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Sodium 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
Chlorine (Cl) 2 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 (pdb code 5ob6). 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, PDB code: 5ob6:

Sodium binding site 1 out of 1 in 5ob6

Go back to Sodium Binding Sites List in 5ob6
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:28.4
occ:1.00
 O A:HOH379 2.2 30.0 1.0
O A:CYS64 2.3 23.6 1.0
O A:SER60 2.4 24.4 1.0
O A:HOH380 2.4 22.9 1.0
OG A:SER72 2.5 35.7 1.0
O A:ARG73 2.5 38.3 1.0
CB A:SER72 3.4 34.2 1.0
C A:CYS64 3.4 23.8 1.0
C A:SER60 3.5 24.1 1.0
C A:ARG73 3.6 39.3 1.0
CA A:ASN65 3.8 25.4 1.0
N A:ASN65 4.0 25.4 1.0
N A:ARG73 4.0 35.5 1.0
CA A:SER60 4.1 22.0 1.0
C A:SER72 4.2 37.7 1.0
CB A:SER60 4.2 19.8 1.0
CA A:ARG73 4.4 33.6 1.0
CA A:SER72 4.4 36.5 1.0
N A:ASN74 4.4 31.0 1.0
N A:CYS64 4.4 22.6 1.0
CA A:ASN74 4.6 34.9 1.0
O A:HOH361 4.6 50.7 1.0
CA A:CYS64 4.6 22.4 1.0
OD1 A:ASN65 4.6 25.7 1.0
O A:SER72 4.6 33.4 1.0
N A:ARG61 4.6 27.5 1.0
N A:ASP66 4.7 24.1 1.0
CB A:ASN74 4.7 33.9 1.0
CB A:ASN65 4.7 25.7 1.0
CL A:CL204 4.7 35.5 1.0
C A:ARG61 4.7 30.6 1.0
CB A:THR69 4.7 28.1 1.0
O A:ARG61 4.8 32.5 1.0
C A:ASN65 4.8 24.5 1.0
O A:HOH400 4.8 41.8 1.0
CA A:ARG61 4.9 30.5 0.5
CA A:ARG61 5.0 31.5 0.5

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 23:09:53 2024

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