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Sodium 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
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 5ob7

Go back to Sodium Binding Sites List in 5ob7
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na202

b:42.0
occ:1.00
 O A:HOH369 2.3 23.5 1.0
O A:SER60 2.3 34.3 1.0
O A:CYS64 2.4 26.8 1.0
O A:HOH365 2.6 28.8 1.0
OG A:SER72 2.6 39.8 1.0
O A:ARG73 2.7 44.2 1.0
C A:SER60 3.4 31.6 1.0
C A:CYS64 3.5 27.0 1.0
CB A:SER72 3.6 46.2 1.0
C A:ARG73 3.7 43.4 1.0
CA A:ASN65 3.9 29.1 1.0
CA A:SER60 3.9 30.5 1.0
CB A:SER60 4.0 29.0 1.0
N A:ASN65 4.1 28.6 1.0
N A:ARG73 4.2 42.0 1.0
C A:SER72 4.4 47.0 1.0
N A:ASN74 4.5 38.0 1.0
O A:ARG61 4.5 43.1 1.0
N A:ARG61 4.5 35.4 1.0
N A:ASP66 4.5 27.7 1.0
N A:CYS64 4.5 25.7 1.0
CA A:ARG73 4.5 45.6 1.0
CB A:THR69 4.6 28.0 1.0
CA A:ASN74 4.6 36.6 1.0
OD1 A:ASN65 4.6 37.6 1.0
C A:ARG61 4.6 37.6 1.0
CA A:SER72 4.6 47.5 1.0
CA A:CYS64 4.7 27.0 1.0
C A:ASN65 4.7 27.6 1.0
CL A:CL203 4.7 42.4 1.0
CB A:ASN65 4.8 31.1 1.0
CB A:ASN74 4.8 37.9 1.0
CA A:ARG61 4.8 38.1 1.0
O A:SER72 4.8 41.2 1.0
OG A:SER60 4.8 25.7 1.0
OG1 A:THR69 5.0 24.9 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: Mon Oct 7 23:09:52 2024

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