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Sodium in PDB 7bb1: Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1

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

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

Protein crystallography data

The structure of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1, PDB code: 7bb1 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) 27.92 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.964, 78.964, 37.093, 90, 90, 90
R / Rfree (%) 10.9 / 14.1

Other elements in 7bb1:

The structure of Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1 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-Glutamic Acid 2:1 (pdb code 7bb1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1, PDB code: 7bb1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7bb1

Go back to Sodium Binding Sites List in 7bb1
Sodium binding site 1 out of 4 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1


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-Glutamic Acid 2:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na217

b:7.0
occ:0.79
 O A:SER60 2.3 9.1 1.0
O A:HOH396 2.4 11.3 1.0
O A:CYS64 2.4 7.7 1.0
O A:ARG73 2.4 11.5 1.0
O A:HOH372 2.5 9.1 1.0
OG A:SER72 2.5 11.5 1.0
HB2 A:SER72 2.9 13.2 1.0
HA A:ASN65 3.1 9.6 1.0
CB A:SER72 3.2 11.0 1.0
C A:SER60 3.5 7.9 1.0
C A:ARG73 3.5 10.7 1.0
HB2 A:SER60 3.5 8.9 1.0
C A:CYS64 3.5 7.5 1.0
HA A:SER60 3.8 8.4 1.0
HB A:THR69 3.8 10.2 1.0
HB3 A:SER72 3.9 13.2 1.0
H A:CYS64 3.9 8.9 1.0
CA A:ASN65 4.0 8.0 1.0
N A:ARG73 4.0 11.8 1.0
HB2 A:ASN74 4.0 12.8 1.0
H A:ASP66 4.0 8.9 1.0
H A:ARG73 4.0 14.1 1.0
CA A:SER60 4.0 7.0 1.0
HA A:ASN74 4.1 12.1 1.0
C A:SER72 4.2 11.9 1.0
N A:ASN65 4.2 7.9 1.0
CB A:SER60 4.2 7.4 1.0
CA A:ARG73 4.3 11.9 1.0
CA A:SER72 4.3 11.6 1.0
N A:ASN74 4.4 10.0 1.0
O A:HOH328 4.4 31.0 0.8
N A:CYS64 4.5 7.4 1.0
CA A:ASN74 4.6 10.1 1.0
N A:ARG61 4.6 8.6 1.0
C A:ARG61 4.6 9.6 1.0
HA A:ARG61 4.6 11.7 1.0
HB2 A:ASN65 4.6 11.8 1.0
CA A:CYS64 4.7 7.7 1.0
OD1 A:ASN65 4.7 12.7 1.0
CB A:THR69 4.7 8.5 1.0
N A:ASP66 4.7 7.5 1.0
O A:ARG61 4.7 10.3 1.0
CL A:CL208 4.7 10.2 0.8
HA A:ARG73 4.7 14.3 1.0
O A:SER72 4.7 13.4 1.0
CB A:ASN74 4.7 10.7 1.0
HG21 A:THR69 4.8 10.9 1.0
H A:TRP63 4.8 8.6 1.0
CB A:ASN65 4.8 9.8 1.0
HG A:SER60 4.9 8.2 1.0
N A:TRP62 4.9 8.3 1.0
CA A:ARG61 4.9 9.7 1.0
C A:ASN65 4.9 7.7 1.0
HG1 A:THR69 4.9 10.2 1.0
HA A:SER72 4.9 13.9 1.0
HB3 A:SER60 4.9 8.9 1.0
O A:HOH428 5.0 16.1 0.6
H A:ASN65 5.0 9.5 1.0

Sodium binding site 2 out of 4 in 7bb1

Go back to Sodium Binding Sites List in 7bb1
Sodium binding site 2 out of 4 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1


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

b:17.8
occ:0.59
 O A:GLY67 2.7 10.9 0.9
O A:HOH484 2.9 26.5 0.9
HA2 A:GLY67 3.6 10.8 0.9
C A:GLY67 3.7 9.3 0.9
HA3 A:GLY67 3.9 10.8 0.9
CA A:GLY67 4.0 9.0 0.9
O A:HOH444 4.3 23.1 1.0
O A:HOH449 4.4 31.9 1.0
O A:HOH414 4.5 36.2 0.9
HA A:ARG68 4.7 12.0 0.6
HA A:ARG68 4.8 12.1 0.4
N A:ARG68 4.9 9.2 1.0

Sodium binding site 3 out of 4 in 7bb1

Go back to Sodium Binding Sites List in 7bb1
Sodium binding site 3 out of 4 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1


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

b:17.6
occ:0.74
 OE1 A:GLU35 2.7 8.3 1.0
O A:HOH353 2.7 24.8 0.9
O A:HOH308 2.8 16.2 0.8
O A:HOH350 2.8 12.1 1.0
O A:HOH471 2.8 28.1 1.0
OD2 A:ASP52 3.2 12.5 1.0
HB3 A:GLN57 3.5 7.6 1.0
CD A:GLU35 3.6 7.9 1.0
OE2 A:GLU35 3.8 8.6 1.0
O A:HOH406 3.9 30.5 1.0
HB2 A:GLN57 3.9 7.6 1.0
O A:HOH327 3.9 27.3 1.0
HG22 A:VAL109 4.1 15.6 0.2
CB A:GLN57 4.1 6.3 1.0
HG3 A:GLN57 4.1 7.7 1.0
O A:HOH373 4.3 19.7 0.9
CG A:ASP52 4.3 9.2 1.0
HG23 A:VAL109 4.5 15.6 0.2
O A:HOH343 4.6 11.3 0.9
CG A:GLN57 4.6 6.4 1.0
HB3 A:ASP52 4.7 8.2 1.0
H A:ALA110 4.7 12.8 1.0
CG2 A:VAL109 4.7 13.0 0.2
HA A:GLU35 4.7 7.8 1.0
O A:GLN57 4.8 7.4 1.0
HB2 A:ALA110 4.8 14.9 1.0
OE1 A:GLN57 4.9 7.3 1.0
HB A:VAL109 4.9 18.5 0.8
HG21 A:VAL109 4.9 15.6 0.2
HB2 A:ASP52 5.0 8.2 1.0
CB A:ASP52 5.0 6.8 1.0
CG A:GLU35 5.0 7.2 1.0
HB3 A:GLU35 5.0 7.8 1.0
H A:VAL109 5.0 13.2 0.2
H A:VAL109 5.0 13.2 0.8

Sodium binding site 4 out of 4 in 7bb1

Go back to Sodium Binding Sites List in 7bb1
Sodium binding site 4 out of 4 in the Lysozyme Crystallized in the Presence of the Hydrated Deep Eutectic Solvent Choline Chloride-Glutamic Acid 2:1


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-Glutamic Acid 2:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na220

b:20.7
occ:0.85
 HZ3 A:TRP123 2.7 18.2 1.0
O A:HOH377 2.8 33.2 0.9
O A:HOH389 2.9 21.8 1.0
HD3 A:ARG5 3.0 14.2 1.0
HE2 A:PHE38 3.0 9.1 1.0
O A:HOH434 3.0 33.5 0.7
HB3 A:ARG5 3.3 12.5 1.0
CZ3 A:TRP123 3.6 15.1 1.0
O A:HOH384 3.6 37.0 0.8
CE2 A:PHE38 3.9 7.5 1.0
CD A:ARG5 3.9 11.8 1.0
HZ3 A:LYS33 4.0 20.3 1.0
HG2 A:ARG5 4.1 13.6 1.0
C6 A:CHT202 4.1 35.4 1.0
HD3 A:LYS33 4.1 14.8 1.0
CB A:ARG5 4.2 10.4 1.0
HE3 A:TRP123 4.3 15.7 1.0
CG A:ARG5 4.3 11.3 1.0
HH2 A:TRP123 4.3 19.3 1.0
HZ A:PHE38 4.3 8.3 1.0
H A:ARG5 4.3 10.8 1.0
HE A:ARG5 4.4 14.7 1.0
CE3 A:TRP123 4.4 13.1 1.0
CH2 A:TRP123 4.4 16.1 1.0
HD2 A:ARG5 4.5 14.2 1.0
CZ A:PHE38 4.6 6.9 1.0
C7 A:CHT202 4.6 35.0 1.0
NE A:ARG5 4.6 12.2 1.0
HE2 A:LYS33 4.7 18.1 1.0
O A:HOH479 4.7 42.1 1.0
HB2 A:ARG5 4.7 12.5 1.0
HD2 A:PHE38 4.8 9.2 1.0
NZ A:LYS33 4.8 16.9 1.0
CD2 A:PHE38 4.8 7.7 1.0
N A:ARG5 5.0 9.0 1.0
CD A:LYS33 5.0 12.3 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 16:08:34 2024

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