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Sodium in PDB 5e9r: X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole

Enzymatic activity of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole

All present enzymatic activity of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole, PDB code: 5e9r was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.50 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.500, 78.500, 36.309, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 23.7

Other elements in 5e9r:

The structure of X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole (pdb code 5e9r). 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 Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole, PDB code: 5e9r:

Sodium binding site 1 out of 1 in 5e9r

Go back to Sodium Binding Sites List in 5e9r
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole


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 Complex Between Lysozyme and the Compound Fac, Cis-[Ruii(Co)3CL2(N3-Mbi), Mbi=N-Methyl-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:31.2
occ:1.00
O A:CYS64 2.3 29.4 1.0
O A:SER60 2.3 28.3 1.0
OG A:SER72 2.5 30.0 1.0
O A:HOH367 2.5 24.6 1.0
O A:HOH319 2.5 30.4 1.0
O A:ARG73 2.6 39.8 1.0
CB A:SER72 3.4 33.4 1.0
C A:SER60 3.4 27.3 1.0
C A:CYS64 3.4 27.1 1.0
C A:ARG73 3.5 36.4 1.0
N A:ARG73 3.9 37.6 1.0
CA A:ASN65 4.0 27.3 1.0
C A:SER72 4.0 36.4 1.0
CA A:SER60 4.0 26.5 1.0
N A:ASN65 4.1 27.9 1.0
CB A:SER60 4.2 27.2 1.0
CA A:ARG73 4.2 40.9 1.0
N A:ASN74 4.3 33.0 1.0
CA A:SER72 4.3 35.1 1.0
O A:ARG61 4.4 31.7 1.0
N A:CYS64 4.4 25.9 1.0
O A:SER72 4.4 37.6 1.0
CA A:ASN74 4.4 32.3 1.0
OD1 A:ASN65 4.5 28.0 1.0
C A:ARG61 4.5 34.4 1.0
CA A:CYS64 4.5 26.9 1.0
N A:ARG61 4.6 30.9 1.0
CB A:ASN74 4.7 31.1 1.0
O A:HOH421 4.7 44.7 1.0
CB A:THR69 4.8 28.1 1.0
CB A:ASN65 4.8 28.3 1.0
N A:ASP66 4.8 25.6 1.0
CL A:CL204 4.8 36.2 1.0
N A:TRP62 4.8 33.5 1.0
CA A:ARG61 4.9 34.7 1.0
C A:TRP62 4.9 30.6 1.0
N A:TRP63 4.9 28.4 1.0
C A:ASN65 5.0 25.9 1.0

Reference:

A.Merlino, A.Merlino. N/A N/A.
Page generated: Tue Dec 15 10:55:58 2020

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