Atomistry » Rhodium » PDB 165d-8oqd » 7z6d
Atomistry »
  Rhodium »
    PDB 165d-8oqd »
      7z6d »

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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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

Go back to Rhodium Binding Sites List in 7z6d
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: Thu Oct 10 12:38:08 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy