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Cadmium in PDB 6msx: Iron Containing Ferritin at 1.43A

Protein crystallography data

The structure of Iron Containing Ferritin at 1.43A, PDB code: 6msx was solved by A.Blackburn, S.H.Partowmah, H.M.Brennan, K.E.Mestizo, C.D.Stivala, J.Petreczky, A.Perez, A.Horn, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.43
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.590, 181.590, 181.590, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.2

Other elements in 6msx:

The structure of Iron Containing Ferritin at 1.43A also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Iron Containing Ferritin at 1.43A (pdb code 6msx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Iron Containing Ferritin at 1.43A, PDB code: 6msx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 6msx

Go back to Cadmium Binding Sites List in 6msx
Cadmium binding site 1 out of 5 in the Iron Containing Ferritin at 1.43A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Iron Containing Ferritin at 1.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:19.3
occ:0.25
CD A:CD203 0.0 19.3 0.2
CD A:CD203 1.1 37.9 0.2
OD1 A:ASP80 2.4 24.2 1.0
OD2 A:ASP80 2.5 31.1 1.0
O A:HOH498 2.5 27.1 1.0
CG A:ASP80 2.9 28.1 1.0
O A:HOH383 4.3 31.9 1.0
CB A:ASP80 4.3 27.4 1.0
O A:HOH322 4.5 31.8 0.8

Cadmium binding site 2 out of 5 in 6msx

Go back to Cadmium Binding Sites List in 6msx
Cadmium binding site 2 out of 5 in the Iron Containing Ferritin at 1.43A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Iron Containing Ferritin at 1.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:37.9
occ:0.25
CD A:CD203 0.0 37.9 0.2
CD A:CD203 1.1 19.3 0.2
OD2 A:ASP80 1.7 31.1 1.0
OD1 A:ASP80 2.2 24.2 1.0
CG A:ASP80 2.3 28.1 1.0
O A:HOH498 3.3 27.1 1.0
O A:HOH322 3.6 31.8 0.8
CB A:ASP80 3.7 27.4 1.0
O A:HOH481 4.0 58.2 0.2
O A:HOH383 4.4 31.9 1.0
CA A:ASP80 4.8 24.1 1.0

Cadmium binding site 3 out of 5 in 6msx

Go back to Cadmium Binding Sites List in 6msx
Cadmium binding site 3 out of 5 in the Iron Containing Ferritin at 1.43A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Iron Containing Ferritin at 1.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:46.4
occ:0.16
O A:HOH329 1.6 35.3 1.0
OE1 A:GLU130 2.4 46.0 1.0
CD A:GLU130 3.3 44.5 1.0
O A:HOH511 3.5 0.0 0.3
OE2 A:GLU130 3.6 38.5 1.0
O A:HOH304 3.6 54.5 1.0
CD A:CD206 4.2 49.1 0.2
O A:HOH443 4.4 46.0 0.5
CG A:GLU130 4.7 34.7 1.0
CB A:GLU130 5.0 34.2 1.0

Cadmium binding site 4 out of 5 in 6msx

Go back to Cadmium Binding Sites List in 6msx
Cadmium binding site 4 out of 5 in the Iron Containing Ferritin at 1.43A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Iron Containing Ferritin at 1.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:52.0
occ:0.40
O A:HOH430 1.8 50.8 0.5
O A:HOH313 1.8 57.1 1.0
O A:HOH379 2.1 57.9 1.0
OE1 A:GLU11 2.4 33.4 1.0
OE2 A:GLU11 2.6 43.9 1.0
CD A:GLU11 2.9 44.0 1.0
O A:HOH417 2.9 39.4 1.0
OG1 A:THR10 4.0 35.3 1.0
CG A:GLU11 4.5 33.6 1.0
CB A:SER9 4.5 27.2 1.0
OE1 A:GLN120 4.5 40.0 1.0
NE2 A:GLN120 4.6 45.1 1.0
N A:THR10 4.7 25.5 1.0
CD A:GLN120 4.9 44.7 1.0
N A:GLU11 4.9 25.2 1.0

Cadmium binding site 5 out of 5 in 6msx

Go back to Cadmium Binding Sites List in 6msx
Cadmium binding site 5 out of 5 in the Iron Containing Ferritin at 1.43A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Iron Containing Ferritin at 1.43A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:49.1
occ:0.17
O A:HOH304 2.3 54.5 1.0
O A:HOH522 3.1 52.1 0.3
OD1 A:ASP127 3.6 41.8 1.0
CD A:CD204 4.2 46.4 0.2
OG A:SER131 4.2 53.4 1.0
OE1 A:GLU130 4.2 46.0 1.0
CG A:ASP127 4.8 42.2 1.0

Reference:

A.Blackburn, S.H.Partowmah, H.M.Brennan, K.E.Mestizo, C.D.Stivala, J.Petreczky, A.Perez, A.Horn, S.Mcsweeney. A Simple Technique to Improve Microcrystals Using Gel Exclusion of Nucleation Inducing Elements To Be Published.
Page generated: Sat Dec 12 08:28:48 2020

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