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Ruthenium in PDB 3wvv: Crystal Structure of Ruco/Apo-E45C_C48AFR

Protein crystallography data

The structure of Crystal Structure of Ruco/Apo-E45C_C48AFR, PDB code: 3wvv was solved by K.Fujita, Y.Tanaka, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.44 / 1.82
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.672, 181.672, 181.672, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.1

Other elements in 3wvv:

The structure of Crystal Structure of Ruco/Apo-E45C_C48AFR also contains other interesting chemical elements:

Cadmium (Cd) 4 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Crystal Structure of Ruco/Apo-E45C_C48AFR (pdb code 3wvv). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the Crystal Structure of Ruco/Apo-E45C_C48AFR, PDB code: 3wvv:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 3wvv

Go back to Ruthenium Binding Sites List in 3wvv
Ruthenium binding site 1 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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 Ruco/Apo-E45C_C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru213

b:41.2
occ:0.50
NE2 A:HIS114 2.3 24.7 1.0
CE1 A:HIS114 2.5 23.6 1.0
OE2 A:GLU130 2.7 31.4 1.0
CB A:CYS126 3.3 28.8 1.0
CD2 A:HIS114 3.6 21.4 1.0
CD A:CD203 3.7 42.9 0.4
ND1 A:HIS114 3.8 27.1 1.0
SG A:CYS126 3.8 33.3 1.0
CD A:GLU130 3.9 35.1 1.0
OG A:SER118 4.1 40.9 1.0
CG A:HIS114 4.3 20.8 1.0
CA A:CYS126 4.5 22.1 1.0
OE1 A:GLU130 4.7 34.1 1.0
C A:CYS126 4.9 23.6 1.0
CG A:GLU130 4.9 28.7 1.0
O A:CYS126 5.0 22.6 1.0

Ruthenium binding site 2 out of 4 in 3wvv

Go back to Ruthenium Binding Sites List in 3wvv
Ruthenium binding site 2 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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 Ruco/Apo-E45C_C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru214

b:37.8
occ:0.40
NE2 A:HIS132 2.3 46.2 1.0
CE1 A:HIS132 2.9 51.2 1.0
CD2 A:HIS132 3.4 42.8 1.0
ND1 A:HIS132 4.1 43.3 1.0
CG A:HIS132 4.4 38.7 1.0
NH2 A:ARG64 4.4 53.7 1.0
OG A:SER131 4.7 46.5 1.0

Ruthenium binding site 3 out of 4 in 3wvv

Go back to Ruthenium Binding Sites List in 3wvv
Ruthenium binding site 3 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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 Ruco/Apo-E45C_C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru215

b:48.4
occ:0.70
SG A:CYS45 2.2 34.1 1.0
NE2 A:HIS49 2.5 47.1 1.0
RU A:RU216 2.7 43.4 0.8
CD2 A:HIS49 3.1 43.8 1.0
CB A:CYS45 3.5 24.8 1.0
CE1 A:HIS49 3.7 49.5 1.0
CA A:CYS45 4.1 17.1 1.0
CG A:HIS49 4.4 37.8 1.0
O A:CYS45 4.4 14.6 1.0
C A:CYS45 4.5 14.9 1.0
ND1 A:HIS49 4.7 48.7 1.0
CB A:HIS173 5.0 71.5 1.0

Ruthenium binding site 4 out of 4 in 3wvv

Go back to Ruthenium Binding Sites List in 3wvv
Ruthenium binding site 4 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Crystal Structure of Ruco/Apo-E45C_C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru216

b:43.4
occ:0.80
SG A:CYS45 2.2 34.1 1.0
RU A:RU215 2.7 48.4 0.7
CB A:HIS173 3.1 71.5 1.0
CB A:CYS45 3.5 24.8 1.0
NE2 A:HIS49 3.9 47.1 1.0
O A:HOH445 4.1 47.7 1.0
CD2 A:HIS49 4.3 43.8 1.0
CA A:HIS173 4.6 78.2 1.0
CE1 A:HIS49 4.7 49.5 1.0
CA A:CYS45 4.7 17.1 1.0
C A:CYS45 4.8 14.9 1.0

Reference:

K.Fujita, Y.Tanaka, T.Sho, S.Ozeki, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno. Intracellular Co Release From Composite of Ferritin and Ruthenium Carbonyl Complexes. J.Am.Chem.Soc. V. 136 16902 2014.
ISSN: ISSN 0002-7863
PubMed: 25352251
DOI: 10.1021/JA508938F
Page generated: Wed Dec 16 02:08:10 2020

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