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Sodium in PDB 7b9j: Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2

Enzymatic activity of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2

All present enzymatic activity of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2, PDB code: 7b9j was solved by B.D.Belviso, R.Caliandro, B.Carrozzini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.60 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.05, 80.05, 36.769, 90, 90, 90
R / Rfree (%) 17.8 / 22.5

Other elements in 7b9j:

The structure of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 (pdb code 7b9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2, PDB code: 7b9j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7b9j

Go back to Sodium Binding Sites List in 7b9j
Sodium binding site 1 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na217

b:17.2
occ:0.77
 O A:HOH328 2.3 17.1 0.9
OG A:SER72 2.3 15.1 1.0
O A:CYS64 2.4 16.4 1.0
O A:SER60 2.5 19.6 1.0
O A:HOH319 2.5 18.0 0.9
O A:ARG73 2.7 21.7 1.0
CB A:SER72 3.1 18.7 1.0
C A:CYS64 3.6 14.4 1.0
C A:SER60 3.6 27.4 1.0
C A:ARG73 3.7 19.8 1.0
N A:ARG73 3.9 23.7 1.0
CA A:ASN65 3.9 18.1 1.0
C A:SER72 4.1 24.9 1.0
N A:ASN65 4.2 16.6 1.0
CA A:SER60 4.2 16.6 1.0
CB A:SER60 4.2 11.8 1.0
CA A:SER72 4.2 25.4 1.0
CA A:ARG73 4.4 26.2 1.0
N1 A:URE224 4.5 16.6 1.0
N A:ASN74 4.6 16.6 1.0
OD1 A:ASN65 4.6 19.3 1.0
CB A:THR69 4.6 21.8 1.0
N A:CYS64 4.6 19.0 1.0
N A:ASP66 4.7 16.7 1.0
CB A:ASN65 4.7 20.8 1.0
N A:ARG61 4.7 19.3 1.0
O A:URE224 4.7 18.1 1.0
CA A:CYS64 4.7 15.4 1.0
C A:ARG61 4.8 24.4 1.0
O A:SER72 4.8 25.4 1.0
C A:ASN65 4.8 18.0 1.0
CA A:ASN74 4.9 22.8 1.0
O A:ARG61 4.9 20.6 1.0
O A:HOH380 4.9 26.9 1.0
OG1 A:THR69 4.9 17.4 1.0
OG A:SER60 4.9 16.5 1.0
O A:THR69 4.9 20.0 1.0
CA A:ARG61 5.0 23.6 1.0
OD1 A:ASP66 5.0 20.1 1.0

Sodium binding site 2 out of 5 in 7b9j

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Sodium binding site 2 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na218

b:31.0
occ:0.74
 O A:GLY67 2.7 23.5 1.0
O A:HOH324 3.6 22.9 1.0
C A:GLY67 3.6 24.4 1.0
CA A:GLY67 3.8 17.2 1.0
N2 A:URE224 4.2 21.2 1.0
O A:HOH346 4.2 22.4 0.9
N A:ARG68 4.8 16.5 1.0
O A:HOH373 4.8 26.9 1.0
C A:URE224 4.9 21.5 1.0
O A:URE224 4.9 18.1 1.0
O A:HOH378 5.0 13.5 1.0

Sodium binding site 3 out of 5 in 7b9j

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Sodium binding site 3 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na219

b:36.2
occ:1.00
 O A:GLY117 3.4 22.5 1.0
C A:THR118 3.5 19.1 1.0
O A:THR118 3.6 16.0 1.0
N A:ASP119 3.6 21.4 1.0
O A:HOH391 3.7 17.9 1.0
CA A:ASP119 3.9 22.8 1.0
CA A:THR118 4.1 14.9 1.0
CB A:ASP119 4.3 21.0 1.0
C A:GLY117 4.3 21.6 1.0
N A:THR118 4.6 15.2 1.0
O A:HOH315 4.9 19.5 1.0
O A:HOH362 4.9 25.7 1.0

Sodium binding site 4 out of 5 in 7b9j

Go back to Sodium Binding Sites List in 7b9j
Sodium binding site 4 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na220

b:23.0
occ:0.74
 OE1 A:GLU35 2.6 13.6 1.0
O A:HOH312 2.9 18.4 1.0
OD2 A:ASP52 3.4 18.0 1.0
CD A:GLU35 3.6 12.0 1.0
OE2 A:GLU35 3.7 12.8 1.0
O A:HOH359 4.0 20.9 1.0
CG2 A:VAL109 4.1 17.7 0.5
O A:HOH306 4.2 25.5 1.0
CB A:GLN57 4.3 14.2 1.0
O A:HOH308 4.3 25.8 1.0
O A:HOH379 4.5 30.2 1.0
CG A:ASP52 4.6 19.7 1.0
CG A:GLN57 4.7 16.0 1.0
OE1 A:GLN57 4.9 16.8 1.0
CG A:GLU35 5.0 17.4 1.0
O A:GLN57 5.0 11.9 1.0

Sodium binding site 5 out of 5 in 7b9j

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Sodium binding site 5 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Urea 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na221

b:33.9
occ:0.81
 CE2 A:PHE38 3.6 17.7 1.0
NZ A:LYS33 3.8 29.9 1.0
CZ3 A:TRP123 3.9 24.6 1.0
CD A:ARG5 4.2 24.2 1.0
CE A:LYS33 4.2 25.7 1.0
CD A:LYS33 4.3 19.8 1.0
CZ A:PHE38 4.3 19.0 1.0
CB A:ARG5 4.3 21.0 1.0
C5 A:CHT202 4.5 28.8 0.7
CD2 A:PHE38 4.6 20.3 1.0
CE3 A:TRP123 4.7 18.4 1.0
CG A:ARG5 4.7 20.5 1.0
NE A:ARG5 4.7 24.1 1.0
CH2 A:TRP123 4.8 21.1 1.0

Reference:

B.D.Belviso, F.M.Perna, B.Carrozzini, M.Trotta, V.Capriati, R.Caliandro. Introducing Protein Crystallization in Hydrated Deep Eutectic Solvents Acs Sustain Chem Eng V. 9 8435 2021.
ISSN: ESSN 2168-0485
DOI: 10.1021/ACSSUSCHEMENG.1C01230
Page generated: Tue Oct 8 16:08:33 2024

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