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Rhodium in PDB 8oqd: 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: 8oqd 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) 21.64 / 1.54
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.142, 67.142, 64.791, 90, 90, 120
R / Rfree (%) 19.5 / 22.2

Other elements in 8oqd:

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 8oqd). 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: 8oqd:
Jump to Rhodium binding site number: 1; 2; 3; 4;

Rhodium binding site 1 out of 4 in 8oqd

Go back to Rhodium Binding Sites List in 8oqd
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:31.8
occ:0.50
 RH1 A:D1O201 0.0 31.8 0.5
O7 A:D1O201 2.1 26.2 0.5
O1 A:D1O201 2.1 28.7 0.5
O0 A:D1O201 2.1 30.6 0.5
O3 A:D1O201 2.1 27.2 0.5
ND1 A:HIS119 2.2 35.0 1.0
RH2 A:D1O201 2.4 36.9 0.5
C5 A:D1O201 2.7 32.5 0.5
O4 A:D1O201 3.0 34.0 0.5
O9 A:D1O201 3.0 36.4 0.5
C1 A:D1O201 3.0 26.7 0.5
O8 A:D1O201 3.1 31.8 0.5
O2 A:D1O201 3.1 34.0 0.5
CE1 A:HIS119 3.1 34.5 1.0
C3 A:D1O201 3.1 29.4 0.5
CG A:HIS119 3.2 30.9 1.0
CB A:HIS119 3.6 22.1 1.0
O A:HOH319 3.7 46.5 1.0
O A:HOH324 3.9 21.0 1.0
NE2 A:HIS119 4.2 32.6 1.0
C6 A:D1O201 4.2 28.5 0.5
CA A:HIS119 4.2 17.2 1.0
CD2 A:HIS119 4.3 29.4 1.0
O A:VAL118 4.3 18.4 1.0
C2 A:D1O201 4.5 20.8 0.5
C4 A:D1O201 4.6 19.7 0.5
CL A:CL204 4.9 41.2 0.5

Rhodium binding site 2 out of 4 in 8oqd

Go back to Rhodium Binding Sites List in 8oqd
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:36.9
occ:0.50
 RH2 A:D1O201 0.0 36.9 0.5
O4 A:D1O201 2.1 34.0 0.5
O9 A:D1O201 2.1 36.4 0.5
O2 A:D1O201 2.1 34.0 0.5
O8 A:D1O201 2.1 31.8 0.5
RH1 A:D1O201 2.4 31.8 0.5
CL A:CL204 2.6 41.2 0.5
C5 A:D1O201 2.9 32.5 0.5
O7 A:D1O201 2.9 26.2 0.5
C1 A:D1O201 3.0 26.7 0.5
O1 A:D1O201 3.0 28.7 0.5
C3 A:D1O201 3.1 29.4 0.5
O3 A:D1O201 3.3 27.2 0.5
O0 A:D1O201 3.3 30.6 0.5
O A:HOH354 3.4 45.1 1.0
C6 A:D1O201 3.8 28.5 0.5
NZ A:LYS7 4.3 44.7 1.0
C2 A:D1O201 4.5 20.8 0.5
CE A:LYS7 4.5 36.1 1.0
ND1 A:HIS119 4.6 35.0 1.0
C4 A:D1O201 4.7 19.7 0.5
O A:HOH331 4.7 28.9 1.0

Rhodium binding site 3 out of 4 in 8oqd

Go back to Rhodium Binding Sites List in 8oqd
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:16.9
occ:0.72
 RH1 A:VVU205 0.0 16.9 0.7
O7 A:VVU205 2.0 17.9 0.7
O1 A:VVU205 2.0 17.3 0.7
O3 A:VVU205 2.1 15.9 0.7
O0 A:VVU205 2.1 18.9 0.7
NE2 A:HIS105 2.2 18.1 1.0
RH2 A:VVU205 2.4 18.5 0.7
C5 A:VVU205 2.7 22.5 0.7
C3 A:VVU205 2.8 18.8 0.7
C1 A:VVU205 2.9 19.7 0.7
C7 A:VVU205 2.9 16.3 0.7
O9 A:VVU205 3.0 20.0 0.7
O2 A:VVU205 3.0 17.5 0.7
O8 A:VVU205 3.1 17.1 0.7
O4 A:VVU205 3.1 16.3 0.7
CE1 A:HIS105 3.2 18.9 1.0
CD2 A:HIS105 3.2 17.1 1.0
O A:HOH385 4.1 20.7 1.0
C4 A:VVU205 4.2 15.3 0.7
C6 A:VVU205 4.2 22.7 0.7
O A:HOH352 4.3 35.1 1.0
C2 A:VVU205 4.3 18.8 0.7
C8 A:VVU205 4.3 14.5 0.7
ND1 A:HIS105 4.4 17.8 1.0
CG A:HIS105 4.4 15.8 1.0
CG2 A:THR78 4.6 18.7 1.0
CL A:CL203 5.0 21.6 0.7

Rhodium binding site 4 out of 4 in 8oqd

Go back to Rhodium Binding Sites List in 8oqd
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:18.5
occ:0.72
 RH2 A:VVU205 0.0 18.5 0.7
O8 A:VVU205 2.0 17.1 0.7
O9 A:VVU205 2.1 20.0 0.7
O4 A:VVU205 2.1 16.3 0.7
O2 A:VVU205 2.1 17.5 0.7
RH1 A:VVU205 2.4 16.9 0.7
CL A:CL203 2.6 21.6 0.7
C3 A:VVU205 2.8 18.8 0.7
C5 A:VVU205 2.8 22.5 0.7
C7 A:VVU205 2.8 16.3 0.7
C1 A:VVU205 2.9 19.7 0.7
O7 A:VVU205 3.0 17.9 0.7
O3 A:VVU205 3.0 15.9 0.7
O1 A:VVU205 3.1 17.3 0.7
O0 A:VVU205 3.2 18.9 0.7
O A:HOH303 3.6 37.5 1.0
O A:HOH360 3.7 48.7 1.0
C6 A:VVU205 4.1 22.7 0.7
C4 A:VVU205 4.2 15.3 0.7
C2 A:VVU205 4.3 18.8 0.7
C8 A:VVU205 4.3 14.5 0.7
O A:HOH422 4.4 50.8 1.0
NE2 A:HIS105 4.6 18.1 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: Thu Oct 10 12:40:44 2024

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