Atomistry » Chlorine » PDB 5o5r-5oeg » 5ob7
Atomistry »
  Chlorine »
    PDB 5o5r-5oeg »
      5ob7 »

Chlorine in PDB 5ob7: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2), PDB code: 5ob7 was solved by N.Pontillo, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.84 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.968, 78.968, 36.604, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 23.4

Other elements in 5ob7:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) also contains other interesting chemical elements:

Ruthenium (Ru) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) (pdb code 5ob7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2), PDB code: 5ob7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5ob7

Go back to Chlorine Binding Sites List in 5ob7
Chlorine binding site 1 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:33.4
occ:1.00
OH A:TYR23 3.0 25.0 1.0
O A:HOH348 3.4 29.2 1.0
CE2 A:TYR23 3.6 23.6 1.0
CZ A:TYR23 3.6 23.8 1.0
CA A:GLY104 4.1 31.5 1.0
O A:ARG21 4.5 29.1 0.5
O A:ARG21 4.5 29.4 0.5
N A:GLY104 4.7 29.1 1.0
CE1 A:TYR23 4.8 23.1 1.0
CD2 A:TYR23 4.8 24.6 1.0
NH2 A:ARG21 5.0 38.2 0.5

Chlorine binding site 2 out of 3 in 5ob7

Go back to Chlorine Binding Sites List in 5ob7
Chlorine binding site 2 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:42.4
occ:1.00
N A:THR69 3.0 29.6 1.0
O A:HOH400 3.0 39.0 1.0
O A:HOH369 3.2 23.5 1.0
O A:HOH402 3.2 57.7 1.0
O A:THR69 3.2 33.7 1.0
N A:ARG68 3.4 30.7 0.5
N A:ARG68 3.4 32.4 0.5
C A:GLY67 3.5 32.2 1.0
C A:THR69 3.6 30.7 1.0
CA A:GLY67 3.6 30.2 1.0
N A:GLY67 3.7 29.2 1.0
CA A:THR69 3.7 30.0 1.0
OD1 A:ASN65 3.7 37.6 1.0
O A:HOH320 3.7 38.5 1.0
OG A:SER72 3.8 39.8 1.0
C A:ARG68 4.0 30.3 0.5
C A:ARG68 4.0 31.9 0.5
CB A:THR69 4.0 28.0 1.0
CA A:ARG68 4.1 28.7 0.5
CA A:ARG68 4.1 31.2 0.5
O A:GLY67 4.2 33.1 1.0
O A:HOH365 4.2 28.8 1.0
OD1 A:ASP66 4.3 28.5 1.0
N A:PRO70 4.5 37.0 1.0
OG1 A:THR69 4.6 24.9 1.0
NA A:NA202 4.7 42.0 1.0
C A:ASP66 4.8 30.4 1.0
CB A:SER72 4.9 46.2 1.0
CG A:ASN65 4.9 36.4 1.0
N A:ASP66 5.0 27.7 1.0

Chlorine binding site 3 out of 3 in 5ob7

Go back to Chlorine Binding Sites List in 5ob7
Chlorine binding site 3 out of 3 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (Crystal 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:41.4
occ:0.80
CL1 A:9QB204 0.0 41.4 0.8
RU1 A:9QB204 2.0 44.2 0.8
C2 A:9QB204 2.3 47.3 0.8
C1 A:9QB204 2.7 39.9 0.8
NE2 A:HIS15 3.0 44.2 1.0
O2 A:9QB204 3.1 44.8 0.8
O4 A:9QB204 3.1 40.4 0.8
OD1 A:ASP87 3.3 46.0 1.0
O1 A:9QB204 3.5 41.9 0.8
CD2 A:HIS15 3.8 45.6 1.0
CE1 A:HIS15 3.8 49.1 1.0
N A:ILE88 3.8 38.2 1.0
CG1 A:ILE88 3.9 36.4 1.0
C3 A:9QB204 3.9 45.6 0.8
O A:HOH353 3.9 51.3 1.0
CA A:ASP87 4.1 36.4 1.0
CG A:ASP87 4.3 45.5 1.0
C A:ASP87 4.5 35.7 1.0
CB A:ASP87 4.6 43.1 1.0
O A:SER86 4.7 35.5 1.0
CB A:ILE88 4.8 34.3 1.0
CA A:ILE88 4.8 35.6 1.0
ND1 A:HIS15 4.8 43.4 1.0
CG A:HIS15 4.8 43.4 1.0
CD1 A:ILE88 4.8 36.9 1.0
O3 A:9QB204 5.0 42.5 0.8
CB A:ALA11 5.0 35.6 1.0

Reference:

N.Pontillo, G.Ferraro, L.Messori, G.Tamasi, A.Merlino. Ru-Based Co Releasing Molecules with Azole Ligands: Interaction with Proteins and the Co Release Mechanism Disclosed By X-Ray Crystallography. Dalton Trans V. 46 9621 2017.
ISSN: ESSN 1477-9234
PubMed: 28702564
DOI: 10.1039/C7DT01991B
Page generated: Sat Dec 12 12:11:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy