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Rhodium in PDB 7z6j: X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl

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

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl, PDB code: 7z6j 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) 39.31 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.61, 78.61, 37.41, 90, 90, 90
R / Rfree (%) 19.5 / 24.9

Other elements in 7z6j:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl also contains other interesting chemical elements:

Sodium (Na) 1 atom

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 Hewl (pdb code 7z6j). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 5 binding sites of Rhodium where determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl, PDB code: 7z6j:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5;

Rhodium binding site 1 out of 5 in 7z6j

Go back to Rhodium Binding Sites List in 7z6j
Rhodium binding site 1 out of 5 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


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

b:55.0
occ:0.25
 O A:HOH438 2.2 25.2 0.2
OD2 A:ASP101 2.2 43.1 1.0
O A:HOH411 2.6 42.5 1.0
O A:HOH415 2.7 60.2 1.0
O A:HOH429 3.0 59.0 1.0
CG A:ASP101 3.2 40.4 1.0
OD1 A:ASP101 3.4 40.7 1.0
CB A:ASP101 4.5 37.6 1.0
O A:ASP101 4.6 42.8 1.0
HZ2 A:TRP63 4.6 24.6 1.0
HB3 A:ASP101 4.6 37.5 1.0
O A:HOH417 4.8 42.0 1.0
HH2 A:TRP63 4.8 25.2 1.0

Rhodium binding site 2 out of 5 in 7z6j

Go back to Rhodium Binding Sites List in 7z6j
Rhodium binding site 2 out of 5 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


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 Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh204

b:62.8
occ:0.25
 HD1 A:HIS15 1.7 47.1 0.0
RH1 A:RH205 2.4 60.2 0.2
ND1 A:HIS15 2.5 47.1 1.0
O A:HOH389 2.9 58.2 1.0
HE1 A:HIS15 3.0 46.4 1.0
HA A:HIS15 3.1 36.1 1.0
CE1 A:HIS15 3.1 46.7 1.0
O A:HOH437 3.7 52.4 1.0
CG A:HIS15 3.7 41.9 1.0
HH21 A:ARG14 3.9 29.8 0.5
NH2 A:ARG14 3.9 28.1 0.5
HH22 A:ARG14 3.9 29.8 0.5
CA A:HIS15 4.0 36.8 1.0
HG23 A:THR89 4.0 33.0 1.0
CB A:HIS15 4.2 36.5 1.0
HB3 A:HIS15 4.2 37.7 1.0
O A:HOH394 4.3 48.2 1.0
NE2 A:HIS15 4.4 46.4 1.0
CZ A:ARG14 4.4 32.8 0.5
O A:ARG14 4.4 34.0 0.5
O A:ARG14 4.5 33.6 0.5
HH11 A:ARG14 4.6 31.5 0.5
HH12 A:ARG14 4.6 31.5 0.5
CD2 A:HIS15 4.7 43.9 1.0
HG2 A:ARG14 4.7 35.6 0.5
HG2 A:ARG14 4.7 35.6 0.5
O A:HIS15 4.8 39.2 1.0
NH1 A:ARG14 4.8 31.3 0.5
C A:HIS15 4.8 34.7 1.0
HE A:ARG14 4.9 34.0 0.5
HG22 A:THR89 4.9 33.1 1.0
N A:HIS15 4.9 35.3 1.0
CG2 A:THR89 4.9 33.5 1.0
NE A:ARG14 4.9 34.7 0.5
NH1 A:ARG14 4.9 32.1 0.5
HH12 A:ARG14 4.9 32.3 0.5
C A:ARG14 5.0 32.9 0.5
C A:ARG14 5.0 32.6 0.5

Rhodium binding site 3 out of 5 in 7z6j

Go back to Rhodium Binding Sites List in 7z6j
Rhodium binding site 3 out of 5 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


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 Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh205

b:60.2
occ:0.25
 RH1 A:RH204 2.4 62.8 0.2
O A:HOH437 3.0 52.4 1.0
O A:HOH389 3.6 58.2 1.0
HD1 A:HIS15 4.1 47.1 0.0
HH22 A:ARG14 4.5 29.8 0.5
HA A:HIS15 4.8 36.1 1.0
ND1 A:HIS15 4.9 47.1 1.0
NH2 A:ARG14 4.9 28.1 0.5
HH12 A:ARG14 5.0 32.3 0.5

Rhodium binding site 4 out of 5 in 7z6j

Go back to Rhodium Binding Sites List in 7z6j
Rhodium binding site 4 out of 5 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


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 Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh206

b:54.8
occ:0.30
 O A:HOH427 2.1 21.9 0.3
HZ2 A:LYS33 2.2 32.6 1.0
HZ3 A:LYS33 2.2 32.6 1.0
NZ A:LYS33 2.6 33.9 1.0
HZ1 A:LYS33 3.3 32.5 1.0
HE2 A:LYS33 3.5 29.9 1.0
CE A:LYS33 3.6 29.8 1.0
HE3 A:LYS33 4.0 29.9 1.0
O A:HOH428 4.2 47.3 1.0
OD1 A:ASN37 4.5 35.8 1.0
HD21 A:ASN37 4.6 36.1 1.0
CD A:LYS33 4.9 26.7 1.0
HD3 A:LYS33 4.9 26.3 1.0

Rhodium binding site 5 out of 5 in 7z6j

Go back to Rhodium Binding Sites List in 7z6j
Rhodium binding site 5 out of 5 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [RH2(OCOCH3) (OCOCF3)3] with Hewl


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 Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh207

b:47.8
occ:0.30
 O A:LEU129 2.4 47.5 1.0
OXT A:LEU129 2.4 43.5 1.0
C A:LEU129 2.8 45.5 1.0
HZ3 A:LYS13 3.4 50.6 1.0
HZ1 A:LYS13 3.8 50.6 1.0
NZ A:LYS13 3.9 51.3 1.0
HZ2 A:LYS13 4.0 50.6 1.0
CA A:LEU129 4.3 41.5 1.0
HB3 A:LEU129 4.6 43.0 1.0
HA A:LEU129 4.8 42.1 1.0
H A:LEU129 4.8 39.9 1.0
N A:LEU129 5.0 40.3 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: Thu Oct 10 12:38:23 2024

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