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Sodium in PDB 6pl9: Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl

Enzymatic activity of Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl

All present enzymatic activity of Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl:
3.2.1.17;

Protein crystallography data

The structure of Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl, PDB code: 6pl9 was solved by M.P.Sullivan, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.99 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.425, 80.425, 37.794, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.3

Other elements in 6pl9:

The structure of Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl also contains other interesting chemical elements:

Rhodium (Rh) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl (pdb code 6pl9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl, PDB code: 6pl9:

Sodium binding site 1 out of 1 in 6pl9

Go back to Sodium Binding Sites List in 6pl9
Sodium binding site 1 out of 1 in the Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Adduct Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidaz Ol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Rhodium(III) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:15.2
occ:1.00
 O A:SER60 2.3 15.9 1.0
O A:CYS64 2.4 13.8 1.0
OG A:SER72 2.4 18.6 1.0
O A:ARG73 2.4 17.2 1.0
O A:HOH416 2.4 19.3 1.0
O A:HOH407 2.7 16.7 1.0
CB A:SER72 3.3 18.5 1.0
C A:CYS64 3.5 13.3 1.0
C A:SER60 3.5 14.4 1.0
C A:ARG73 3.5 17.6 1.0
O A:HOH402 3.7 29.8 1.0
N A:ARG73 3.8 19.1 1.0
CA A:ASN65 4.0 13.6 1.0
N A:ASN65 4.1 13.6 1.0
CA A:SER60 4.1 12.9 1.0
C A:SER72 4.1 20.2 1.0
CA A:ARG73 4.3 19.8 1.0
CA A:SER72 4.3 19.8 1.0
CB A:SER60 4.3 12.4 1.0
N A:ASN74 4.4 17.0 1.0
N A:CYS64 4.4 13.0 1.0
C A:ARG61 4.4 15.7 1.0
O A:ARG61 4.5 18.8 1.0
N A:ARG61 4.5 14.9 1.0
CA A:CYS64 4.6 12.9 1.0
CA A:ASN74 4.6 16.4 1.0
O A:HOH399 4.6 33.2 1.0
O A:HOH387 4.7 25.3 1.0
CA A:ARG61 4.7 17.1 1.0
O A:SER72 4.7 22.0 1.0
CB A:ASN74 4.7 16.2 1.0
CB A:THR69 4.7 14.8 1.0
N A:TRP62 4.8 15.3 1.0
CB A:ASN65 4.8 15.6 1.0
N A:ASP66 4.8 13.1 1.0
O A:THR69 4.8 17.8 1.0
C A:ASN65 4.9 13.2 1.0
OD1 A:ASN65 4.9 20.2 1.0

Reference:

M.P.Sullivan, D.C.Goldstone, C.G.Hartinger. Linking Biological Activity to Chemical Properties: Structure-(Re)Activity Relationships of Anticancer N-Heterocyclic Carbene Organometallics To Be Published.
Page generated: Tue Dec 15 12:45:43 2020

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