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Rhodium in PDB 8oqe: Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 H Soaking)

Enzymatic activity of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 H Soaking)

All present enzymatic activity of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 H Soaking):
4.6.1.18;

Protein crystallography data

The structure of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 H Soaking), PDB code: 8oqe 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) 21.60 / 1.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.795, 66.795, 64.904, 90, 90, 120
R / Rfree (%) 17.9 / 21.6

Other elements in 8oqe:

The structure of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 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 (6 H Soaking) (pdb code 8oqe). 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 (6 H Soaking), PDB code: 8oqe:
Jump to Rhodium binding site number: 1; 2; 3; 4;

Rhodium binding site 1 out of 4 in 8oqe

Go back to Rhodium Binding Sites List in 8oqe
Rhodium binding site 1 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 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 (6 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:12.7
occ:0.78
 RH1 A:VVU201 0.0 12.7 0.8
O1 A:VVU201 2.0 14.5 0.8
O7 A:VVU201 2.1 11.8 0.8
O0 A:VVU201 2.1 13.7 0.8
O3 A:VVU201 2.1 15.2 0.8
NE2 A:HIS105 2.2 14.2 1.0
RH2 A:VVU201 2.4 14.1 0.8
C5 A:VVU201 2.7 14.4 0.8
C7 A:VVU201 2.9 15.7 0.8
C3 A:VVU201 2.9 12.9 0.8
C1 A:VVU201 2.9 14.8 0.8
O2 A:VVU201 3.0 14.3 0.8
O4 A:VVU201 3.0 15.7 0.8
O8 A:VVU201 3.1 13.3 0.8
O9 A:VVU201 3.1 15.1 0.8
CE1 A:HIS105 3.2 13.2 1.0
CD2 A:HIS105 3.3 12.8 1.0
O A:HOH371 4.1 14.9 1.0
C6 A:VVU201 4.2 20.1 0.8
O A:HOH391 4.3 33.2 1.0
C4 A:VVU201 4.3 12.9 0.8
C2 A:VVU201 4.3 17.1 0.8
C8 A:VVU201 4.3 15.5 0.8
O A:HOH355 4.4 40.3 1.0
ND1 A:HIS105 4.4 12.8 1.0
CG A:HIS105 4.4 11.2 1.0
CG2 A:THR78 4.7 15.1 1.0
CL A:CL204 5.0 20.2 0.8

Rhodium binding site 2 out of 4 in 8oqe

Go back to Rhodium Binding Sites List in 8oqe
Rhodium binding site 2 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 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 (6 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:14.1
occ:0.78
 RH2 A:VVU201 0.0 14.1 0.8
O2 A:VVU201 2.0 14.3 0.8
O4 A:VVU201 2.0 15.7 0.8
O8 A:VVU201 2.1 13.3 0.8
O9 A:VVU201 2.1 15.1 0.8
RH1 A:VVU201 2.4 12.7 0.8
CL A:CL204 2.6 20.2 0.8
C5 A:VVU201 2.8 14.4 0.8
C3 A:VVU201 2.9 12.9 0.8
C1 A:VVU201 2.9 14.8 0.8
C7 A:VVU201 2.9 15.7 0.8
O1 A:VVU201 3.0 14.5 0.8
O7 A:VVU201 3.1 11.8 0.8
O3 A:VVU201 3.1 15.2 0.8
O0 A:VVU201 3.1 13.7 0.8
O A:HOH373 3.8 47.0 1.0
O A:HOH321 3.9 45.4 1.0
C6 A:VVU201 4.2 20.1 0.8
C2 A:VVU201 4.3 17.1 0.8
C8 A:VVU201 4.3 15.5 0.8
C4 A:VVU201 4.3 12.9 0.8
NE2 A:HIS105 4.6 14.2 1.0
O A:HOH448 4.7 42.2 1.0

Rhodium binding site 3 out of 4 in 8oqe

Go back to Rhodium Binding Sites List in 8oqe
Rhodium binding site 3 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 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 (6 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:23.9
occ:0.55
 RH1 A:D1O202 0.0 23.9 0.6
O1 A:D1O202 2.1 23.3 0.6
O0 A:D1O202 2.1 25.4 0.6
O7 A:D1O202 2.1 19.6 0.6
O3 A:D1O202 2.1 24.5 0.6
ND1 A:HIS119 2.2 26.4 1.0
RH2 A:D1O202 2.4 29.6 0.6
C5 A:D1O202 2.7 26.1 0.6
O9 A:D1O202 2.9 28.9 0.6
C1 A:D1O202 2.9 22.2 0.6
O4 A:D1O202 3.0 26.7 0.6
CE1 A:HIS119 3.0 27.1 1.0
O8 A:D1O202 3.1 24.4 0.6
C3 A:D1O202 3.1 22.6 0.6
O2 A:D1O202 3.1 26.0 0.6
CG A:HIS119 3.3 22.6 1.0
CB A:HIS119 3.6 17.2 1.0
O A:HOH341 3.8 18.8 1.0
O A:HOH412 4.0 53.4 1.0
C6 A:D1O202 4.2 26.8 0.6
NE2 A:HIS119 4.2 25.1 1.0
CA A:HIS119 4.2 14.7 1.0
C2 A:D1O202 4.3 20.8 0.6
CD2 A:HIS119 4.4 23.3 1.0
O A:VAL118 4.4 15.7 1.0
C4 A:D1O202 4.5 17.6 0.6
CL A:CL205 5.0 40.2 0.6

Rhodium binding site 4 out of 4 in 8oqe

Go back to Rhodium Binding Sites List in 8oqe
Rhodium binding site 4 out of 4 in the Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (6 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 (6 H Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:29.6
occ:0.55
 RH2 A:D1O202 0.0 29.6 0.6
O9 A:D1O202 2.1 28.9 0.6
O4 A:D1O202 2.1 26.7 0.6
O2 A:D1O202 2.1 26.0 0.6
O8 A:D1O202 2.1 24.4 0.6
RH1 A:D1O202 2.4 23.9 0.6
CL A:CL205 2.6 40.2 0.6
C1 A:D1O202 2.9 22.2 0.6
C5 A:D1O202 2.9 26.1 0.6
O7 A:D1O202 2.9 19.6 0.6
O1 A:D1O202 3.0 23.3 0.6
C3 A:D1O202 3.0 22.6 0.6
O3 A:D1O202 3.2 24.5 0.6
O0 A:D1O202 3.4 25.4 0.6
NZ A:LYS7 3.7 21.9 0.2
C6 A:D1O202 3.8 26.8 0.6
C2 A:D1O202 4.3 20.8 0.6
CE A:LYS7 4.6 21.5 0.6
ND1 A:HIS119 4.6 26.4 1.0
C4 A:D1O202 4.6 17.6 0.6
O A:HOH339 4.8 25.1 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: Fri Jul 28 03:56:00 2023

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