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Cadmium in PDB 3f38: Apoferritin: Complex with 2,6-Dimethylphenol

Protein crystallography data

The structure of Apoferritin: Complex with 2,6-Dimethylphenol, PDB code: 3f38 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) 20.88 / 1.75
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.988, 181.988, 181.988, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with 2,6-Dimethylphenol (pdb code 3f38). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Apoferritin: Complex with 2,6-Dimethylphenol, PDB code: 3f38:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 3f38

Go back to Cadmium Binding Sites List in 3f38
Cadmium binding site 1 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:19.0
occ:0.25
 CD A:CD1001 0.0 19.0 0.2
CD A:CD1001 1.4 21.3 0.2
OD2 A:ASP80 1.8 36.3 1.0
CG A:ASP80 2.5 25.0 1.0
OD1 A:ASP80 2.5 24.2 1.0
CB A:ASP80 3.9 22.5 1.0
O A:HOH222 4.2 33.8 1.0
CA A:ASP80 5.0 25.2 1.0

Cadmium binding site 2 out of 10 in 3f38

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Cadmium binding site 2 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:21.3
occ:0.25
 CD A:CD1001 0.0 21.3 0.2
CD A:CD1001 1.4 19.0 0.2
OD1 A:ASP80 2.9 24.2 1.0
OD2 A:ASP80 3.0 36.3 1.0
CG A:ASP80 3.4 25.0 1.0
O A:HOH222 4.9 33.8 1.0
CB A:ASP80 4.9 22.5 1.0

Cadmium binding site 3 out of 10 in 3f38

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Cadmium binding site 3 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:31.7
occ:0.16
 CD A:CD1002 0.0 31.7 0.2
CD A:CD1002 1.8 47.0 0.2
OE2 A:GLU130 3.2 36.5 1.0
OE1 A:GLU130 3.3 33.6 1.0
CD A:GLU130 3.7 33.5 1.0
O A:HOH270 3.9 52.2 1.0
O A:HOH287 4.2 43.6 1.0
CB A:CYS126 4.5 26.4 1.0
N A:ASP127 4.7 25.4 1.0
CA A:ASP127 4.8 23.8 1.0
C A:CYS126 5.0 26.2 1.0
CB A:ASP127 5.0 26.2 1.0

Cadmium binding site 4 out of 10 in 3f38

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Cadmium binding site 4 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:47.0
occ:0.16
 CD A:CD1002 0.0 47.0 0.2
CD A:CD1002 1.8 31.7 0.2
OE2 A:GLU130 2.5 36.5 1.0
CD A:GLU130 3.4 33.5 1.0
OE1 A:GLU130 3.6 33.6 1.0
CD A:CD1003 4.2 39.5 0.2
CG A:GLU130 4.8 25.6 1.0
OD2 A:ASP127 4.9 49.1 1.0

Cadmium binding site 5 out of 10 in 3f38

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Cadmium binding site 5 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:39.5
occ:0.16
 OD2 A:ASP127 3.2 49.1 1.0
OG A:SER131 4.1 46.8 0.5
CD A:CD1002 4.2 47.0 0.2
OE2 A:GLU130 4.4 36.5 1.0
CG A:ASP127 4.4 45.9 1.0

Cadmium binding site 6 out of 10 in 3f38

Go back to Cadmium Binding Sites List in 3f38
Cadmium binding site 6 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:43.8
occ:0.30
 CD A:CD1004 0.0 43.8 0.3
CD A:CD1004 1.6 22.3 0.1
CD A:CD1004 1.6 23.2 0.1
OE2 A:GLU60 2.6 37.7 1.0
OE1 A:GLU57 2.6 67.5 1.0
OE1 A:GLU60 2.7 45.2 1.0
CD A:GLU60 3.0 40.6 1.0
OE2 A:GLU56 3.2 64.5 1.0
CD A:GLU57 3.7 88.8 1.0
CD A:GLU56 3.7 65.1 1.0
CG A:GLU56 3.9 30.9 1.0
OE2 A:GLU57 4.1 64.9 1.0
CG A:GLU60 4.5 27.6 1.0
OE1 A:GLU56 4.6 49.6 1.0
O A:HOH202 4.6 45.4 1.0
CG A:GLU57 4.9 32.3 1.0

Cadmium binding site 7 out of 10 in 3f38

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Cadmium binding site 7 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:23.2
occ:0.10
 CD A:CD1004 0.0 23.2 0.1
CD A:CD1004 1.6 43.8 0.3
OE2 A:GLU60 2.4 37.7 1.0
OE1 A:GLU57 2.5 67.5 1.0
OE2 A:GLU57 3.0 64.9 1.0
CD A:CD1004 3.0 22.3 0.1
CD A:GLU57 3.1 88.8 1.0
CD A:GLU60 3.4 40.6 1.0
OE1 A:GLU60 3.6 45.2 1.0
CG A:GLU57 4.6 32.3 1.0
NH2 A:ARG64 4.6 50.8 0.5
CG A:GLU60 4.8 27.6 1.0
OE2 A:GLU56 4.8 64.5 1.0

Cadmium binding site 8 out of 10 in 3f38

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Cadmium binding site 8 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:22.3
occ:0.10
 CD A:CD1004 0.0 22.3 0.1
CD A:CD1004 1.6 43.8 0.3
OE1 A:GLU60 2.1 45.2 1.0
OE2 A:GLU56 2.2 64.5 1.0
CD A:GLU60 3.0 40.6 1.0
CD A:CD1004 3.0 23.2 0.1
CD A:GLU56 3.1 65.1 1.0
OE2 A:GLU60 3.3 37.7 1.0
CG A:GLU56 3.6 30.9 1.0
OE1 A:GLU57 4.0 67.5 1.0
OE1 A:GLU56 4.1 49.6 1.0
CG A:GLU60 4.4 27.6 1.0
O A:HOH202 4.4 45.4 1.0

Cadmium binding site 9 out of 10 in 3f38

Go back to Cadmium Binding Sites List in 3f38
Cadmium binding site 9 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:32.2
occ:0.15
 O A:HOH202 1.6 45.4 1.0
OE1 A:GLU56 2.3 49.6 1.0
OE2 A:GLU53 2.5 53.8 1.0
OE1 A:GLU53 2.9 62.6 1.0
CD A:GLU53 3.1 0.9 1.0
CD A:GLU56 3.3 65.1 1.0
OE2 A:GLU56 3.5 64.5 1.0
CG A:GLU53 4.6 47.8 1.0
CG A:GLU56 4.7 30.9 1.0
CB A:GLU56 4.9 20.5 1.0

Cadmium binding site 10 out of 10 in 3f38

Go back to Cadmium Binding Sites List in 3f38
Cadmium binding site 10 out of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol


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

b:51.8
occ:0.30
 OE2 A:GLU11 2.6 28.7 1.0
OE1 A:GLU11 2.6 32.9 1.0
CD A:GLU11 2.9 30.2 1.0
O A:HOH252 3.2 33.3 1.0
OG1 A:THR10 4.1 27.0 1.0
CG A:GLU11 4.5 24.2 1.0
NE2 A:GLN120 4.6 38.0 1.0
OE1 A:GLN120 4.6 34.5 1.0
CB A:SER9 4.7 22.3 1.0
N A:THR10 5.0 22.2 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 Jul 19 15:54:21 2024

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