Chlorine 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:

Sodium (Na) 5 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 13 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 7b9j

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Chlorine binding site 1 out of 13 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 Chlorine with other atoms in the Cl 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:Cl204

b:11.6
occ:0.66
 OH A:TYR23 2.9 14.3 1.0
O A:HOH340 3.4 20.2 1.0
CE2 A:TYR23 3.6 14.9 1.0
CZ A:TYR23 3.6 17.9 1.0
CA A:GLY104 4.1 21.3 1.0
O A:ARG21 4.6 21.0 1.0
N A:GLY104 4.8 25.9 1.0
CE1 A:TYR23 4.8 12.7 1.0
CD2 A:TYR23 4.8 15.0 1.0
O A:HOH317 4.9 29.7 1.0

Chlorine binding site 2 out of 13 in 7b9j

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Chlorine binding site 2 out of 13 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 Chlorine with other atoms in the Cl 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:Cl205

b:17.4
occ:0.59
 OG A:SER24 3.0 18.1 1.0
N A:GLY26 3.0 12.7 1.0
CA A:GLY26 3.5 12.2 1.0
CB A:SER24 3.5 17.5 1.0
CA A:GLN121 3.8 21.7 1.0
CD1 A:ILE124 3.8 25.4 1.0
N A:LEU25 4.1 15.6 1.0
N A:GLN121 4.1 20.4 1.0
CB A:GLN121 4.2 25.8 1.0
C A:LEU25 4.2 18.9 1.0
C A:SER24 4.3 14.6 1.0
O A:VAL120 4.3 18.1 1.0
CG2 A:VAL120 4.3 16.9 1.0
C A:VAL120 4.4 20.9 1.0
CG1 A:ILE124 4.4 23.0 1.0
CG A:GLN121 4.4 31.7 1.0
CA A:SER24 4.5 19.4 1.0
CA A:LEU25 4.6 18.3 1.0
C A:GLY26 4.6 17.2 1.0
O A:SER24 4.8 17.7 1.0
N A:ASN27 4.8 16.3 1.0
CB A:LEU25 4.9 19.0 1.0
C A:GLN121 4.9 22.4 1.0

Chlorine binding site 3 out of 13 in 7b9j

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Chlorine binding site 3 out of 13 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 Chlorine with other atoms in the Cl 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:Cl206

b:21.5
occ:0.67
 O A:HOH333 3.4 25.1 1.0
O A:HOH304 3.5 18.0 0.6
N A:ILE88 3.5 21.9 1.0
NH2 A:ARG14 3.7 36.1 1.0
CG1 A:ILE88 3.7 24.6 1.0
CA A:ASP87 4.0 24.3 1.0
CE1 A:HIS15 4.0 24.8 1.0
CB A:ALA11 4.1 19.1 1.0
CG2 A:ILE88 4.1 18.6 1.0
OD1 A:ASP87 4.1 27.9 1.0
O A:SER86 4.2 24.7 1.0
CZ A:PHE3 4.2 22.7 1.0
C A:ASP87 4.2 23.0 1.0
CB A:ILE88 4.3 18.3 1.0
CG A:ASP87 4.4 28.5 1.0
CA A:ILE88 4.5 20.8 1.0
CD1 A:ILE88 4.5 22.8 1.0
CE2 A:PHE3 4.7 24.4 1.0
CZ A:ARG14 4.7 29.3 1.0
CB A:ASP87 4.7 24.7 1.0
ND1 A:HIS15 4.8 26.8 1.0
OD2 A:ASP87 4.9 39.0 1.0
N A:ASP87 5.0 22.3 1.0
C A:SER86 5.0 25.2 1.0

Chlorine binding site 4 out of 13 in 7b9j

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Chlorine binding site 4 out of 13 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 Chlorine with other atoms in the Cl 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:Cl207

b:15.0
occ:0.40
 N A:LYS1 2.5 18.1 1.0
OD1 A:ASN39 2.9 16.3 1.0
NE2 A:GLN41 3.0 15.5 1.0
CA A:LYS1 3.3 24.7 1.0
C A:LYS1 3.6 27.1 1.0
CG A:GLN41 3.8 16.6 1.0
CG A:ASN39 3.8 19.1 1.0
CD A:GLN41 3.8 15.0 1.0
O A:LYS1 4.0 17.3 1.0
N A:VAL2 4.0 21.5 1.0
CB A:GLN41 4.0 13.0 1.0
ND2 A:ASN39 4.2 17.3 1.0
CG2 A:VAL2 4.3 20.2 1.0
O A:HOH377 4.4 34.2 1.0
N A:GLN41 4.5 14.6 1.0
OG1 A:THR40 4.5 23.3 1.0
CB A:LYS1 4.7 22.7 1.0
N A:THR40 4.9 14.2 1.0
CA A:GLN41 4.9 18.0 1.0

Chlorine binding site 5 out of 13 in 7b9j

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Chlorine binding site 5 out of 13 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 Chlorine with other atoms in the Cl 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:Cl208

b:26.3
occ:0.64
 O A:GLY22 3.0 17.1 1.0
N A:SER24 3.0 14.5 1.0
O A:HOH338 3.4 16.8 0.9
CB A:SER24 3.4 17.5 1.0
OG A:SER24 3.7 18.1 1.0
ND2 A:ASN27 3.7 16.8 1.0
CA A:SER24 3.8 19.4 1.0
CA A:TYR23 3.9 16.0 1.0
C A:TYR23 3.9 17.6 1.0
C A:GLY22 4.1 20.0 1.0
N A:TYR23 4.5 17.9 1.0
OD1 A:ASN19 5.0 23.4 0.6
CG A:ASN27 5.0 19.4 1.0

Chlorine binding site 6 out of 13 in 7b9j

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Chlorine binding site 6 out of 13 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl209

b:32.6
occ:0.53
 N A:ASN74 3.1 16.6 1.0
NE A:ARG73 3.3 38.2 1.0
C A:ASN74 3.7 20.6 1.0
CA A:ASN74 3.8 22.8 1.0
O A:ASN74 3.9 23.3 1.0
NH2 A:ARG73 4.0 36.7 1.0
CB A:ARG73 4.0 25.0 1.0
CA A:ARG73 4.0 26.2 1.0
C A:ARG73 4.0 19.8 1.0
N A:LEU75 4.0 20.9 1.0
CZ A:ARG73 4.1 42.2 1.0
CB A:ASN74 4.1 16.2 1.0
CD A:ARG73 4.1 29.3 1.0
CD2 A:LEU75 4.2 20.8 1.0
O A:HOH380 4.6 26.9 1.0
CA A:LEU75 4.6 20.8 1.0
CG A:ARG73 4.7 26.0 1.0
CG A:LEU75 4.8 24.6 1.0

Chlorine binding site 7 out of 13 in 7b9j

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Chlorine binding site 7 out of 13 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl210

b:14.6
occ:0.44
 N A:LEU56 2.8 15.2 1.0
O A:TYR53 2.8 13.2 1.0
N A:ILE55 3.0 17.4 1.0
OG A:SER91 3.2 20.4 1.0
C A:GLY54 3.3 15.9 1.0
N A:GLN57 3.4 14.6 1.0
CA A:GLY54 3.5 12.5 1.0
CA A:LEU56 3.5 15.6 1.0
C A:LEU56 3.6 18.8 1.0
CB A:SER91 3.7 18.6 1.0
C A:ILE55 3.7 17.6 1.0
C A:TYR53 3.8 16.1 1.0
CG1 A:ILE58 3.8 12.6 1.0
CD1 A:ILE58 3.8 16.1 1.0
CB A:LEU56 3.9 15.9 1.0
CA A:ILE55 3.9 18.1 1.0
O A:GLY54 3.9 13.0 1.0
N A:ILE58 4.0 14.9 1.0
CG2 A:ILE55 4.0 18.7 1.0
N A:GLY54 4.1 14.6 1.0
O A:HOH301 4.2 18.2 0.9
O A:LEU83 4.3 20.7 1.0
CB A:ILE58 4.3 15.8 1.0
CA A:GLN57 4.4 15.3 1.0
O A:LEU56 4.5 15.8 1.0
CB A:ILE55 4.5 25.6 1.0
CB A:LEU83 4.5 16.0 1.0
C A:GLN57 4.7 17.0 1.0
CA A:SER91 4.8 19.8 1.0
CG A:LEU56 4.8 17.2 1.0
CA A:ILE58 4.8 16.9 1.0
O A:ILE55 4.9 16.4 1.0

Chlorine binding site 8 out of 13 in 7b9j

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Chlorine binding site 8 out of 13 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl211

b:25.8
occ:0.50
 O A:HOH329 2.6 25.6 0.8
N A:GLU7 2.9 23.0 1.0
N A:CYS6 3.4 16.5 1.0
CB A:GLU7 3.5 22.2 1.0
CA A:GLY4 3.6 20.8 1.0
C A:GLY4 3.6 19.6 1.0
CB A:CYS6 3.7 21.0 1.0
C A:CYS6 3.7 20.7 1.0
CA A:GLU7 3.7 20.6 1.0
N A:ARG5 3.8 21.2 1.0
CA A:CYS6 3.8 17.0 1.0
O A:GLY4 4.1 21.9 1.0
C A:ARG5 4.2 20.1 1.0
N A:GLY4 4.5 21.0 1.0
CA A:ARG5 4.6 18.9 1.0
O A:HOH363 4.7 28.3 0.9
O A:CYS6 4.9 21.2 1.0
OE1 A:GLU7 4.9 21.7 1.0
CG A:GLU7 4.9 23.8 1.0

Chlorine binding site 9 out of 13 in 7b9j

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Chlorine binding site 9 out of 13 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl212

b:22.7
occ:0.63
 ND2 A:ASN65 3.1 18.0 1.0
O A:HOH341 3.2 31.0 1.0
CG A:PRO79 3.4 22.7 0.6
CB A:PRO79 3.6 20.9 0.6
CB A:PRO79 3.6 21.3 0.4
O A:HOH392 3.7 26.7 1.0
CA A:PRO79 3.8 21.6 0.6
CA A:PRO79 3.8 21.3 0.4
CB A:ASN65 3.9 20.8 1.0
CG A:ASN65 4.0 21.1 1.0
N A:PRO79 4.1 22.0 0.6
N A:PRO79 4.1 22.0 0.4
CD A:PRO79 4.2 20.8 0.6
O A:ASN65 4.3 19.7 1.0
CD A:PRO79 4.3 21.2 0.4
CG A:PRO79 4.4 22.4 0.4
C A:ILE78 4.7 23.2 1.0
C A:ASN65 4.8 18.0 1.0
O A:ILE78 4.8 20.7 1.0
CA A:ASN65 4.9 18.1 1.0

Chlorine binding site 10 out of 13 in 7b9j

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Chlorine binding site 10 out of 13 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl213

b:32.9
occ:0.64
 N A:GLY126 3.6 27.2 1.0
NE2 A:GLN121 3.9 36.3 1.0
CA A:ARG125 4.0 23.5 0.6
CA A:ARG125 4.0 23.4 0.4
O A:HOH371 4.0 34.5 1.0
CG A:ARG125 4.3 27.6 0.6
C A:ARG125 4.3 26.0 1.0
O A:ILE124 4.5 24.3 1.0
CA A:GLY126 4.5 25.2 1.0
CB A:ARG125 4.7 25.6 0.4
CB A:ARG125 4.7 25.5 0.6
CG A:ARG125 4.9 27.4 0.4
N A:ARG125 4.9 24.6 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: Fri Nov 5 12:20:23 2021

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