Chlorine in PDB 6pla: Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl

Enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl

All present enzymatic activity of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl:
3.2.1.17;

Protein crystallography data

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl, PDB code: 6pla 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) 34.21 / 1.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.448, 76.448, 37.763, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.4

Other elements in 6pla:

The structure of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl also contains other interesting chemical elements:

Osmium (Os) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl (pdb code 6pla). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl, PDB code: 6pla:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6pla

Go back to Chlorine Binding Sites List in 6pla
Chlorine binding site 1 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:33.6
occ:0.80
 CL1 A:O1N202 0.0 33.6 0.8
OS A:O1N202 2.4 16.1 0.8
ND2 A:ASN103 2.8 16.4 1.0
C1 A:O1N202 3.1 17.2 0.8
C5 A:O1N202 3.2 18.4 0.8
C14 A:O1N202 3.3 16.8 0.8
O A:HOH360 3.4 27.3 1.0
N2 A:O1N202 3.4 15.6 0.8
C15 A:O1N202 3.4 18.3 0.8
OD2 A:ASP101 3.7 17.4 1.0
CB A:ALA107 3.7 15.4 1.0
C16 A:O1N202 3.7 20.7 0.8
C13 A:O1N202 3.9 17.8 0.8
CG A:ASN103 4.0 17.7 1.0
C19 A:O1N202 4.1 17.4 0.8
CA A:ALA107 4.1 13.7 1.0
C17 A:O1N202 4.2 21.7 0.8
N1 A:O1N202 4.2 16.2 0.8
CZ3 A:TRP62 4.5 31.8 1.0
C11 A:O1N202 4.5 19.7 0.8
C10 A:O1N202 4.5 18.3 0.8
CZ2 A:TRP63 4.5 14.8 1.0
CG A:ASP101 4.6 17.3 1.0
CE3 A:TRP62 4.6 30.6 1.0
C4 A:O1N202 4.6 17.9 0.8
OD1 A:ASP101 4.6 16.8 1.0
CB A:ASN103 4.7 15.8 1.0
CH2 A:TRP62 4.8 35.4 1.0
O A:ALA107 4.9 18.4 1.0
OD1 A:ASN103 4.9 19.6 1.0
NE1 A:TRP63 4.9 16.0 1.0

Chlorine binding site 2 out of 3 in 6pla

Go back to Chlorine Binding Sites List in 6pla
Chlorine binding site 2 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:40.9
occ:0.60
 CL1 A:O1N203 0.0 40.9 0.6
OS A:O1N203 2.4 28.5 0.6
CL2 A:O1N203 3.1 39.9 0.6
C18 A:O1N203 3.2 36.5 0.6
C14 A:O1N203 3.2 29.6 0.6
C15 A:O1N203 3.3 29.6 0.6
C1 A:O1N203 3.4 24.3 0.6
C2 A:O1N203 3.4 19.7 0.6
C16 A:O1N203 3.5 35.2 0.6
N1 A:O1N203 3.7 18.6 0.6
C19 A:O1N203 3.8 30.0 0.6
C13 A:O1N203 3.9 30.2 0.6
CZ3 A:TRP123 4.2 22.7 1.0
CD A:ARG5 4.4 20.8 1.0
C10 A:O1N203 4.4 31.6 0.6
C11 A:O1N203 4.5 31.8 0.6
NE A:ARG5 4.5 21.5 1.0
N2 A:O1N203 4.6 23.6 0.6
CH2 A:TRP123 4.8 25.1 1.0
CE2 A:PHE38 5.0 16.3 1.0
NZ A:LYS33 5.0 24.2 1.0
C3 A:O1N203 5.0 20.2 0.6

Chlorine binding site 3 out of 3 in 6pla

Go back to Chlorine Binding Sites List in 6pla
Chlorine binding site 3 out of 3 in the Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Adducts Formed After 1 Month in the Reaction of Dichlorido(1,3- Dimethylbenzimidazol-2-Ylidene)(ETA6-P-Cymene)Osmium(II) with Hewl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:39.9
occ:0.60
 CL2 A:O1N203 0.0 39.9 0.6
OS A:O1N203 2.4 28.5 0.6
C1 A:O1N203 2.9 24.3 0.6
CL1 A:O1N203 3.1 40.9 0.6
C5 A:O1N203 3.2 25.8 0.6
N2 A:O1N203 3.2 23.6 0.6
C10 A:O1N203 3.3 31.6 0.6
C19 A:O1N203 3.4 30.0 0.6
NZ A:LYS33 3.6 24.2 1.0
CE A:LYS33 3.7 21.8 1.0
O A:HOH380 3.9 31.6 1.0
C15 A:O1N203 4.0 29.6 0.6
N1 A:O1N203 4.0 18.6 0.6
C11 A:O1N203 4.0 31.8 0.6
CH2 A:TRP123 4.2 25.1 1.0
C18 A:O1N203 4.2 36.5 0.6
C4 A:O1N203 4.4 21.0 0.6
C14 A:O1N203 4.5 29.6 0.6
CZ3 A:TRP123 4.5 22.7 1.0
C13 A:O1N203 4.5 30.2 0.6
CD A:LYS33 4.6 19.3 1.0
C16 A:O1N203 4.7 35.2 0.6
C3 A:O1N203 4.8 20.2 0.6
C2 A:O1N203 4.8 19.7 0.6
C12 A:O1N203 4.9 36.4 0.6

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: Sat Dec 12 13:30:46 2020

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