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Cadmium in PDB 7emm: Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr, PDB code: 7emm was solved by M.Taher, B.Maity, T.Nakane, S.Abe, T.Ueno, S.Mazumdar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.77 / 1.25
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.064, 182.064, 182.064, 90, 90, 90
R / Rfree (%) 17.5 / 18.6

Other elements in 7emm:

The structure of Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Iridium (Ir) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr (pdb code 7emm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr, PDB code: 7emm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 7emm

Go back to Cadmium Binding Sites List in 7emm
Cadmium binding site 1 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:10.9
occ:0.35
CD A:CD205 1.3 10.8 0.1
OD2 A:ASP80 2.4 16.4 1.0
OD1 A:ASP80 2.4 13.8 1.0
CL A:CL216 2.5 25.4 1.0
CG A:ASP80 2.8 16.0 1.0
CB A:ASP80 4.3 14.1 1.0
O A:HOH413 4.4 19.4 1.0
O A:HOH326 4.5 23.0 1.0

Cadmium binding site 2 out of 6 in 7emm

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Cadmium binding site 2 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:10.8
occ:0.15
CD A:CD204 1.3 10.9 0.3
OD2 A:ASP80 1.6 16.4 1.0
CG A:ASP80 2.2 16.0 1.0
OD1 A:ASP80 2.3 13.8 1.0
CL A:CL216 3.4 25.4 1.0
O A:HOH326 3.5 23.0 1.0
CB A:ASP80 3.5 14.1 1.0
O A:HOH413 4.4 19.4 1.0
CA A:ASP80 4.7 12.3 1.0

Cadmium binding site 3 out of 6 in 7emm

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Cadmium binding site 3 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:44.9
occ:0.10
O A:HOH306 2.2 31.7 1.0
O A:HOH341 2.5 33.4 1.0
CD A:CD207 3.7 24.4 0.1
OD1 A:ASP127 3.7 22.0 1.0
OE1 A:GLU130 3.9 26.4 1.0
O A:HOH344 4.3 43.2 1.0
OG A:SER131 4.4 25.0 1.0
CG A:ASP127 4.8 19.3 1.0
CD A:CD208 4.9 17.8 0.2
CB A:GLU130 4.9 15.1 1.0

Cadmium binding site 4 out of 6 in 7emm

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Cadmium binding site 4 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:24.4
occ:0.10
CD A:CD208 1.7 17.8 0.2
OE1 A:GLU130 2.3 26.4 1.0
CD A:GLU130 3.3 23.1 1.0
O A:HOH306 3.5 31.7 1.0
OE2 A:GLU130 3.6 20.0 1.0
CD A:CD206 3.7 44.9 0.1
O A:HOH316 4.3 31.8 1.0
CG A:GLU130 4.6 16.9 1.0
CB A:GLU130 5.0 15.1 1.0

Cadmium binding site 5 out of 6 in 7emm

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Cadmium binding site 5 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:17.8
occ:0.20
CD A:CD207 1.7 24.4 0.1
OE1 A:GLU130 2.4 26.4 1.0
OE2 A:GLU130 2.9 20.0 1.0
CD A:GLU130 3.0 23.1 1.0
O A:HOH306 3.9 31.7 1.0
IR A:IR210 4.0 26.8 0.1
N A:ASP127 4.3 11.3 1.0
CA A:ASP127 4.3 12.5 1.0
O A:HOH316 4.3 31.8 1.0
CG A:GLU130 4.5 16.9 1.0
C A:CYS126 4.6 11.3 1.0
CB A:ASP127 4.6 16.7 1.0
CB A:CYS126 4.6 12.1 1.0
O A:CYS126 4.8 12.5 1.0
CD A:CD206 4.9 44.9 0.1

Cadmium binding site 6 out of 6 in 7emm

Go back to Cadmium Binding Sites List in 7emm
Cadmium binding site 6 out of 6 in the Crystal Structure of Ircp* Immobilized Apo-R52H-Rhlfr


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 Ircp* Immobilized Apo-R52H-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:22.2
occ:0.15
O A:HOH372 1.9 41.1 1.0
NE2 A:HIS132 2.2 24.0 1.0
CE1 A:HIS132 2.8 23.4 1.0
CD2 A:HIS132 3.4 21.1 1.0
O A:HOH350 4.0 44.3 1.0
ND1 A:HIS132 4.1 21.9 1.0
CG A:HIS132 4.4 18.6 1.0
NH1 A:ARG64 4.5 34.7 1.0

Reference:

M.Taher, B.Maity, T.Nakane, S.Abe, T.Ueno, S.Mazumdar. Controlled Uptake of An Iridium Complex Inside Engineered Apo-Ferritin Nanocages: Study of Structure and Catalysis. Angew.Chem.Int.Ed.Engl. V. 61 16623 2022.
ISSN: ESSN 1521-3773
PubMed: 35005820
DOI: 10.1002/ANIE.202116623
Page generated: Thu Jul 10 15:26:13 2025

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