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Cadmium in PDB 7bom: Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.

Protein crystallography data

The structure of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions., PDB code: 7bom was solved by Y.Hishikawa, B.Maity, N.Ito, S.Abe, D.Lu, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.73 / 1.93
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.716, 181.716, 181.716, 90, 90, 90
R / Rfree (%) 16.3 / 19.6

Other elements in 7bom:

The structure of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. also contains other interesting chemical elements:

Gold (Au) 12 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. (pdb code 7bom). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions., PDB code: 7bom:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 7bom

Go back to Cadmium Binding Sites List in 7bom
Cadmium binding site 1 out of 5 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd213

b:27.4
occ:0.30
OE1 X:GLU130 2.3 35.9 1.0
OE2 X:GLU130 2.4 34.6 1.0
CD X:GLU130 2.7 33.4 1.0
O X:HOH313 4.1 37.1 1.0
CG X:GLU130 4.2 32.1 1.0
CB X:GLU130 5.0 34.1 1.0

Cadmium binding site 2 out of 5 in 7bom

Go back to Cadmium Binding Sites List in 7bom
Cadmium binding site 2 out of 5 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd214

b:33.9
occ:0.12
O X:HOH313 2.1 37.1 1.0
O X:HOH394 2.2 53.2 1.0
OD1 X:ASP127 4.0 34.7 1.0
OE1 X:GLU130 4.1 35.9 1.0
OG X:SER131 4.6 37.7 1.0
CB X:GLU130 4.9 34.1 1.0

Cadmium binding site 3 out of 5 in 7bom

Go back to Cadmium Binding Sites List in 7bom
Cadmium binding site 3 out of 5 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd215

b:32.0
occ:0.50
OD1 X:ASP80 1.9 24.1 1.0
CL X:CL220 2.3 54.2 0.8
OD2 X:ASP80 2.6 17.1 1.0
CG X:ASP80 2.6 20.1 1.0
CB X:ASP80 4.1 24.7 1.0
O X:HOH326 4.6 30.1 1.0

Cadmium binding site 4 out of 5 in 7bom

Go back to Cadmium Binding Sites List in 7bom
Cadmium binding site 4 out of 5 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd216

b:53.3
occ:0.45
OE1 X:GLU57 2.4 60.2 1.0
OE2 X:GLU60 2.5 58.0 1.0
OE2 X:GLU57 2.5 57.4 1.0
OE1 X:GLU60 2.5 62.5 1.0
CD X:GLU57 2.8 47.2 1.0
CD X:GLU60 2.8 49.1 1.0
OE2 X:GLU136 3.9 78.3 1.0
CG X:GLU57 4.3 41.0 1.0
CG X:GLU60 4.3 39.3 1.0
CD X:GLU136 4.8 63.7 1.0
OE1 X:GLU136 4.9 82.2 1.0

Cadmium binding site 5 out of 5 in 7bom

Go back to Cadmium Binding Sites List in 7bom
Cadmium binding site 5 out of 5 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions.


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr Immobilized with Gold Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd217

b:49.9
occ:0.50
NE2 X:HIS132 2.2 58.6 1.0
CE1 X:HIS132 2.8 58.5 1.0
CD2 X:HIS132 3.4 54.8 1.0
ND1 X:HIS132 4.0 58.6 1.0
CG X:HIS132 4.3 51.0 1.0
CB X:SER131 4.8 39.2 1.0

Reference:

Y.Hishikawa, B.Maity, N.Ito, S.Abe, D.Lu, T.Ueno. Design of Multinuclear Gold Binding Site at the Two-Fold Symmetric Interface of the Ferritin Cage Chem Lett. V. 49 840 2021.
ISSN: ESSN 1348-0715
DOI: 10.1246/CL.200217
Page generated: Sat Apr 17 14:38:34 2021

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