU88 2.9 30.4 1.0
CG A:GLU88 4.4 23.5 1.0
NH2 A:ARG39 4.4 22.1 1.0
O A:HOH202 4.4 46.0 1.0
O A:HOH336 4.6 47.4 1.0
NH1 A:ARG39 4.8 21.9 1.0
CB A:GLU88 4.9 18.8 1.0
O A:HOH186 5.0 46.6 1.0

Cadmium binding site 6 out of 8 in 3f33

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Cadmium binding site 6 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:29.3
occ:0.25
 CD A:CD1005 0.0 29.3 0.2
CD A:CD1005 1.5 28.6 0.2
OE2 A:GLU56 2.1 36.5 1.0
OE1 A:GLU60 2.2 33.9 1.0
O A:HOH185 3.0 27.5 1.0
CD A:GLU60 3.0 29.3 1.0
OE2 A:GLU60 3.1 33.5 1.0
CD A:GLU56 3.1 33.6 1.0
OE2 A:GLU57 3.5 37.8 1.0
CG A:GLU56 3.6 24.6 1.0
OE1 A:GLU56 4.2 36.2 1.0
O A:HOH370 4.3 39.5 1.0
CG A:GLU60 4.4 23.2 1.0
CD A:GLU57 4.7 33.6 1.0
CD A:CD1003 4.9 0.0 1.0

Cadmium binding site 7 out of 8 in 3f33

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Cadmium binding site 7 out of 8 in the Apoferritin: Complex with Propofol


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:28.6
occ:0.25
 CD A:CD1005 0.0 28.6 0.2
CD A:CD1005 1.5 29.3 0.2
O A:HOH185 1.6 27.5 1.0
OE2 A:GLU57 2.4 37.8 1.0
OE2 A:GLU60 2.5 33.5 1.0
OE1 A:GLU60 2.8 33.9 1.0
OE2 A:GLU56 2.9 36.5 1.0
CD A:GLU60 3.0 29.3 1.0
CD A:GLU57 3.4 33.6 1.0
OE1 A:GLU57 3.6 36.3 1.0
O A:HOH370 3.8 39.5 1.0
CD A:GLU56 3.8 33.6 1.0
CG A:GLU56 4.0 24.6 1.0
CG A:GLU60 4.5 23.2 1.0
CG A:GLU57 4.7 24.0 1.0
O A:HOH346 4.9 46.9 1.0
OE1 A:GLU56 4.9 36.2 1.0

Cadmium binding site 8 out of 8 in 3f33

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


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 Propofol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:59.2
occ:0.50
 OE2 A:GLU11 2.5 25.1 1.0
OE1 A:GLU11 2.6 30.8 1.0
CD A:GLU11 2.9 29.1 1.0
O A:HOH292 3.0 33.8 1.0
OG1 A:THR10 4.0 23.2 1.0
CG A:GLU11 4.5 22.5 1.0
CB A:SER9 4.6 19.3 1.0
NE2 A:GLN120 4.6 34.9 1.0
OE1 A:GLN120 4.7 35.4 1.0
N A:THR10 4.9 19.8 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 13:34:32 2020
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