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Rhodium in PDB 7z6d: X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1):
4.6.1.18;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1), PDB code: 7z6d was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.85 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.69, 33.12, 73.45, 90, 90.13, 90
R / Rfree (%) 20.2 / 23.2

Rhodium Binding Sites:

The binding sites of Rhodium atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) (pdb code 7z6d). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 8 binding sites of Rhodium where determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1), PDB code: 7z6d:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rhodium binding site 1 out of 8 in 7z6d

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Rhodium binding site 1 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:30.7
occ:0.50
 RH3 A:F3I202 0.0 30.7 0.5
HE2 A:HIS105 1.2 17.5 0.0
NE2 A:HIS105 2.0 17.5 1.0
O12 A:F3I202 2.1 32.4 0.5
O14 A:F3I202 2.1 34.1 0.5
O9 A:F3I202 2.1 31.2 0.5
RH4 A:F3I202 2.4 38.9 0.5
H9 A:F3I202 2.7 31.1 0.0
C1 A:F3I202 2.8 25.4 0.5
CE1 A:HIS105 3.0 18.3 1.0
CD2 A:HIS105 3.0 19.0 1.0
O16 A:F3I202 3.1 34.2 0.5
O11 A:F3I202 3.2 23.3 0.5
HE1 A:HIS105 3.2 17.7 1.0
HD2 A:HIS105 3.2 17.5 1.0
C2 A:F3I202 3.9 21.7 0.5
HG21 A:THR78 4.0 21.2 1.0
ND1 A:HIS105 4.1 16.6 1.0
CG A:HIS105 4.1 14.4 1.0
HG23 A:THR78 4.2 21.2 1.0
CG2 A:THR78 4.5 21.1 1.0
O A:HOH338 4.5 30.2 1.0
HG22 A:THR78 4.5 21.2 1.0
HD1 A:HIS105 4.9 16.6 0.0

Rhodium binding site 2 out of 8 in 7z6d

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Rhodium binding site 2 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:38.9
occ:0.50
 RH4 A:F3I202 0.0 38.9 0.5
O16 A:F3I202 2.1 34.2 0.5
RH3 A:F3I202 2.4 30.7 0.5
O11 A:F3I202 2.4 23.3 0.5
HE2 A:HIS105 2.9 17.5 0.0
C1 A:F3I202 3.0 25.4 0.5
O9 A:F3I202 3.1 31.2 0.5
O14 A:F3I202 3.1 34.1 0.5
O12 A:F3I202 3.2 32.4 0.5
NE2 A:HIS105 3.4 17.5 1.0
H9 A:F3I202 3.6 31.1 0.0
HD2 A:HIS105 3.7 17.5 1.0
CD2 A:HIS105 3.8 19.0 1.0
C2 A:F3I202 4.1 21.7 0.5
O A:HOH408 4.2 36.9 1.0
CE1 A:HIS105 4.3 18.3 1.0
HE1 A:HIS105 4.6 17.7 1.0
HE22 A:GLN74 4.8 15.8 1.0
CG A:HIS105 4.9 14.4 1.0
O A:HOH375 4.9 26.9 1.0

Rhodium binding site 3 out of 8 in 7z6d

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Rhodium binding site 3 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh203

b:36.4
occ:0.40
 HD1 A:HIS119 1.5 16.5 0.0
HD1 A:HIS119 1.8 11.6 0.0
ND1 A:HIS119 2.2 11.7 0.5
RH1 A:RH204 2.3 44.2 0.4
ND1 A:HIS119 2.3 16.6 0.5
O A:HOH355 2.7 23.6 0.6
HB3 A:HIS119 2.7 10.9 0.5
O A:HOH463 2.9 17.3 0.6
CG A:HIS119 2.9 11.3 0.5
CE1 A:HIS119 3.0 12.1 0.5
HB2 A:HIS119 3.0 14.2 0.5
CE1 A:HIS119 3.2 18.0 0.5
HE1 A:HIS119 3.2 12.1 0.5
CG A:HIS119 3.2 15.4 0.5
CB A:HIS119 3.3 10.9 0.5
HE1 A:HIS119 3.3 17.1 0.5
CB A:HIS119 3.5 14.5 0.5
O A:HOH402 3.6 20.9 1.0
CD2 A:HIS119 3.8 12.3 0.5
HA A:HIS119 3.8 12.7 0.5
NE2 A:HIS119 3.8 12.5 0.5
HB2 A:HIS119 4.0 10.9 0.5
HA A:HIS119 4.0 10.8 0.5
O A:HOH434 4.2 28.4 1.0
CA A:HIS119 4.3 12.6 0.5
NE2 A:HIS119 4.3 16.0 0.5
CA A:HIS119 4.3 10.7 0.5
CD2 A:HIS119 4.3 16.3 0.5
HB3 A:HIS119 4.4 14.2 0.5
HE2 A:HIS119 4.6 12.4 0.0
HD2 A:HIS119 4.6 12.1 0.5
H A:PHE120 4.7 10.8 1.0
O A:VAL118 4.7 13.9 1.0
O A:HOH359 4.9 14.2 0.5

Rhodium binding site 4 out of 8 in 7z6d

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Rhodium binding site 4 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh204

b:44.2
occ:0.40
 RH1 A:RH203 2.3 36.4 0.4
HD1 A:HIS119 2.9 11.6 0.0
HE1 A:HIS119 2.9 12.1 0.5
O A:HOH355 3.3 23.6 0.6
ND1 A:HIS119 3.3 11.7 0.5
CE1 A:HIS119 3.3 12.1 0.5
O A:HOH463 3.4 17.3 0.6
HD1 A:HIS119 3.7 16.5 0.0
HE2 A:LYS7 4.4 25.6 1.0
HZ3 A:LYS7 4.4 27.5 1.0
CG A:HIS119 4.5 11.3 0.5
NE2 A:HIS119 4.5 12.5 0.5
ND1 A:HIS119 4.5 16.6 0.5
HB2 A:HIS119 4.7 14.2 0.5
O A:HOH460 4.8 31.6 1.0
HZ2 A:LYS7 4.9 27.5 1.0
HB3 A:HIS119 4.9 10.9 0.5
O A:HOH456 4.9 34.5 1.0
NZ A:LYS7 4.9 28.4 1.0

Rhodium binding site 5 out of 8 in 7z6d

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Rhodium binding site 5 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 5 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh401

b:25.2
occ:0.20
 RH1 B:RH401 0.0 25.2 0.2
O B:HOH666 1.6 27.7 0.4
H1 B:HOH666 1.9 27.9 0.0
O B:HOH666 2.1 24.2 0.2
RH1 B:RH402 2.5 22.9 0.2
HD2 B:HIS119 2.6 16.5 0.5
O B:HOH654 2.6 26.8 0.4
H1 B:HOH666 2.7 29.5 0.0
CD2 B:HIS119 3.4 17.1 0.5
RH1 B:RH401 3.5 26.9 0.4
HE2 B:LYS7 3.6 27.8 1.0
HE2 B:HIS119 3.6 16.7 0.0
HD1 B:HIS119 3.8 16.7 0.0
NE2 B:HIS119 3.8 16.6 0.5
O B:HOH621 3.8 29.1 0.4
HD3 B:LYS7 4.3 22.4 1.0
HZ3 B:LYS7 4.3 31.9 1.0
CE B:LYS7 4.5 28.0 1.0
O B:HOH607 4.6 26.1 1.0
CG B:HIS119 4.6 15.4 0.5
ND1 B:HIS119 4.6 16.9 0.6
HZ2 B:LYS7 4.7 31.9 1.0
O B:HOH513 4.7 19.8 1.0
NZ B:LYS7 4.7 33.8 1.0
H1 B:HOH621 4.8 29.2 0.0
RH1 B:RH402 4.8 28.1 0.4
HE21 B:GLN11 4.8 22.7 1.0
O B:HOH558 4.9 37.2 1.0
O B:HOH573 4.9 18.9 1.0
CD B:LYS7 5.0 22.7 1.0

Rhodium binding site 6 out of 8 in 7z6d

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Rhodium binding site 6 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 6 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh401

b:26.9
occ:0.40
 RH1 B:RH401 0.0 26.9 0.4
HE2 B:HIS119 1.5 16.7 0.0
H1 B:HOH666 2.1 29.5 0.0
O B:HOH621 2.1 29.1 0.4
O B:HOH615 2.1 24.7 0.4
O B:HOH666 2.1 27.7 0.4
NE2 B:HIS119 2.3 16.6 0.5
RH1 B:RH402 2.4 28.1 0.4
H1 B:HOH621 2.6 29.2 0.0
H1 B:HOH666 2.7 27.9 0.0
RH1 B:RH402 2.7 22.9 0.2
O B:HOH666 2.8 24.2 0.2
HE1 B:HIS119 3.0 18.8 0.6
O B:HOH662 3.2 26.2 0.4
CD2 B:HIS119 3.2 17.1 0.5
CE1 B:HIS119 3.3 16.9 0.5
HD2 B:HIS119 3.4 16.5 0.5
HD1 B:HIS119 3.4 16.7 0.0
HE1 B:HIS119 3.5 16.6 0.5
RH1 B:RH401 3.5 25.2 0.2
CE1 B:HIS119 3.7 20.0 0.6
O B:HOH649 3.7 31.1 0.6
ND1 B:HIS119 3.9 16.9 0.6
H1 B:HOH662 3.9 26.8 0.4
O B:HOH654 4.1 26.8 0.4
O B:HOH573 4.2 18.9 1.0
CG B:HIS119 4.4 15.4 0.5
ND1 B:HIS119 4.4 15.9 0.5
O B:HOH510 4.6 34.5 1.0
HE21 B:GLN11 4.8 22.7 1.0
HZ2 B:LYS41 4.9 26.2 1.0
O B:HOH627 4.9 21.2 0.5
NE2 B:HIS119 4.9 18.4 0.6

Rhodium binding site 7 out of 8 in 7z6d

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Rhodium binding site 7 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 7 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh402

b:22.9
occ:0.20
 RH1 B:RH402 0.0 22.9 0.2
HD2 B:HIS119 0.8 16.5 0.5
CD2 B:HIS119 1.0 17.1 0.5
HD1 B:HIS119 1.4 16.7 0.0
NE2 B:HIS119 1.6 16.6 0.5
HE2 B:HIS119 1.8 16.7 0.0
ND1 B:HIS119 2.2 16.9 0.6
CG B:HIS119 2.3 15.4 0.5
O B:HOH666 2.4 27.7 0.4
RH1 B:RH401 2.5 25.2 0.2
H1 B:HOH666 2.7 29.5 0.0
RH1 B:RH401 2.7 26.9 0.4
CE1 B:HIS119 2.8 16.9 0.5
CE1 B:HIS119 2.9 20.0 0.6
HE1 B:HIS119 3.0 18.8 0.6
ND1 B:HIS119 3.0 15.9 0.5
O B:HOH666 3.2 24.2 0.2
CG B:HIS119 3.3 15.5 0.6
H1 B:HOH666 3.3 27.9 0.0
O B:HOH621 3.4 29.1 0.4
HB2 B:HIS119 3.4 13.9 0.6
HB2 B:HIS119 3.4 13.7 0.5
CB B:HIS119 3.4 13.9 0.5
HE1 B:HIS119 3.6 16.6 0.5
O B:HOH573 3.6 18.9 1.0
HA B:HIS119 3.7 12.0 0.6
CB B:HIS119 3.8 14.2 0.6
HA B:HIS119 3.8 12.0 0.5
HD1 B:HIS119 4.0 16.1 0.0
NE2 B:HIS119 4.1 18.4 0.6
HB3 B:HIS119 4.2 13.7 0.5
CA B:HIS119 4.2 11.9 0.5
H1 B:HOH621 4.2 29.2 0.0
CA B:HIS119 4.3 11.9 0.6
O B:HOH615 4.3 24.7 0.4
CD2 B:HIS119 4.3 17.5 0.6
O B:HOH638 4.3 27.8 1.0
H B:PHE120 4.5 11.4 1.0
O B:HOH654 4.5 26.8 0.4
O B:VAL118 4.7 14.0 1.0
HB3 B:HIS119 4.7 13.9 0.6
O B:HOH607 4.7 26.1 1.0
O B:HOH562 4.9 18.2 1.0
HE2 B:HIS119 4.9 18.5 0.0
RH1 B:RH402 5.0 28.1 0.4

Rhodium binding site 8 out of 8 in 7z6d

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Rhodium binding site 8 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 8 of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh402

b:28.1
occ:0.40
 RH1 B:RH402 0.0 28.1 0.4
O B:HOH662 2.1 26.2 0.4
RH1 B:RH401 2.4 26.9 0.4
H1 B:HOH662 2.7 26.8 0.4
O B:HOH615 3.1 24.7 0.4
H1 B:HOH666 3.1 27.9 0.0
H1 B:HOH621 3.2 29.2 0.0
O B:HOH621 3.2 29.1 0.4
H1 B:HOH666 3.3 29.5 0.0
O B:HOH666 3.3 27.7 0.4
O B:HOH666 3.5 24.2 0.2
HE2 B:HIS119 3.9 16.7 0.0
HE3 B:LYS41 4.0 23.8 1.0
O B:HOH654 4.0 26.8 0.4
O B:HOH636 4.3 40.5 1.0
O B:HOH558 4.4 37.2 1.0
HZ2 B:LYS41 4.4 26.2 1.0
O B:HOH649 4.7 31.1 0.6
HE2 B:LYS41 4.7 23.8 1.0
NE2 B:HIS119 4.7 16.6 0.5
CE B:LYS41 4.7 24.0 1.0
RH1 B:RH401 4.8 25.2 0.2
RH1 B:RH402 5.0 22.9 0.2

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins To Be Published.
Page generated: Tue Aug 19 00:42:49 2025

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