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Sodium in PDB 6plb: Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl

Enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl

All present enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl:
3.2.1.17;

Protein crystallography data

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl, PDB code: 6plb 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) 39.20 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.338, 78.338, 37.833, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19

Other elements in 6plb:

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Iridium (Ir) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl (pdb code 6plb). 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 Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl, PDB code: 6plb:

Sodium binding site 1 out of 1 in 6plb

Go back to Sodium Binding Sites List in 6plb
Sodium binding site 1 out of 1 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(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 Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimida Zol-2-Ylidene)(ETA5-Pentamethylcyclopentadienyl) Iridium(III) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:21.1
occ:1.00
 O A:SER60 2.2 18.9 1.0
O A:HOH392 2.4 26.5 1.0
O A:ARG73 2.4 24.9 1.0
O A:CYS64 2.4 17.9 1.0
OG A:SER72 2.4 27.8 1.0
O A:HOH381 2.6 22.4 1.0
CB A:SER72 3.3 27.6 1.0
C A:SER60 3.4 17.7 1.0
C A:CYS64 3.5 17.0 1.0
C A:ARG73 3.5 23.6 1.0
CA A:ASN65 4.0 18.0 1.0
N A:ARG73 4.1 26.3 1.0
C A:SER72 4.1 29.0 1.0
N A:ASN65 4.1 17.0 1.0
CA A:SER60 4.1 15.9 1.0
CA A:SER72 4.3 30.0 1.0
CB A:SER60 4.3 15.8 1.0
C A:ARG61 4.4 20.6 1.0
CA A:ARG73 4.4 26.3 0.5
N A:ARG61 4.4 17.8 1.0
N A:CYS64 4.4 17.0 1.0
CA A:ARG73 4.4 26.3 0.5
N A:ASN74 4.4 23.6 1.0
O A:ARG61 4.4 23.7 1.0
O A:HOH384 4.6 31.7 1.0
CA A:CYS64 4.6 17.3 1.0
CA A:ASN74 4.6 20.9 1.0
O A:SER72 4.6 32.4 1.0
CA A:ARG61 4.6 21.1 1.0
CB A:THR69 4.7 19.6 1.0
N A:TRP62 4.7 19.5 1.0
CB A:ASN74 4.8 20.4 1.0
O A:THR69 4.8 24.8 1.0
N A:ASP66 4.8 16.8 1.0
CB A:ASN65 4.9 19.7 1.0
C A:ASN65 4.9 16.8 1.0
N A:TRP63 5.0 16.8 1.0
OD1 A:ASN65 5.0 27.1 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 12:45:53 2020

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