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Chlorine in PDB 5ob8: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl):
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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8 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) 55.56 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.573, 78.573, 36.664, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 23

Other elements in 5ob8:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) also contains other interesting chemical elements:

Ruthenium (Ru) 2 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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) (pdb code 5ob8). 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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl), PDB code: 5ob8:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5ob8

Go back to Chlorine Binding Sites List in 5ob8
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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)


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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:39.7
occ:1.00
 O A:HOH365 2.9 27.6 1.0
N A:THR69 3.0 28.4 1.0
O A:THR69 3.3 27.7 1.0
N A:ARG68 3.4 24.4 1.0
OD1 A:ASN65 3.5 30.3 1.0
O A:HOH413 3.5 39.1 1.0
O A:HOH357 3.5 46.6 1.0
C A:GLY67 3.5 28.6 1.0
N A:GLY67 3.5 25.9 1.0
CA A:GLY67 3.6 29.2 1.0
C A:THR69 3.7 34.0 1.0
CA A:THR69 3.7 29.9 1.0
O A:HOH392 3.8 32.4 1.0
OG A:SER72 3.9 56.4 1.0
C A:ARG68 4.0 28.2 1.0
CB A:THR69 4.0 29.6 1.0
OD1 A:ASP66 4.1 24.4 1.0
CA A:ARG68 4.1 27.3 1.0
O A:GLY67 4.2 34.1 1.0
NA A:NA203 4.6 45.9 1.0
OG1 A:THR69 4.6 23.3 1.0
C A:ASP66 4.6 30.1 1.0
N A:PRO70 4.7 35.5 1.0
CG A:ASN65 4.7 26.7 1.0
N A:ASP66 4.8 28.6 1.0
O A:HOH348 4.9 37.1 0.5

Chlorine binding site 2 out of 3 in 5ob8

Go back to Chlorine Binding Sites List in 5ob8
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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)


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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:36.4
occ:1.00
 OH A:TYR23 3.1 26.5 1.0
O A:HOH328 3.4 27.7 1.0
CE2 A:TYR23 3.7 22.9 1.0
CZ A:TYR23 3.7 26.3 1.0
CA A:GLY104 4.2 30.6 1.0
O A:ARG21 4.6 28.9 1.0
N A:GLY104 4.7 28.6 1.0
CE1 A:TYR23 4.8 24.4 1.0
CD2 A:TYR23 4.9 26.3 1.0
O A:HOH331 4.9 36.2 1.0

Chlorine binding site 3 out of 3 in 5ob8

Go back to Chlorine Binding Sites List in 5ob8
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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl)


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-Mim), Mim=Methyl-Imidazole (Crystals Grown Using Nacl) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:48.8
occ:0.80
 CL1 A:9QB206 0.0 48.8 0.8
RU1 A:9QB206 2.3 43.4 0.8
C1 A:9QB206 2.8 45.9 0.8
O5 A:9QB206 3.0 41.3 0.8
NE2 A:HIS15 3.2 37.9 1.0
O4 A:9QB206 3.3 35.5 0.8
NE A:ARG14 3.4 49.2 1.0
O1 A:9QB206 3.5 38.6 0.8
CG A:ARG14 3.6 48.1 1.0
O A:HOH303 3.7 51.7 1.0
CE1 A:HIS15 3.9 49.2 1.0
C2 A:9QB206 4.0 38.2 0.8
CD2 A:HIS15 4.0 37.0 1.0
CD A:ARG14 4.1 50.6 1.0
CZ A:ARG14 4.4 56.2 1.0
NH2 A:ARG14 4.4 55.4 1.0
O2 A:9QB206 4.8 32.5 0.8
ND1 A:HIS15 4.9 41.5 1.0
CB A:ARG14 4.9 41.3 1.0
CG A:HIS15 5.0 38.8 1.0
O A:HOH339 5.0 44.3 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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