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Cadmium in PDB 3f37: Apoferritin: Complex with 2,6-Dimethylphenol

Protein crystallography data

The structure of Apoferritin: Complex with 2,6-Dimethylphenol, PDB code: 3f37 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) 37.00 / 1.54
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.252, 181.252, 181.252, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apoferritin: Complex with 2,6-Dimethylphenol (pdb code 3f37). 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-Dimethylphenol, PDB code: 3f37:
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 3f37

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Cadmium binding site 1 out of 11 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:16.3
occ:0.25
CD A:CD1001 0.0 16.3 0.2
CD A:CD1001 1.4 14.9 0.2
OD1 A:ASP80 2.7 19.9 1.0
OD2 A:ASP80 2.9 41.8 1.0
CG A:ASP80 3.2 23.0 1.0
O A:HOH248 4.2 26.1 1.0
CB A:ASP80 4.7 19.0 1.0

Cadmium binding site 2 out of 11 in 3f37

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Cadmium binding site 2 out of 11 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:14.9
occ:0.25
CD A:CD1001 0.0 14.9 0.2
CD A:CD1001 1.4 16.3 0.2
OD2 A:ASP80 2.1 41.8 1.0
OD1 A:ASP80 2.7 19.9 1.0
CG A:ASP80 2.8 23.0 1.0
CB A:ASP80 4.2 19.0 1.0
O A:HOH248 4.7 26.1 1.0

Cadmium binding site 3 out of 11 in 3f37

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Cadmium binding site 3 out of 11 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:38.1
occ:0.16
CD A:CD1003 2.4 28.5 0.2
O A:HOH369 2.8 52.9 0.3
OE1 A:GLU130 3.4 38.2 1.0
CD A:GLU130 4.3 35.2 1.0
OE2 A:GLU130 4.4 24.1 1.0
CD A:CD1004 4.4 28.6 0.2
O A:HOH330 4.7 55.5 1.0

Cadmium binding site 4 out of 11 in 3f37

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Cadmium binding site 4 out of 11 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:Cd1003

b:28.5
occ:0.16
O A:HOH369 1.9 52.9 0.3
CD A:CD1002 2.4 38.1 0.2
O A:HOH330 2.4 55.5 1.0
OE1 A:GLU130 2.5 38.2 1.0
OE2 A:GLU130 2.5 24.1 1.0
CD A:GLU130 2.8 35.2 1.0
O A:HOH260 3.7 34.1 1.0
CG A:GLU130 4.3 25.4 1.0
NE2 A:HIS114 4.7 23.3 1.0

Cadmium binding site 5 out of 11 in 3f37

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Cadmium binding site 5 out of 11 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:Cd1004

b:28.6
occ:0.16
O A:HOH186 2.3 44.2 1.0
OD2 A:ASP127 3.4 46.4 1.0
O A:HOH192 3.6 49.1 0.3
OG A:SER131 4.3 66.1 1.0
OE1 A:GLU130 4.4 38.2 1.0
CD A:CD1002 4.4 38.1 0.2
CG A:ASP127 4.7 47.0 1.0

Cadmium binding site 6 out of 11 in 3f37

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Cadmium binding site 6 out of 11 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:Cd1005

b:36.8
occ:0.33
O A:HOH178 2.2 52.6 1.0
OE2 A:GLU11 2.5 23.0 1.0
OE1 A:GLU11 2.7 30.0 1.0
O A:HOH272 2.9 31.4 1.0
CD A:GLU11 2.9 27.6 1.0
O A:HOH376 3.9 43.0 1.0
OG1 A:THR10 4.0 23.2 1.0
CG A:GLU11 4.5 22.6 1.0
CB A:SER9 4.5 18.0 1.0
OE1 A:GLN120 4.6 42.0 1.0
NE2 A:GLN120 4.6 31.2 1.0
N A:THR10 4.7 18.8 1.0
CD A:GLN120 5.0 39.0 1.0

Cadmium binding site 7 out of 11 in 3f37

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Cadmium binding site 7 out of 11 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:Cd1006

b:34.5
occ:0.25
CD A:CD1006 0.0 34.5 0.2
CD A:CD1006 1.3 19.2 0.1
CD A:CD1006 1.5 33.7 0.2
OE2 A:GLU57 2.4 35.7 0.5
OE2 A:GLU60 2.5 35.4 1.0
OE1 A:GLU60 2.8 37.5 1.0
CD A:GLU60 3.0 38.5 1.0
OE2 A:GLU56 3.0 48.2 1.0
CD A:GLU57 3.3 47.0 0.5
OE1 A:GLU57 3.5 33.3 0.5
CD A:GLU56 4.0 75.0 1.0
CG A:GLU56 4.2 25.4 1.0
O A:HOH323 4.4 46.4 1.0
CG A:GLU60 4.5 23.0 1.0
CG A:GLU57 4.7 26.2 0.5
CG A:GLU57 4.7 28.2 0.5

Cadmium binding site 8 out of 11 in 3f37

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Cadmium binding site 8 out of 11 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:Cd1006

b:33.7
occ:0.25
CD A:CD1006 0.0 33.7 0.2
CD A:CD1006 1.5 34.5 0.2
OE2 A:GLU56 2.1 48.2 1.0
OE1 A:GLU60 2.1 37.5 1.0
CD A:CD1006 2.8 19.2 0.1
CD A:GLU60 2.9 38.5 1.0
OE2 A:GLU60 3.0 35.4 1.0
CD A:GLU56 3.1 75.0 1.0
OE2 A:GLU57 3.4 35.7 0.5
CG A:GLU56 3.6 25.4 1.0
OE1 A:GLU56 4.2 42.9 1.0
CG A:GLU60 4.4 23.0 1.0
CD A:GLU57 4.5 47.0 0.5
CD A:CD1007 4.6 96.4 0.3
OE1 A:GLU57 4.9 33.3 0.5
CB A:GLU56 5.0 18.6 1.0

Cadmium binding site 9 out of 11 in 3f37

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Cadmium binding site 9 out of 11 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:Cd1006

b:19.2
occ:0.10
CD A:CD1006 0.0 19.2 0.1
CD A:CD1006 1.3 34.5 0.2
OE2 A:GLU57 2.4 35.7 0.5
OE2 A:GLU60 2.4 35.4 1.0
OE1 A:GLU57 2.6 33.3 0.5
CD A:CD1006 2.8 33.7 0.2
CD A:GLU57 2.8 47.0 0.5
CD A:GLU60 3.4 38.5 1.0
OE1 A:GLU60 3.6 37.5 1.0
OE2 A:GLU56 4.3 48.2 1.0
CG A:GLU57 4.3 26.2 0.5
CG A:GLU57 4.4 28.2 0.5
O A:HOH323 4.7 46.4 1.0
CG A:GLU60 4.7 23.0 1.0
CA A:GLU57 5.0 16.5 0.5
CA A:GLU57 5.0 16.8 0.5

Cadmium binding site 10 out of 11 in 3f37

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Cadmium binding site 10 out of 11 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:Cd1007

b:75.0
occ:0.70
CD A:CD1007 0.0 75.0 0.7
OE1 A:GLU56 2.6 42.9 1.0
OE1 A:GLU53 2.7 42.0 1.0
OE2 A:GLU53 2.8 45.5 1.0
CD A:CD1007 2.9 96.4 0.3
CD A:GLU53 3.1 0.6 1.0
CD A:GLU56 3.3 75.0 1.0
OE2 A:GLU56 3.3 48.2 1.0
CG A:GLU53 4.6 35.0 1.0
O A:HOH323 4.6 46.4 1.0
CG A:GLU56 4.7 25.4 1.0
CB A:GLU56 5.0 18.6 1.0

Cadmium binding site 11 out of 11 in 3f37

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

b:96.4
occ:0.30
CD A:CD1007 0.0 96.4 0.3
OE1 A:GLU56 2.9 42.9 1.0
CD A:CD1007 2.9 75.0 0.7
OE2 A:GLU56 3.2 48.2 1.0
CD A:GLU56 3.3 75.0 1.0
CD A:CD1006 4.6 33.7 0.2
CG A:GLU56 4.7 25.4 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: Wed Oct 28 10:02:52 2020
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