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Rhodium in PDB 8oqg: Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)

Enzymatic activity of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)

All present enzymatic activity of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection):
4.6.1.18;

Protein crystallography data

The structure of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection), PDB code: 8oqg 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) 22.02 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.278, 67.278, 65.899, 90, 90, 120
R / Rfree (%) 18.2 / 20.2

Other elements in 8oqg:

The structure of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Rhodium Binding Sites:

The binding sites of Rhodium atom in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) (pdb code 8oqg). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 4 binding sites of Rhodium where determined in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection), PDB code: 8oqg:
Jump to Rhodium binding site number: 1; 2; 3; 4;

Rhodium binding site 1 out of 4 in 8oqg

Go back to Rhodium Binding Sites List in 8oqg
Rhodium binding site 1 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:13.7
occ:0.80
 RH1 A:VVU201 0.0 13.7 0.8
O1 A:VVU201 2.0 15.4 0.8
O3 A:VVU201 2.0 13.5 0.8
O0 A:VVU201 2.1 15.7 0.8
O7 A:VVU201 2.1 14.2 0.8
NE2 A:HIS105 2.2 13.9 1.0
RH2 A:VVU201 2.4 16.0 0.8
C5 A:VVU201 2.6 20.3 0.8
C7 A:VVU201 2.8 16.3 0.8
C1 A:VVU201 2.9 20.1 0.8
C3 A:VVU201 2.9 16.6 0.8
O4 A:VVU201 3.0 15.0 0.8
O9 A:VVU201 3.0 15.3 0.8
O2 A:VVU201 3.1 15.4 0.8
O8 A:VVU201 3.1 15.1 0.8
CE1 A:HIS105 3.1 12.8 1.0
CD2 A:HIS105 3.3 13.9 1.0
C6 A:VVU201 4.1 23.9 0.8
C4 A:VVU201 4.2 17.0 0.8
O A:HOH351 4.2 19.4 1.0
C2 A:VVU201 4.3 20.6 0.8
C8 A:VVU201 4.3 16.9 0.8
ND1 A:HIS105 4.3 13.0 1.0
O A:HOH350 4.4 31.8 1.0
CG A:HIS105 4.4 12.4 1.0
CG2 A:THR78 4.6 16.9 1.0

Rhodium binding site 2 out of 4 in 8oqg

Go back to Rhodium Binding Sites List in 8oqg
Rhodium binding site 2 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:16.0
occ:0.80
 RH2 A:VVU201 0.0 16.0 0.8
O2 A:VVU201 2.0 15.4 0.8
O4 A:VVU201 2.0 15.0 0.8
O8 A:VVU201 2.0 15.1 0.8
O9 A:VVU201 2.1 15.3 0.8
RH1 A:VVU201 2.4 13.7 0.8
CL A:CL204 2.6 24.4 0.8
C5 A:VVU201 2.7 20.3 0.8
C1 A:VVU201 2.8 20.1 0.8
C3 A:VVU201 2.8 16.6 0.8
C7 A:VVU201 2.9 16.3 0.8
O1 A:VVU201 2.9 15.4 0.8
O7 A:VVU201 3.0 14.2 0.8
O3 A:VVU201 3.2 13.5 0.8
O0 A:VVU201 3.2 15.7 0.8
O A:HOH306 3.7 53.9 1.0
O A:HOH354 3.8 58.1 1.0
O A:HOH377 4.0 51.9 1.0
C6 A:VVU201 4.0 23.9 0.8
C2 A:VVU201 4.2 20.6 0.8
C8 A:VVU201 4.3 16.9 0.8
C4 A:VVU201 4.3 17.0 0.8
NE2 A:HIS105 4.6 13.9 1.0

Rhodium binding site 3 out of 4 in 8oqg

Go back to Rhodium Binding Sites List in 8oqg
Rhodium binding site 3 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:48.8
occ:0.35
 RH3 A:VW5202 0.0 48.8 0.3
O1 A:VW5202 2.1 43.3 0.3
O4 A:VW5202 2.1 42.9 0.3
RH4 A:VW5202 2.5 44.9 0.3
CE1 A:HIS119 2.9 22.0 0.3
ND1 A:HIS119 3.1 21.7 0.3
O2 A:VW5202 3.1 33.1 0.3
O3 A:VW5202 3.3 36.6 0.3
NZ A:LYS7 4.1 26.9 0.2
NE2 A:HIS119 4.1 22.6 0.3
CG A:HIS119 4.4 20.9 0.3
CE A:LYS7 4.6 26.7 0.6
ND1 A:HIS119 4.6 22.9 0.7
O A:HOH395 4.7 47.5 1.0
O A:HOH326 4.7 30.3 1.0
CD2 A:HIS119 4.9 22.3 0.3
O A:HOH367 5.0 6.5 0.5

Rhodium binding site 4 out of 4 in 8oqg

Go back to Rhodium Binding Sites List in 8oqg
Rhodium binding site 4 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (High Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:44.9
occ:0.35
 RH4 A:VW5202 0.0 44.9 0.3
ND1 A:HIS119 1.8 21.7 0.3
O3 A:VW5202 2.1 36.6 0.3
O2 A:VW5202 2.1 33.1 0.3
ND1 A:HIS119 2.2 22.9 0.7
RH3 A:VW5202 2.5 48.8 0.3
CE1 A:HIS119 2.6 22.0 0.3
CG A:HIS119 2.6 20.9 0.3
CE1 A:HIS119 3.0 21.8 0.7
O1 A:VW5202 3.1 43.3 0.3
CG A:HIS119 3.1 20.2 0.7
CB A:HIS119 3.3 18.4 0.3
O4 A:VW5202 3.3 42.9 0.3
NE2 A:HIS119 3.4 22.6 0.3
CB A:HIS119 3.5 17.9 0.7
CD2 A:HIS119 3.5 22.3 0.3
O A:HOH367 3.7 6.5 0.5
O A:HOH308 3.8 52.6 1.0
CA A:HIS119 4.1 16.6 0.3
CA A:HIS119 4.1 16.3 0.7
NE2 A:HIS119 4.1 20.6 0.7
CD2 A:HIS119 4.2 20.0 0.7
O A:VAL118 4.4 18.8 1.0
O A:HOH348 4.8 37.9 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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