Cadmium in PDB 8i6l: Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.

Protein crystallography data

The structure of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius., PDB code: 8i6l was solved by B.Maity, J.Tian, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.58 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.058, 182.058, 182.058, 90, 90, 90
R / Rfree (%) 15.5 / 17.4

Other elements in 8i6l:

The structure of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. (pdb code 8i6l). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius., PDB code: 8i6l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 8i6l

Go back to Cadmium Binding Sites List in 8i6l
Cadmium binding site 1 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:15.3
occ:0.10
 CD A:CD608 1.6 13.7 0.2
OE1 A:GLU130 2.3 23.0 1.0
CD A:CD606 3.2 86.7 0.2
CD A:GLU130 3.3 21.1 1.0
OE2 A:GLU130 3.6 17.6 1.0
OD1 A:ASP127 3.8 16.8 0.5
O A:HOH717 4.3 23.0 1.0
CG A:GLU130 4.6 15.5 1.0
CG A:ASP127 4.7 14.5 0.5
CB A:ASP127 4.8 12.2 0.5
CB A:GLU130 5.0 14.4 1.0

Cadmium binding site 2 out of 9 in 8i6l

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Cadmium binding site 2 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd606

b:86.7
occ:0.20
 OD1 A:ASP127 2.3 16.8 0.5
O A:HOH748 2.9 36.7 1.0
CD A:CD605 3.2 15.3 0.1
OE1 A:GLU130 3.4 23.0 1.0
CG A:ASP127 3.5 14.5 0.5
OD1 A:ASP127 3.7 12.4 0.5
OD2 A:ASP127 4.2 17.7 0.5
CD A:CD608 4.4 13.7 0.2
CB A:ASP127 4.6 12.2 0.5
OG A:SER131 4.7 23.9 1.0
CD A:GLU130 4.7 21.1 1.0
CB A:GLU130 4.8 14.4 1.0
CG A:ASP127 4.8 9.4 0.5

Cadmium binding site 3 out of 9 in 8i6l

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Cadmium binding site 3 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd607

b:11.8
occ:0.50
 OD2 A:ASP80 1.9 9.9 1.0
OD1 A:ASP80 2.3 8.4 1.0
CL A:CL618 2.5 21.9 1.0
CG A:ASP80 2.6 11.8 1.0
CB A:ASP80 4.1 10.9 1.0
O A:HOH801 4.4 14.3 1.0
O A:HOH842 4.7 16.4 1.0

Cadmium binding site 4 out of 9 in 8i6l

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Cadmium binding site 4 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd608

b:13.7
occ:0.20
 CD A:CD605 1.6 15.3 0.1
OE1 A:GLU130 2.6 23.0 1.0
OE2 A:GLU130 2.9 17.6 1.0
O A:HOH717 2.9 23.0 1.0
CD A:GLU130 3.0 21.1 1.0
CG A:GLU130 4.3 15.5 1.0
CD A:CD606 4.4 86.7 0.2

Cadmium binding site 5 out of 9 in 8i6l

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Cadmium binding site 5 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd609

b:16.8
occ:0.20
 O A:HOH756 2.1 35.3 1.0
NE2 A:HIS132 2.2 21.7 1.0
O A:HOH876 2.8 50.7 1.0
CE1 A:HIS132 2.9 21.2 1.0
CD2 A:HIS132 3.4 19.4 1.0
O A:HOH752 3.9 32.1 1.0
ND1 A:HIS132 4.1 20.0 1.0
CG A:HIS132 4.3 16.0 1.0
NH2 A:ARG64 4.4 32.8 1.0

Cadmium binding site 6 out of 9 in 8i6l

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Cadmium binding site 6 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd610

b:30.6
occ:0.20
 O A:HOH784 2.0 30.4 1.0
NE2 A:HIS49 2.2 10.3 0.5
CE1 A:HIS49 2.8 9.7 0.5
CD2 A:HIS49 3.4 10.2 0.5
CG A:GLU45 3.7 14.2 1.0
CD A:GLU45 3.8 21.6 1.0
OD2 A:ASP174 3.8 57.1 1.0
OE2 A:GLU45 4.0 31.7 1.0
ND1 A:HIS49 4.1 11.6 0.5
O1 A:EDO603 4.2 32.4 1.0
O A:HOH749 4.2 19.5 1.0
CG A:HIS49 4.4 9.5 0.5
OE1 A:GLU45 4.4 22.0 1.0
O A:HOH705 4.5 34.2 1.0
CG A:ASP174 4.6 55.7 1.0
OD1 A:ASP174 4.7 54.1 1.0
O A:HOH766 4.8 49.2 1.0
O2 A:EDO603 5.0 39.8 1.0

Cadmium binding site 7 out of 9 in 8i6l

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Cadmium binding site 7 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd611

b:28.2
occ:0.20
 OE2 A:GLU56 2.1 37.7 1.0
OE2 A:GLU60 2.2 27.8 1.0
CD A:CD613 2.2 33.1 0.2
CD A:GLU60 2.9 23.5 1.0
OE1 A:GLU60 2.9 25.4 1.0
CD A:GLU56 3.2 30.6 1.0
CG A:GLU56 3.6 18.4 1.0
OE1 A:GLU56 4.3 37.5 1.0
CG A:GLU60 4.4 15.5 1.0
CB A:GLU56 4.9 12.6 1.0
O A:HOH716 5.0 41.4 1.0

Cadmium binding site 8 out of 9 in 8i6l

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Cadmium binding site 8 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd612

b:35.6
occ:0.20
 O A:HOH754 1.9 37.8 1.0
O A:HOH827 1.9 35.4 1.0
OE1 A:GLU11 2.5 13.0 1.0
OE2 A:GLU11 2.7 19.1 1.0
CD A:GLU11 2.9 15.7 1.0
O A:HOH831 3.0 21.2 1.0
O A:HOH909 3.5 34.0 1.0
OG1 A:THR10 4.0 16.0 1.0
CG A:GLU11 4.5 12.4 1.0
NE2 A:GLN120 4.5 24.4 1.0
CB A:SER9 4.6 8.3 1.0
OE1 A:GLN120 4.7 20.9 1.0
N A:THR10 4.8 8.6 1.0
CD A:GLN120 5.0 19.1 1.0

Cadmium binding site 9 out of 9 in 8i6l

Go back to Cadmium Binding Sites List in 8i6l
Cadmium binding site 9 out of 9 in the Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd613

b:33.1
occ:0.20
 CD A:CD611 2.2 28.2 0.2
OE1 A:GLU60 2.4 25.4 1.0
CD A:GLU60 3.3 23.5 1.0
OE2 A:GLU60 3.4 27.8 1.0
OE2 A:GLU56 4.0 37.7 1.0
O A:HOH738 4.5 37.7 1.0
CG A:GLU57 4.5 18.5 1.0
CG A:GLU60 4.7 15.5 1.0
CD A:GLU56 4.9 30.6 1.0
CG A:GLU56 5.0 18.4 1.0

Reference:

B.Maity, J.Tian, S.Abe, T.Ueno. Crystal Structure of Horse Spleen L-Ferritin at -180DEG Celsius. To Be Published.
Page generated: Fri Jul 19 20:30:03 2024

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