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

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

All present enzymatic activity of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glycerol 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-Glycerol 1:2, PDB code: 7baz 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) 55.79 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.901, 78.901, 37.124, 90, 90, 90
R / Rfree (%) 12.7 / 16.4

Other elements in 7baz:

The structure of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glycerol 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-Glycerol 1:2 (pdb code 7baz). 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-Glycerol 1:2, PDB code: 7baz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7baz

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Sodium binding site 1 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glycerol 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-Glycerol 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na217

b:10.0
occ:0.64
 O A:SER60 2.1 12.8 1.0
CB A:SER72 2.2 14.8 0.4
O A:HOH301 2.3 12.6 0.8
O A:HOH411 2.3 11.5 1.0
O A:ARG73 2.4 14.2 0.6
OG A:SER72 2.6 10.8 0.6
O A:CYS64 2.6 8.4 1.0
OG A:SER72 3.0 15.7 0.4
HA A:ASN65 3.1 9.9 1.0
CB A:SER72 3.3 11.8 0.6
C A:SER60 3.3 11.9 1.0
CA A:SER72 3.3 12.9 0.4
C A:ARG73 3.5 12.6 0.6
HB2 A:SER60 3.5 9.1 1.0
C A:CYS64 3.7 7.9 1.0
HA A:SER60 3.7 9.9 1.0
C A:SER72 3.9 10.6 0.4
CA A:SER60 3.9 8.2 1.0
N A:ARG73 3.9 12.4 0.6
H A:ASP66 4.0 8.5 1.0
CA A:ASN65 4.1 8.3 1.0
N A:ARG73 4.1 10.1 0.4
H A:CYS64 4.1 11.4 1.0
CB A:SER60 4.2 7.6 1.0
C A:SER72 4.2 12.8 0.6
O A:HOH418 4.2 30.8 0.7
CA A:ARG73 4.3 13.6 0.6
N A:ASN65 4.3 7.8 1.0
HA A:ARG61 4.3 20.6 1.0
CB A:THR69 4.4 8.7 0.4
CA A:SER72 4.4 12.2 0.6
N A:ARG61 4.4 13.6 1.0
C A:ARG61 4.4 15.4 1.0
N A:ASN74 4.4 11.7 0.6
N A:ASN74 4.5 10.0 0.4
N A:SER72 4.5 12.0 0.4
O A:ARG61 4.5 16.6 1.0
CB A:THR69 4.6 9.6 0.6
N A:CYS64 4.6 9.5 1.0
CA A:ARG61 4.6 17.2 1.0
CG2 A:THR69 4.6 8.8 0.4
CA A:ASN74 4.6 10.8 0.6
O A:THR69 4.7 9.3 0.4
N A:ASP66 4.7 7.1 1.0
OD1 A:ASN65 4.7 14.2 1.0
CB A:ASN74 4.7 9.8 0.6
N A:TRP62 4.7 13.1 1.0
CL A:CL208 4.7 13.7 0.8
HB2 A:ASN65 4.7 13.6 1.0
O A:SER72 4.8 10.3 0.4
CA A:CYS64 4.8 8.4 1.0
O A:SER72 4.8 13.9 0.6
H A:TRP63 4.8 10.9 1.0
HB3 A:SER60 4.9 9.1 1.0
OG A:SER60 4.9 7.2 1.0
OG1 A:THR69 4.9 9.2 0.6
H A:TRP62 4.9 15.7 1.0
CB A:ASN65 4.9 11.3 1.0
C A:ASN65 4.9 7.5 1.0
OG1 A:THR69 4.9 8.4 0.4
O A:THR69 5.0 9.9 0.6
CA A:ASN74 5.0 10.9 0.4

Sodium binding site 2 out of 5 in 7baz

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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-Glycerol 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-Glycerol 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na218

b:29.6
occ:0.96
 O A:GLY67 2.7 13.0 1.0
O A:HOH491 2.9 29.4 1.0
O A:HOH486 3.3 35.5 1.0
C A:GLY67 3.8 10.6 1.0
HA2 A:GLY67 3.8 12.8 1.0
O A:HOH468 4.1 26.5 0.5
HA3 A:GLY67 4.1 12.8 1.0
CA A:GLY67 4.2 10.6 1.0
O A:HOH459 4.4 23.6 1.0
HA A:ARG68 4.5 13.1 1.0
O A:HOH468 4.6 26.1 0.5
O A:HOH416 4.7 35.5 1.0
N A:ARG68 4.9 9.1 1.0
O A:HOH476 4.9 32.1 1.0

Sodium binding site 3 out of 5 in 7baz

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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-Glycerol 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-Glycerol 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na219

b:66.6
occ:1.00
 HA A:ASP119 2.6 14.7 1.0
O A:HOH434 3.0 21.1 1.0
O A:HOH509 3.1 41.6 0.9
CA A:ASP119 3.5 12.2 1.0
O A:THR118 3.6 10.8 1.0
HB2 A:ASP119 3.7 17.8 1.0
N A:ASP119 4.0 10.9 1.0
C A:THR118 4.0 10.2 1.0
CB A:ASP119 4.1 14.8 1.0
OD1 A:ASP119 4.1 18.2 1.0
O A:HOH474 4.1 24.6 0.9
H A:VAL120 4.1 12.4 1.0
CG A:ASP119 4.4 17.3 1.0
C A:ASP119 4.5 10.7 1.0
N A:VAL120 4.6 10.3 1.0
H A:ASP119 4.6 13.1 1.0
O A:HOH371 4.6 13.5 1.0
O A:HOH381 4.8 17.9 0.7
H A:GLN121 5.0 13.4 1.0
HB3 A:ASP119 5.0 17.8 1.0
HG22 A:VAL120 5.0 13.8 1.0
O A:GLY117 5.0 15.1 1.0

Sodium binding site 4 out of 5 in 7baz

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Sodium binding site 4 out of 5 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glycerol 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-Glycerol 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na220

b:15.0
occ:0.67
 O A:HOH384 2.7 18.5 0.9
O A:HOH358 2.7 10.9 1.0
OE1 A:GLU35 2.8 8.7 1.0
O A:HOH318 3.1 11.2 0.8
OD2 A:ASP52 3.1 13.4 1.0
HB3 A:GLN57 3.4 7.9 1.0
O A:HOH386 3.6 11.3 0.3
CD A:GLU35 3.7 8.0 1.0
HB2 A:GLN57 3.8 7.9 1.0
OE2 A:GLU35 3.9 8.4 1.0
O A:HOH334 3.9 29.3 1.0
CB A:GLN57 4.0 6.5 1.0
HG3 A:GLN57 4.1 8.3 1.0
O A:HOH386 4.1 18.0 0.7
O A:HOH349 4.1 16.4 0.9
O A:HOH479 4.2 18.6 0.9
CG A:ASP52 4.3 10.7 1.0
HG22 A:VAL109 4.4 17.1 0.4
CG A:GLN57 4.6 6.9 1.0
HB3 A:ASP52 4.6 8.8 1.0
O A:HOH423 4.6 20.9 0.5
O A:HOH376 4.7 12.2 1.0
O A:GLN57 4.7 8.4 1.0
OE1 A:GLN57 4.8 7.7 1.0
HA A:GLU35 4.8 7.4 1.0
HB2 A:ASP52 4.8 8.8 1.0
CB A:ASP52 4.9 7.4 1.0
H A:ALA110 4.9 14.7 1.0

Sodium binding site 5 out of 5 in 7baz

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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-Glycerol 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-Glycerol 1:2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na221

b:20.2
occ:1.00
 O A:HOH314 2.4 43.6 1.0
HE2 A:PHE38 2.8 9.9 1.0
HZ3 A:TRP123 2.9 17.0 1.0
O A:HOH444 3.0 35.2 1.0
HD3 A:ARG5 3.1 11.0 0.3
HD3 A:ARG5 3.2 13.1 0.7
HB3 A:ARG5 3.2 12.3 0.3
O A:HOH378 3.3 39.1 0.9
HB2 A:ARG5 3.3 14.1 0.7
HZ3 A:LYS33 3.4 22.5 1.0
CE2 A:PHE38 3.7 8.3 1.0
HD3 A:LYS33 3.7 14.9 1.0
CZ3 A:TRP123 3.8 14.2 1.0
CB A:ARG5 4.1 10.2 0.3
CD A:ARG5 4.1 10.9 0.7
CD A:ARG5 4.1 9.2 0.3
HE2 A:LYS33 4.1 18.8 1.0
HZ A:PHE38 4.1 9.6 1.0
HE A:ARG5 4.1 13.4 0.7
NZ A:LYS33 4.2 18.8 1.0
CB A:ARG5 4.2 11.7 0.7
C7 A:CHT203 4.2 41.4 0.7
HB2 A:ARG5 4.3 12.3 0.3
CZ A:PHE38 4.3 8.0 1.0
HE3 A:TRP123 4.4 15.2 1.0
HZ1 A:LYS33 4.5 22.5 1.0
CE A:LYS33 4.5 15.6 1.0
HG3 A:ARG5 4.5 12.6 0.7
CD A:LYS33 4.5 12.4 1.0
CG A:ARG5 4.5 9.3 0.3
CG A:ARG5 4.5 10.5 0.7
HG2 A:ARG5 4.5 11.1 0.3
NE A:ARG5 4.5 11.2 0.7
CE3 A:TRP123 4.6 12.7 1.0
HD2 A:ARG5 4.6 11.0 0.3
HD2 A:PHE38 4.6 9.0 1.0
CD2 A:PHE38 4.6 7.5 1.0
HH2 A:TRP123 4.6 17.4 1.0
HB3 A:ARG5 4.6 14.1 0.7
HE A:ARG5 4.7 10.4 0.3
CH2 A:TRP123 4.7 14.5 1.0
HD2 A:ARG5 4.8 13.1 0.7
H A:ARG5 4.8 11.4 0.7
C6 A:CHT203 4.8 41.4 0.7
O A:HOH454 4.8 37.0 0.8
H A:ARG5 4.8 11.4 0.3
HZ2 A:LYS33 4.9 22.5 1.0
NE A:ARG5 4.9 8.7 0.3

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 16:08:34 2024

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