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

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

All present enzymatic activity of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection), PDB code: 8oqf 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) 22.06 / 1.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.389, 67.389, 64.42, 90, 90, 120
R / Rfree (%) 18.5 / 22.4

Other elements in 8oqf:

The structure of Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection) (pdb code 8oqf). 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 (Low Temperature Data Collection), PDB code: 8oqf:
Jump to Rhodium binding site number: 1; 2; 3; 4;

Rhodium binding site 1 out of 4 in 8oqf

Go back to Rhodium Binding Sites List in 8oqf
Rhodium binding site 1 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh203

b:50.4
occ:0.35
 RH3 A:F3I203 0.0 50.4 0.3
ND1 A:HIS119 2.0 17.6 0.3
O9 A:F3I203 2.1 48.2 0.3
O12 A:F3I203 2.1 46.5 0.3
ND1 A:HIS119 2.3 28.6 0.7
RH4 A:F3I203 2.5 55.0 0.3
CE1 A:HIS119 2.7 18.1 0.3
CG A:HIS119 2.7 17.5 0.3
C1 A:F3I203 3.0 42.2 0.3
O13 A:F3I203 3.2 49.1 0.3
CE1 A:HIS119 3.3 26.6 0.7
CG A:HIS119 3.3 24.8 0.7
CB A:HIS119 3.3 15.9 0.3
O11 A:F3I203 3.5 47.2 0.3
CB A:HIS119 3.5 19.7 0.7
NE2 A:HIS119 3.5 18.7 0.3
CD2 A:HIS119 3.6 17.6 0.3
O A:HOH408 3.8 18.4 1.0
O A:HOH459 4.1 41.2 1.0
CA A:HIS119 4.2 15.2 0.3
CA A:HIS119 4.2 16.8 0.7
C2 A:F3I203 4.2 35.1 0.3
NE2 A:HIS119 4.4 28.8 0.7
O A:VAL118 4.4 15.6 1.0
CD2 A:HIS119 4.4 25.4 0.7
O A:HOH475 4.8 25.8 0.3

Rhodium binding site 2 out of 4 in 8oqf

Go back to Rhodium Binding Sites List in 8oqf
Rhodium binding site 2 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh203

b:55.0
occ:0.35
 RH4 A:F3I203 0.0 55.0 0.3
O13 A:F3I203 2.1 49.1 0.3
O11 A:F3I203 2.1 47.2 0.3
RH3 A:F3I203 2.5 50.4 0.3
C1 A:F3I203 2.7 42.2 0.3
O12 A:F3I203 2.9 46.5 0.3
O A:HOH475 3.0 25.8 0.3
O9 A:F3I203 3.0 48.2 0.3
CE1 A:HIS119 3.0 18.1 0.3
ND1 A:HIS119 3.1 17.6 0.3
NZ A:LYS7 3.8 25.9 0.2
C2 A:F3I203 4.2 35.1 0.3
NE2 A:HIS119 4.3 18.7 0.3
CG A:HIS119 4.4 17.5 0.3
CE A:LYS7 4.4 25.8 0.6
O A:HOH325 4.5 28.2 1.0
ND1 A:HIS119 4.8 28.6 0.7
O A:VAL118 4.9 15.6 1.0
CD A:LYS7 4.9 26.1 1.0
O A:HOH438 5.0 37.6 1.0
CD2 A:HIS119 5.0 17.6 0.3

Rhodium binding site 3 out of 4 in 8oqf

Go back to Rhodium Binding Sites List in 8oqf
Rhodium binding site 3 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh204

b:17.2
occ:0.75
 RH1 A:VVU204 0.0 17.2 0.8
O3 A:VVU204 2.0 18.4 0.8
O7 A:VVU204 2.0 18.7 0.8
O0 A:VVU204 2.1 16.7 0.8
O1 A:VVU204 2.1 16.6 0.8
RH2 A:VVU204 2.4 15.5 0.8
CL A:CL205 2.6 22.2 0.8
C5 A:VVU204 2.7 15.7 0.8
C3 A:VVU204 2.8 21.0 0.8
C7 A:VVU204 2.8 19.9 0.8
C1 A:VVU204 3.0 16.6 0.8
O4 A:VVU204 3.0 18.8 0.8
O9 A:VVU204 3.1 14.0 0.8
O8 A:VVU204 3.1 19.0 0.8
O2 A:VVU204 3.2 17.6 0.8
O A:HOH307 3.6 20.3 0.5
O A:HOH364 3.7 49.3 1.0
O A:HOH396 3.9 44.1 1.0
C4 A:VVU204 4.2 23.3 0.8
C6 A:VVU204 4.2 17.3 0.8
C8 A:VVU204 4.3 22.4 0.8
O A:HOH449 4.3 60.3 1.0
C2 A:VVU204 4.4 17.2 0.8
O A:HOH307 4.5 26.4 0.5
NE2 A:HIS105 4.6 17.2 1.0

Rhodium binding site 4 out of 4 in 8oqf

Go back to Rhodium Binding Sites List in 8oqf
Rhodium binding site 4 out of 4 in the Cross-Linked Crystal of Dirhodium Tetraacetate/Ribonuclease A Adduct in the P3221 Space Group (Low 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 (Low Temperature Data Collection) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh204

b:15.5
occ:0.75
 RH2 A:VVU204 0.0 15.5 0.8
O4 A:VVU204 2.0 18.8 0.8
O8 A:VVU204 2.1 19.0 0.8
O9 A:VVU204 2.1 14.0 0.8
O2 A:VVU204 2.1 17.6 0.8
NE2 A:HIS105 2.3 17.2 1.0
RH1 A:VVU204 2.4 17.2 0.8
C5 A:VVU204 2.8 15.7 0.8
C3 A:VVU204 2.8 21.0 0.8
C7 A:VVU204 2.9 19.9 0.8
C1 A:VVU204 2.9 16.6 0.8
O1 A:VVU204 3.0 16.6 0.8
O7 A:VVU204 3.1 18.7 0.8
O3 A:VVU204 3.1 18.4 0.8
O0 A:VVU204 3.2 16.7 0.8
CE1 A:HIS105 3.2 16.0 1.0
CD2 A:HIS105 3.3 14.8 1.0
O A:HOH390 4.1 18.8 1.0
C6 A:VVU204 4.2 17.3 0.8
C4 A:VVU204 4.2 23.3 0.8
C8 A:VVU204 4.3 22.4 0.8
ND1 A:HIS105 4.4 15.7 1.0
C2 A:VVU204 4.4 17.2 0.8
CG A:HIS105 4.4 14.1 1.0
CG2 A:THR78 4.6 16.4 1.0
CL A:CL205 5.0 22.2 0.8

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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