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Cadmium in PDB 9kn7: Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)

Protein crystallography data

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7 was solved by T.Suzuki, Y.Hishikawa, B.Maity, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.94 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.715, 180.715, 180.715, 90, 90, 90
R / Rfree (%) 16.5 / 17.8

Other elements in 9kn7:

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) 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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) (pdb code 9kn7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 1 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:14.7
occ:0.41
O A:HOH453 2.3 35.6 1.0
OD1 A:ASP38 2.5 13.2 1.0
SG A:CYS48 2.6 14.2 1.0
CG A:ASP38 3.3 9.9 1.0
CB A:ASP38 3.5 8.8 1.0
CB A:CYS48 3.5 10.9 1.0
CA A:ASP38 4.0 8.1 1.0
CD A:CD208 4.3 53.5 0.2
OD2 A:ASP38 4.4 10.8 1.0
CD2 A:HIS49 4.4 26.7 1.0
NE2 A:HIS49 4.5 30.0 1.0
N A:ASP38 4.8 7.5 1.0
NH1 A:ARG52 4.8 32.0 0.5
CG A:GLU45 4.8 18.7 1.0
CA A:GLU45 4.9 9.7 1.0
CA A:CYS48 4.9 9.2 1.0
NE A:ARG52 5.0 24.8 0.5

Cadmium binding site 2 out of 8 in 9kn7

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Cadmium binding site 2 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:9.8
occ:0.45
OD2 A:ASP80 2.3 14.8 1.0
OD1 A:ASP80 2.3 9.0 1.0
CL A:CL211 2.5 23.2 1.0
CG A:ASP80 2.7 11.5 1.0
CB A:ASP80 4.2 10.1 1.0
O A:HOH348 4.3 14.6 1.0
O A:HOH334 4.6 17.6 1.0

Cadmium binding site 3 out of 8 in 9kn7

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Cadmium binding site 3 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:25.0
occ:0.13
O A:HOH314 2.3 29.1 1.0
O A:HOH482 3.0 39.2 0.1
OD1 A:ASP127 3.6 20.2 1.0
OG A:SER131 3.7 23.4 1.0
CD A:CD204 4.2 17.1 0.1
OE1 A:GLU130 4.3 21.5 1.0
CG A:ASP127 4.7 16.7 1.0

Cadmium binding site 4 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 4 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:17.1
occ:0.08
CD A:CD205 1.6 18.2 0.3
OE1 A:GLU130 2.2 21.5 1.0
CD A:GLU130 3.2 20.3 1.0
OE2 A:GLU130 3.6 15.6 1.0
CD A:CD203 4.2 25.0 0.1
CG A:GLU130 4.6 15.7 1.0
CB A:GLU130 4.9 13.5 1.0

Cadmium binding site 5 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 5 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:18.2
occ:0.26
CD A:CD204 1.6 17.1 0.1
OE1 A:GLU130 2.4 21.5 1.0
OE2 A:GLU130 2.9 15.6 1.0
CD A:GLU130 3.0 20.3 1.0
N A:ASP127 4.4 11.1 1.0
CG A:GLU130 4.5 15.7 1.0
CA A:ASP127 4.5 12.2 1.0
O A:HOH506 4.7 33.4 1.0
CB A:CYS126 4.7 10.6 1.0
C A:CYS126 4.7 10.5 1.0
CB A:ASP127 4.8 15.0 1.0
O A:CYS126 5.0 11.5 1.0

Cadmium binding site 6 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 6 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:26.6
occ:0.23
NE2 A:HIS132 2.6 27.9 1.0
CD2 A:HIS132 3.5 22.4 1.0
CE1 A:HIS132 3.6 27.5 1.0
O A:HOH310 4.5 15.9 1.0
O A:HOH304 4.6 31.0 1.0
CG A:HIS132 4.7 21.1 1.0
OD2 A:ASP127 4.7 24.1 1.0
ND1 A:HIS132 4.8 24.1 1.0
CD1 A:PHE128 4.9 11.9 1.0

Cadmium binding site 7 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 7 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:30.3
occ:0.17
OE1 A:GLU11 2.4 14.1 1.0
O A:HOH429 2.7 20.5 1.0
OE2 A:GLU11 2.9 19.8 1.0
CD A:GLU11 3.0 16.2 1.0
OG1 A:THR10 4.0 16.4 1.0
CB A:SER9 4.3 8.8 1.0
NE2 A:GLN120 4.3 11.8 0.4
OE1 A:GLN120 4.5 16.9 0.6
CG A:GLU11 4.5 13.3 1.0
N A:THR10 4.6 10.3 1.0
O A:HOH432 4.6 44.5 1.0
NE2 A:GLN120 4.7 18.2 0.6
N A:GLU11 4.9 9.8 1.0
CD A:GLN120 4.9 15.2 0.6
CA A:SER9 5.0 8.5 1.0

Cadmium binding site 8 out of 8 in 9kn7

Go back to Cadmium Binding Sites List in 9kn7
Cadmium binding site 8 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:53.5
occ:0.22
NE2 A:HIS49 2.5 30.0 1.0
CE1 A:HIS49 3.0 28.0 1.0
CD A:GLU45 3.6 28.3 1.0
CG A:GLU45 3.6 18.7 1.0
CD2 A:HIS49 3.7 26.7 1.0
OE2 A:GLU45 3.8 38.8 1.0
OE1 A:GLU45 4.0 30.8 1.0
ND1 A:HIS49 4.2 31.9 1.0
CD A:CD201 4.3 14.7 0.4
NH1 A:ARG52 4.5 32.0 0.5
CG A:HIS49 4.6 21.2 1.0
O A:HOH453 5.0 35.6 1.0
CB A:GLU45 5.0 12.8 1.0

Reference:

Y.Hishikawa, T.Suzuki, B.Maity, H.Noya, M.Yoshizawa, A.Asanuma, Y.Katagiri, S.Abe, S.Nagatoishi, K.Tsumoto, T.Ueno. Design of Aromatic Interaction Networks in A Protein Cage Modulated By Fluorescent Ligand Binding. Adv Sci 17030 2025.
ISSN: ESSN 2198-3844
PubMed: 39973762
DOI: 10.1002/ADVS.202417030
Page generated: Thu Jul 10 16:04:07 2025

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