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Cadmium in PDB 6ra8: Horse Spleen Apoferritin Under 2 Kbar of Argon

Protein crystallography data

The structure of Horse Spleen Apoferritin Under 2 Kbar of Argon, PDB code: 6ra8 was solved by T.Prange, P.Carpentier, N.Colloc'h, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.26 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.873, 180.873, 180.873, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.1

Other elements in 6ra8:

The structure of Horse Spleen Apoferritin Under 2 Kbar of Argon also contains other interesting chemical elements:

Argon (Ar) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Horse Spleen Apoferritin Under 2 Kbar of Argon (pdb code 6ra8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Horse Spleen Apoferritin Under 2 Kbar of Argon, PDB code: 6ra8:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 1 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:24.7
occ:0.50
OD2 A:ASP80 2.3 25.0 1.0
OD1 A:ASP80 2.3 21.8 1.0
O A:HOH479 2.6 12.9 1.0
CG A:ASP80 2.6 24.6 1.0
CB A:ASP80 4.2 21.4 1.0
O A:HOH343 4.4 23.6 1.0
O A:HOH370 4.6 31.1 1.0

Cadmium binding site 2 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 2 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:56.0
occ:0.10
O A:HOH320 2.3 49.4 1.0
OE1 A:GLU130 2.3 67.0 1.0
CD A:GLU130 3.2 61.2 1.0
OE2 A:GLU130 3.4 60.0 1.0
CG A:GLU130 4.7 55.6 1.0

Cadmium binding site 3 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 3 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:42.0
occ:0.10
O A:HOH506 2.3 51.5 0.5
OE2 A:GLU11 2.4 52.4 1.0
OE1 A:GLU11 2.6 41.2 1.0
CD A:GLU11 2.9 48.9 1.0
O A:HOH450 3.2 44.5 1.0
OG1 A:THR10 3.7 41.4 1.0
O A:HOH473 3.7 69.7 1.0
CG A:GLU11 4.4 41.1 1.0
OE1 A:GLN120 4.8 51.9 1.0
CB A:SER9 4.9 27.9 1.0
N A:THR10 5.0 30.2 1.0

Cadmium binding site 4 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 4 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:53.7
occ:0.20
O A:HOH338 2.2 56.6 0.5
OE2 A:GLU45 2.2 66.7 1.0
OE1 A:GLU45 2.5 51.1 1.0
CD A:GLU45 2.7 54.3 1.0
O A:HOH452 2.7 60.0 1.0
O A:HOH402 3.3 50.6 0.5
CG A:GLU45 4.2 40.3 1.0
O A:HOH365 4.6 55.1 1.0

Cadmium binding site 5 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 5 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:46.8
occ:0.40
O A:HOH310 2.2 41.6 1.0
OE2 A:GLU56 2.3 48.3 1.0
OE2 A:GLU60 2.3 49.2 1.0
OE1 A:GLU60 2.4 46.0 1.0
CD A:GLU60 2.7 37.4 1.0
CD A:GLU56 3.1 42.7 1.0
OE2 A:GLU57 3.4 58.0 1.0
CG A:GLU56 3.5 30.1 1.0
OE1 A:GLU56 4.0 48.9 1.0
CG A:GLU60 4.2 35.9 1.0
CD A:GLU57 4.6 62.0 1.0
O A:HOH316 4.8 49.4 1.0
CB A:GLU56 4.9 23.6 1.0

Cadmium binding site 6 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 6 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:44.6
occ:0.20
O A:HOH316 2.0 49.4 1.0
OE1 A:GLU56 2.3 48.9 1.0
OE2 A:GLU53 2.5 60.4 1.0
OE1 A:GLU53 2.6 61.3 1.0
CD A:GLU53 2.9 56.4 1.0
CD A:GLU56 3.4 42.7 1.0
OE2 A:GLU56 3.8 48.3 1.0
CG A:GLU53 4.4 45.2 1.0
CG A:GLU56 4.6 30.1 1.0
CB A:GLU56 4.9 23.6 1.0

Cadmium binding site 7 out of 7 in 6ra8

Go back to Cadmium Binding Sites List in 6ra8
Cadmium binding site 7 out of 7 in the Horse Spleen Apoferritin Under 2 Kbar of Argon


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Horse Spleen Apoferritin Under 2 Kbar of Argon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:52.9
occ:0.10
OE2 A:GLU88 1.9 58.5 1.0
O A:HOH454 2.0 61.7 1.0
O A:HOH307 2.0 60.1 1.0
OE1 A:GLU88 2.3 62.7 1.0
CD A:GLU88 2.4 57.0 1.0
O A:HOH426 3.4 49.3 0.5
O A:HOH443 3.9 65.3 1.0
CG A:GLU88 3.9 44.8 1.0
NH2 A:ARG39 4.1 36.4 1.0
NH1 A:ARG39 4.4 29.9 1.0
CZ A:ARG39 4.8 33.0 1.0
CB A:GLU88 4.8 32.6 1.0

Reference:

T.Prange, P.Carpentier. Labelling Protein Crystals By Argon at 2 Kbar To Be Published.
Page generated: Sat Dec 12 08:29:08 2020

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