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Chlorine in PDB 5ob6: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole

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

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:
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, PDB code: 5ob6 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) 56.41 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.776, 79.776, 36.637, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 24.2

Other elements in 5ob6:

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 also contains other interesting chemical elements:

Ruthenium (Ru) 6 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 (pdb code 5ob6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 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, PDB code: 5ob6:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5ob6

Go back to Chlorine Binding Sites List in 5ob6
Chlorine binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:32.8
occ:1.00
 OH A:TYR23 3.0 24.8 1.0
CZ A:TYR23 3.6 24.0 1.0
CE1 A:TYR23 3.6 23.3 1.0
CA A:GLY104 4.2 29.1 1.0
O A:ARG21 4.5 28.5 0.6
O A:ARG21 4.5 29.9 0.4
N A:GLY104 4.7 32.1 1.0
CE2 A:TYR23 4.8 23.2 1.0
CD1 A:TYR23 4.9 24.6 1.0
O A:HOH318 5.0 37.9 1.0

Chlorine binding site 2 out of 2 in 5ob6

Go back to Chlorine Binding Sites List in 5ob6
Chlorine binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:35.5
occ:1.00
 O A:HOH417 3.0 35.9 1.0
O A:HOH400 3.1 41.8 1.0
O A:HOH380 3.1 22.9 1.0
O A:HOH363 3.2 53.4 1.0
N A:THR69 3.2 27.6 1.0
O A:THR69 3.3 27.2 1.0
N A:ARG68 3.6 29.6 0.5
OD1 A:ASN65 3.6 25.7 1.0
N A:ARG68 3.6 29.6 0.5
C A:GLY67 3.6 32.5 1.0
CA A:GLY67 3.7 28.6 1.0
C A:THR69 3.7 28.1 1.0
N A:GLY67 3.7 26.8 1.0
OG A:SER72 3.8 35.7 1.0
CA A:THR69 3.9 29.1 1.0
O A:HOH379 4.0 30.0 1.0
CB A:THR69 4.2 28.1 1.0
C A:ARG68 4.3 30.0 0.5
C A:ARG68 4.3 30.0 0.5
O A:GLY67 4.3 30.7 1.0
OD1 A:ASP66 4.3 22.2 1.0
CA A:ARG68 4.3 29.0 0.5
CA A:ARG68 4.4 29.0 0.5
N A:PRO70 4.5 31.4 1.0
NA A:NA203 4.7 28.4 1.0
O A:HOH435 4.7 41.3 1.0
OG1 A:THR69 4.8 25.8 1.0
CG A:ASN65 4.8 27.6 1.0
C A:ASP66 4.8 25.1 1.0
O A:HOH332 4.9 27.9 0.5
N A:ASP66 4.9 24.1 1.0
CB A:SER72 5.0 34.2 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: Fri Jul 26 14:22:13 2024

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