Atomistry » Cadmium » PDB 3heq-3o7s » 3o7r
Atomistry »
  Cadmium »
    PDB 3heq-3o7s »
      3o7r »

Cadmium in PDB 3o7r: Crystal Structure of Ru(P-Cymene)/Apo-H49AFR

Protein crystallography data

The structure of Crystal Structure of Ru(P-Cymene)/Apo-H49AFR, PDB code: 3o7r was solved by Y.Takezawa, P.Bockmann, N.Sugi, Z.Wang, S.Abe, T.Murakami, T.Hikage, G.Erker, Y.Watanabe, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.28 / 1.90
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.703, 181.703, 181.703, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.7

Other elements in 3o7r:

The structure of Crystal Structure of Ru(P-Cymene)/Apo-H49AFR also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR (pdb code 3o7r). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR, PDB code: 3o7r:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 3o7r

Go back to Cadmium Binding Sites List in 3o7r
Cadmium binding site 1 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR


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 Ru(P-Cymene)/Apo-H49AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd175

b:23.2
occ:0.50
OD2 A:ASP80 1.6 3.3 1.0
O A:HOH225 2.4 20.7 1.0
OD1 A:ASP80 2.4 14.7 1.0
CG A:ASP80 2.4 15.6 1.0
CB A:ASP80 4.0 14.7 1.0
O A:HOH210 4.4 17.5 1.0

Cadmium binding site 2 out of 3 in 3o7r

Go back to Cadmium Binding Sites List in 3o7r
Cadmium binding site 2 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR


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 Ru(P-Cymene)/Apo-H49AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd176

b:41.2
occ:0.30
OE1 A:GLU60 2.4 29.2 1.0
CD A:GLU60 3.1 26.1 1.0
OE2 A:GLU60 3.1 33.2 1.0
O A:HOH285 3.6 48.8 1.0
OE2 A:GLU56 4.0 32.8 1.0
CD A:GLU56 4.2 23.1 1.0
CG A:GLU56 4.3 20.2 1.0
CG A:GLU60 4.6 19.9 1.0
CG A:GLU57 4.6 17.4 1.0
OE2 A:GLU53 4.7 33.5 1.0
OE1 A:GLU56 4.9 33.3 1.0

Cadmium binding site 3 out of 3 in 3o7r

Go back to Cadmium Binding Sites List in 3o7r
Cadmium binding site 3 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR


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 Ru(P-Cymene)/Apo-H49AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd177

b:42.2
occ:0.70
O A:HOH367 2.2 41.9 1.0
OE1 A:GLU45 2.2 37.6 1.0
O A:HOH346 2.2 38.2 1.0
OD1 A:ASP38 2.5 15.8 1.0
CG A:ASP38 3.4 15.5 1.0
CD A:GLU45 3.5 34.4 1.0
CB A:ASP38 3.7 12.0 1.0
CA A:ASP38 3.8 12.5 1.0
OE2 A:GLU45 4.2 38.5 1.0
SG A:CYS48 4.2 22.3 1.0
CB A:CYS48 4.2 14.5 1.0
CA A:GLU45 4.3 14.5 1.0
O A:HOH222 4.4 20.6 1.0
CB A:GLU45 4.5 15.0 1.0
CG A:GLU45 4.5 22.8 1.0
OD2 A:ASP38 4.6 17.5 1.0
N A:ASP38 4.7 11.9 1.0
O A:PHE37 4.7 13.8 1.0
O A:ASP38 4.8 13.1 1.0
C A:ASP38 4.8 12.7 1.0

Reference:

Y.Takezawa, P.Bockmann, N.Sugi, Z.Wang, S.Abe, T.Murakami, T.Hikage, G.Erker, Y.Watanabe, S.Kitagawa, T.Ueno. Incorporation of Organometallic Ru Complexes Into Apo-Ferritin Cage. J.Chem.Soc.,Dalton Trans. V. 40 2190 2011.
ISSN: ISSN 0300-9246
PubMed: 21113534
DOI: 10.1039/C0DT00955E
Page generated: Sat Dec 12 08:22:40 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy