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Ruthenium in PDB 3o7s: Crystal Structure of Ru(P-Cymene)/Apo-Fr

Protein crystallography data

The structure of Crystal Structure of Ru(P-Cymene)/Apo-Fr, PDB code: 3o7s 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) 37.04 / 1.73
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.443, 181.443, 181.443, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.7

Other elements in 3o7s:

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

Cadmium (Cd) 3 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Crystal Structure of Ru(P-Cymene)/Apo-Fr (pdb code 3o7s). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Crystal Structure of Ru(P-Cymene)/Apo-Fr, PDB code: 3o7s:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 3o7s

Go back to Ruthenium Binding Sites List in 3o7s
Ruthenium binding site 1 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru176

b:34.2
occ:1.00
NE2 A:HIS49 2.1 19.1 1.0
NE2 A:HIS173 2.2 31.6 1.0
OE2 A:GLU53 2.2 26.6 1.0
C9 A:MML179 2.5 42.1 1.0
C10 A:MML179 2.5 42.0 1.0
C2 A:MML179 2.6 42.8 1.0
C5 A:MML179 2.6 42.9 1.0
C4 A:MML179 2.6 42.5 1.0
C3 A:MML179 2.6 42.5 1.0
CD2 A:HIS173 2.9 31.6 1.0
CD2 A:HIS49 3.0 20.5 1.0
CE1 A:HIS49 3.1 21.0 1.0
CD A:GLU53 3.3 19.7 1.0
CE1 A:HIS173 3.4 32.7 1.0
C8 A:MML179 3.5 43.8 1.0
C6 A:MML179 3.6 43.5 1.0
C1 A:MML179 3.6 43.4 1.0
CG A:GLU53 3.8 18.1 1.0
ND1 A:HIS49 4.2 21.1 1.0
CG A:HIS49 4.2 14.6 1.0
CG A:HIS173 4.2 30.2 1.0
ND1 A:HIS173 4.4 31.8 1.0
OE1 A:GLU53 4.4 24.6 1.0
C7 A:MML179 4.8 44.2 1.0

Ruthenium binding site 2 out of 3 in 3o7s

Go back to Ruthenium Binding Sites List in 3o7s
Ruthenium binding site 2 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru178

b:52.5
occ:0.40
NE2 A:HIS114 2.1 45.1 1.0
SG A:CYS126 2.1 53.3 1.0
CD2 A:HIS114 3.0 44.4 1.0
CE1 A:HIS114 3.1 46.0 1.0
O A:HOH331 3.3 32.6 1.0
CB A:CYS126 3.8 52.8 1.0
CG A:HIS114 4.2 43.9 1.0
O A:CYS126 4.2 53.1 1.0
ND1 A:HIS114 4.2 45.5 1.0
CA A:CYS126 4.5 52.6 1.0
C A:CYS126 4.6 52.8 1.0
OG A:SER118 4.8 52.2 1.0

Ruthenium binding site 3 out of 3 in 3o7s

Go back to Ruthenium Binding Sites List in 3o7s
Ruthenium binding site 3 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru180

b:52.5
occ:0.30
CD A:CD177 2.3 27.1 0.5
O A:HOH337 2.8 40.5 1.0
SG A:CYS48 3.0 22.7 1.0
OD1 A:ASP38 3.6 14.6 1.0
O A:HOH317 3.9 40.1 1.0
O A:HOH357 3.9 49.4 1.0
CB A:CYS48 4.0 14.8 1.0
CG A:ASP38 4.2 13.1 1.0
O A:HOH271 4.3 45.6 1.0
O A:HOH338 4.4 26.4 1.0
CG A:GLU45 4.4 18.5 1.0
CB A:ASP38 4.5 10.4 1.0
OE2 A:GLU45 4.5 33.2 1.0
CD A:GLU45 4.8 27.2 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: Wed Dec 16 02:08:05 2020

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