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Rhodium in PDB 7z6g: X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (2)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (2)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Rnase A (2):
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 (2), PDB code: 7z6g 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) 30.99 / 1.71
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.57, 32.57, 72.51, 90, 90.46, 90
R / Rfree (%) 18.3 / 23.6

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 (2) (pdb code 7z6g). 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 (2), PDB code: 7z6g:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rhodium binding site 1 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:35.7
occ:0.70
 RH3 A:F3I201 0.0 35.7 0.7
HE2 A:HIS105 1.3 23.9 0.0
O14 A:F3I201 2.1 43.5 0.7
O12 A:F3I201 2.1 36.4 0.7
NE2 A:HIS105 2.1 24.2 1.0
O10 A:F3I201 2.2 35.4 0.7
RH4 A:F3I201 2.3 57.0 0.7
C1 A:F3I201 2.8 27.1 0.7
O15 A:F3I201 2.9 45.9 0.7
O11 A:F3I201 3.0 23.4 0.7
CD2 A:HIS105 3.1 25.1 1.0
CE1 A:HIS105 3.1 25.7 1.0
HD2 A:HIS105 3.2 24.2 1.0
HE1 A:HIS105 3.3 24.5 1.0
C2 A:F3I201 3.9 23.8 0.7
O A:HOH400 4.0 59.2 1.0
HG21 A:THR78 4.0 36.0 1.0
HG23 A:THR78 4.1 35.9 1.0
ND1 A:HIS105 4.2 22.5 1.0
CG A:HIS105 4.2 22.3 1.0
CG2 A:THR78 4.5 36.5 1.0
O A:HOH316 4.5 45.0 1.0
HG22 A:THR78 4.7 36.0 1.0

Rhodium binding site 2 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:57.0
occ:0.70
 RH4 A:F3I201 0.0 57.0 0.7
O15 A:F3I201 2.1 45.9 0.7
O11 A:F3I201 2.2 23.4 0.7
RH3 A:F3I201 2.3 35.7 0.7
C1 A:F3I201 2.8 27.1 0.7
O10 A:F3I201 2.9 35.4 0.7
HE2 A:HIS105 3.0 23.9 0.0
O12 A:F3I201 3.1 36.4 0.7
O14 A:F3I201 3.1 43.5 0.7
NE2 A:HIS105 3.4 24.2 1.0
HD2 A:HIS105 3.7 24.2 1.0
CD2 A:HIS105 3.8 25.1 1.0
C2 A:F3I201 4.0 23.8 0.7
CE1 A:HIS105 4.3 25.7 1.0
O A:HOH348 4.5 31.7 1.0
HE1 A:HIS105 4.6 24.5 1.0
HE22 A:GLN74 4.7 22.4 1.0
HE21 A:GLN74 4.8 22.4 1.0
CG A:HIS105 4.8 22.3 1.0

Rhodium binding site 3 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:52.1
occ:0.55
 HD1 A:HIS119 1.5 21.9 0.0
HD1 A:HIS119 1.7 21.2 0.0
ND1 A:HIS119 2.0 21.2 0.5
ND1 A:HIS119 2.3 21.9 0.6
RH1 A:RH203 2.5 68.0 0.6
O A:HOH331 2.6 21.2 0.5
O A:HOH409 2.6 25.0 0.5
CG A:HIS119 2.7 20.9 0.5
CE1 A:HIS119 2.8 20.8 0.5
HB3 A:HIS119 2.8 19.5 0.5
HB2 A:HIS119 2.9 18.4 0.6
HE1 A:HIS119 3.1 21.3 0.5
CG A:HIS119 3.2 18.9 0.6
CB A:HIS119 3.2 19.3 0.5
CE1 A:HIS119 3.2 21.8 0.6
O A:HOH381 3.4 14.4 0.6
HE1 A:HIS119 3.4 20.8 0.6
CB A:HIS119 3.5 18.4 0.6
CD2 A:HIS119 3.6 22.2 0.5
NE2 A:HIS119 3.6 22.5 0.5
HA A:HIS119 3.8 17.6 0.6
HA A:HIS119 3.9 18.2 0.5
O A:HOH391 4.0 58.9 1.0
HB2 A:HIS119 4.0 19.4 0.5
CA A:HIS119 4.2 17.8 0.6
CA A:HIS119 4.2 18.4 0.5
HB3 A:HIS119 4.3 18.4 0.6
HE2 A:HIS119 4.3 22.5 0.0
CD2 A:HIS119 4.3 18.8 0.6
NE2 A:HIS119 4.3 18.2 0.6
HD2 A:HIS119 4.4 21.9 0.5
H A:PHE120 4.6 16.2 1.0
O A:VAL118 4.7 21.4 1.0

Rhodium binding site 4 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh203

b:68.0
occ:0.55
 RH1 A:RH202 2.5 52.1 0.6
HE1 A:HIS119 2.6 21.3 0.5
O A:HOH409 3.0 25.0 0.5
HD1 A:HIS119 3.0 21.2 0.0
CE1 A:HIS119 3.1 20.8 0.5
ND1 A:HIS119 3.3 21.2 0.5
O A:HOH331 3.5 21.2 0.5
HD1 A:HIS119 4.0 21.9 0.0
HZ3 A:LYS7 4.1 40.6 1.0
O A:HOH411 4.2 20.4 0.5
NE2 A:HIS119 4.3 22.5 0.5
CG A:HIS119 4.5 20.9 0.5
HE2 A:HIS119 4.7 22.5 0.0
HE21 A:GLN11 4.7 33.8 1.0
ND1 A:HIS119 4.8 21.9 0.6
NZ A:LYS7 4.9 41.6 1.0
HZ2 A:LYS7 4.9 40.6 1.0
HB2 A:HIS119 4.9 18.4 0.6
O A:HOH381 4.9 14.4 0.6
O A:HOH403 5.0 44.2 1.0
CD2 A:HIS119 5.0 22.2 0.5

Rhodium binding site 5 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh301

b:45.2
occ:0.55
 RH1 B:RH301 0.0 45.2 0.6
HE2 B:HIS119 1.3 20.9 0.0
O B:HOH508 2.1 47.6 0.6
O B:HOH524 2.1 47.4 0.6
NE2 B:HIS119 2.1 20.4 0.4
O B:HOH520 2.1 42.1 0.6
RH1 B:RH302 2.5 56.1 0.6
H1 B:HOH524 2.7 47.2 0.0
RH1 B:RH302 2.8 34.2 0.3
CE1 B:HIS119 3.1 20.5 0.4
CD2 B:HIS119 3.1 21.5 0.4
HE1 B:HIS119 3.3 23.2 0.6
HE1 B:HIS119 3.3 20.5 0.4
HD2 B:HIS119 3.3 20.7 0.4
HD1 B:HIS119 3.4 22.8 0.0
O B:HOH504 3.6 50.1 0.6
RH1 B:RH301 3.6 41.1 0.3
O B:HOH464 3.8 63.1 1.0
CE1 B:HIS119 3.8 23.6 0.6
ND1 B:HIS119 3.8 23.1 0.6
O B:HOH482 3.9 26.9 1.0
H1 B:HOH524 3.9 42.1 0.0
O B:HOH524 4.1 36.0 0.3
ND1 B:HIS119 4.2 20.7 0.4
CG B:HIS119 4.2 19.6 0.4
O B:HOH408 4.7 41.1 1.0
HE21 B:GLN11 4.8 28.2 1.0

Rhodium binding site 6 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh301

b:41.1
occ:0.30
 RH1 B:RH301 0.0 41.1 0.3
O B:HOH520 1.9 42.1 0.6
O B:HOH524 2.1 36.0 0.3
RH1 B:RH302 2.5 34.2 0.3
HD2 B:HIS119 2.7 20.7 0.4
H1 B:HOH524 2.7 42.1 0.0
CD2 B:HIS119 3.4 21.5 0.4
HZ3 B:LYS7 3.4 37.6 1.0
RH1 B:RH301 3.6 45.2 0.6
O B:HOH508 3.6 47.6 0.6
HE2 B:HIS119 3.6 20.9 0.0
O B:HOH474 3.8 40.4 1.0
HD1 B:HIS119 3.8 22.8 0.0
NE2 B:HIS119 3.8 20.4 0.4
HD3 B:LYS7 4.2 30.1 1.0
NZ B:LYS7 4.3 38.5 1.0
HE2 B:LYS7 4.5 34.9 1.0
CG B:HIS119 4.5 19.6 0.4
HZ2 B:LYS7 4.5 37.6 1.0
ND1 B:HIS119 4.7 23.1 0.6
O B:HOH406 4.7 23.8 1.0
CE B:LYS7 4.8 35.7 1.0
HB2 B:HIS119 4.8 18.8 0.6
HZ1 B:LYS7 4.9 37.6 1.0
HB2 B:HIS119 4.9 18.4 0.4
RH1 B:RH302 4.9 56.1 0.6
O B:HOH482 4.9 26.9 1.0
CD B:LYS7 5.0 30.2 1.0

Rhodium binding site 7 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh302

b:56.1
occ:0.55
 O B:HOH504 2.1 50.1 0.6
RH1 B:RH301 2.5 45.2 0.6
H1 B:HOH524 2.9 47.2 0.0
O B:HOH524 3.0 47.4 0.6
O B:HOH508 3.1 47.6 0.6
O B:HOH520 3.4 42.1 0.6
HE2 B:HIS119 3.7 20.9 0.0
HE3 B:LYS41 3.8 29.3 1.0
HZ2 B:LYS41 4.4 31.4 1.0
NE2 B:HIS119 4.6 20.4 0.4
CE B:LYS41 4.6 29.4 1.0
O B:HOH408 4.7 41.1 1.0
HE2 B:LYS41 4.8 29.3 1.0
HE21 B:GLN11 4.8 28.2 1.0
RH1 B:RH301 4.9 41.1 0.3
NZ B:LYS41 5.0 32.4 1.0
O B:HOH464 5.0 63.1 1.0

Rhodium binding site 8 out of 8 in 7z6g

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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 (2)


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 (2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh302

b:34.2
occ:0.30
 HD2 B:HIS119 1.1 20.7 0.4
CD2 B:HIS119 1.1 21.5 0.4
HD1 B:HIS119 1.3 22.8 0.0
NE2 B:HIS119 1.6 20.4 0.4
HE2 B:HIS119 2.0 20.9 0.0
ND1 B:HIS119 2.2 23.1 0.6
CG B:HIS119 2.2 19.6 0.4
O B:HOH520 2.4 42.1 0.6
RH1 B:RH301 2.5 41.1 0.3
CE1 B:HIS119 2.7 20.5 0.4
RH1 B:RH301 2.8 45.2 0.6
H1 B:HOH524 2.9 42.1 0.0
ND1 B:HIS119 2.9 20.7 0.4
CE1 B:HIS119 3.1 23.6 0.6
HB2 B:HIS119 3.1 18.8 0.6
O B:HOH524 3.1 36.0 0.3
HE1 B:HIS119 3.2 23.2 0.6
CG B:HIS119 3.2 20.8 0.6
HB2 B:HIS119 3.3 18.4 0.4
O B:HOH508 3.3 47.6 0.6
CB B:HIS119 3.3 18.4 0.4
HE1 B:HIS119 3.5 20.5 0.4
O B:HOH482 3.6 26.9 1.0
CB B:HIS119 3.6 18.8 0.6
HA B:HIS119 3.7 17.2 0.6
HD1 B:HIS119 3.8 21.1 0.0
O B:HOH474 3.8 40.4 1.0
HA B:HIS119 3.9 17.3 0.4
HB3 B:HIS119 4.0 18.4 0.4
O B:HOH497 4.1 40.9 1.0
CA B:HIS119 4.2 16.9 0.6
CA B:HIS119 4.2 17.1 0.4
NE2 B:HIS119 4.3 23.0 0.6
CD2 B:HIS119 4.3 22.5 0.6
O B:HOH524 4.4 47.4 0.6
HB3 B:HIS119 4.5 18.8 0.6
O B:VAL118 4.5 18.3 1.0
H B:PHE120 4.6 17.7 1.0
O B:HOH481 4.9 27.3 1.0
O B:HOH464 5.0 63.1 1.0

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 Apr 11 17:52:27 2023

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