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Rhodium in PDB 8oqc: Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)

Enzymatic activity of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)

All present enzymatic activity of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking):
4.6.1.18;

Protein crystallography data

The structure of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking), PDB code: 8oqc was solved by D.Loreto, A.Merlino, B.Maity, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.97 / 1.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.129, 67.129, 64.979, 90, 90, 120
R / Rfree (%) 18 / 21.5

Other elements in 8oqc:

The structure of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Rhodium Binding Sites:

The binding sites of Rhodium atom in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) (pdb code 8oqc). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 4 binding sites of Rhodium where determined in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking), PDB code: 8oqc:
Jump to Rhodium binding site number: 1; 2; 3; 4;

Rhodium binding site 1 out of 4 in 8oqc

Go back to Rhodium Binding Sites List in 8oqc
Rhodium binding site 1 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:23.8
occ:0.50
 RH1 A:D1O201 0.0 23.8 0.5
ND1 A:HIS119 2.0 33.0 0.5
O1 A:D1O201 2.1 26.7 0.5
O0 A:D1O201 2.1 25.8 0.5
O7 A:D1O201 2.1 19.4 0.5
O3 A:D1O201 2.1 28.8 0.5
ND1 A:HIS119 2.2 16.5 0.5
RH2 A:D1O201 2.4 28.3 0.5
C5 A:D1O201 2.6 28.2 0.5
CE1 A:HIS119 2.6 35.9 0.5
CG A:HIS119 2.8 29.3 0.5
O4 A:D1O201 2.9 27.2 0.5
C1 A:D1O201 3.0 26.3 0.5
O9 A:D1O201 3.0 32.0 0.5
CE1 A:HIS119 3.0 16.1 0.5
O8 A:D1O201 3.1 23.5 0.5
C3 A:D1O201 3.1 20.7 0.5
O2 A:D1O201 3.2 28.4 0.5
CG A:HIS119 3.3 15.0 0.5
CB A:HIS119 3.5 20.9 0.5
NE2 A:HIS119 3.5 34.2 0.5
CD2 A:HIS119 3.7 32.3 0.5
CB A:HIS119 3.7 14.1 0.5
O A:HOH361 3.9 20.7 1.0
O A:HOH395 4.0 46.2 1.0
C6 A:D1O201 4.1 29.1 0.5
NE2 A:HIS119 4.2 14.5 0.5
CA A:HIS119 4.2 14.2 0.5
CA A:HIS119 4.3 16.7 0.5
CD2 A:HIS119 4.4 13.9 0.5
O A:VAL118 4.4 16.2 1.0
C2 A:D1O201 4.4 22.3 0.5
C4 A:D1O201 4.5 15.6 0.5
O A:HOH422 4.8 59.2 1.0

Rhodium binding site 2 out of 4 in 8oqc

Go back to Rhodium Binding Sites List in 8oqc
Rhodium binding site 2 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:28.3
occ:0.50
 RH2 A:D1O201 0.0 28.3 0.5
O9 A:D1O201 2.1 32.0 0.5
O4 A:D1O201 2.1 27.2 0.5
O2 A:D1O201 2.1 28.4 0.5
O8 A:D1O201 2.1 23.5 0.5
RH1 A:D1O201 2.4 23.8 0.5
CL A:CL204 2.6 35.2 0.5
C5 A:D1O201 2.8 28.2 0.5
C1 A:D1O201 2.9 26.3 0.5
O7 A:D1O201 2.9 19.4 0.5
O1 A:D1O201 3.0 26.7 0.5
CE1 A:HIS119 3.0 35.9 0.5
C3 A:D1O201 3.0 20.7 0.5
ND1 A:HIS119 3.2 33.0 0.5
O3 A:D1O201 3.3 28.8 0.5
O0 A:D1O201 3.3 25.8 0.5
O A:HOH345 3.5 41.3 1.0
NZ A:LYS7 3.7 46.9 1.0
C6 A:D1O201 4.0 29.1 0.5
NE2 A:HIS119 4.2 34.2 0.5
C2 A:D1O201 4.3 22.3 0.5
O A:HOH422 4.4 59.2 1.0
CG A:HIS119 4.5 29.3 0.5
CE A:LYS7 4.6 35.9 1.0
C4 A:D1O201 4.6 15.6 0.5
ND1 A:HIS119 4.6 16.5 0.5
O A:HOH335 4.7 25.2 1.0

Rhodium binding site 3 out of 4 in 8oqc

Go back to Rhodium Binding Sites List in 8oqc
Rhodium binding site 3 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh205

b:16.1
occ:0.78
 RH1 A:VVU205 0.0 16.1 0.8
O3 A:VVU205 2.0 17.9 0.8
O7 A:VVU205 2.1 15.9 0.8
O0 A:VVU205 2.1 16.4 0.8
O1 A:VVU205 2.1 17.4 0.8
RH2 A:VVU205 2.4 14.8 0.8
CL A:CL203 2.6 20.5 0.8
C5 A:VVU205 2.7 17.6 0.8
C3 A:VVU205 2.8 15.0 0.8
C7 A:VVU205 2.8 17.1 0.8
C1 A:VVU205 3.0 17.5 0.8
O4 A:VVU205 3.0 17.9 0.8
O8 A:VVU205 3.1 14.2 0.8
O2 A:VVU205 3.1 17.9 0.8
O9 A:VVU205 3.1 17.0 0.8
O A:HOH331 3.5 47.7 1.0
O A:HOH302 3.6 19.1 0.5
O A:HOH332 3.9 42.0 1.0
O A:HOH366 4.0 47.5 1.0
C6 A:VVU205 4.1 19.2 0.8
C4 A:VVU205 4.2 15.7 0.8
C8 A:VVU205 4.2 18.8 0.8
C2 A:VVU205 4.4 16.3 0.8
O A:HOH302 4.5 24.1 0.5
NE2 A:HIS105 4.6 16.7 1.0

Rhodium binding site 4 out of 4 in 8oqc

Go back to Rhodium Binding Sites List in 8oqc
Rhodium binding site 4 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (1 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh205

b:14.8
occ:0.78
 RH2 A:VVU205 0.0 14.8 0.8
O4 A:VVU205 2.0 17.9 0.8
O9 A:VVU205 2.0 17.0 0.8
O8 A:VVU205 2.0 14.2 0.8
O2 A:VVU205 2.1 17.9 0.8
NE2 A:HIS105 2.2 16.7 1.0
RH1 A:VVU205 2.4 16.1 0.8
C5 A:VVU205 2.7 17.6 0.8
C3 A:VVU205 2.8 15.0 0.8
C7 A:VVU205 2.9 17.1 0.8
C1 A:VVU205 2.9 17.5 0.8
O1 A:VVU205 3.1 17.4 0.8
O3 A:VVU205 3.1 17.9 0.8
O7 A:VVU205 3.1 15.9 0.8
O0 A:VVU205 3.1 16.4 0.8
CD2 A:HIS105 3.2 14.9 1.0
CE1 A:HIS105 3.2 15.6 1.0
O A:HOH378 4.1 19.4 1.0
C6 A:VVU205 4.1 19.2 0.8
C4 A:VVU205 4.2 15.7 0.8
C8 A:VVU205 4.3 18.8 0.8
CG A:HIS105 4.4 13.6 1.0
ND1 A:HIS105 4.4 14.3 1.0
C2 A:VVU205 4.4 16.3 0.8
CG2 A:THR78 4.6 15.8 1.0
CL A:CL203 4.9 20.5 0.8
O A:HOH331 4.9 47.7 1.0

Reference:

D.Loreto, B.Maity, T.Morita, H.Nakamura, A.Merlino, T.Ueno. Cross-Linked Crystals of Dirhodium Tetraacetate/Rnase A Adduct Can Be Used As Heterogeneous Catalysts. Inorg.Chem. V. 62 7515 2023.
ISSN: ISSN 0020-1669
PubMed: 37144589
DOI: 10.1021/ACS.INORGCHEM.3C00852
Page generated: Thu Oct 10 12:40:38 2024

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