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Chlorine in PDB 6b7v: Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa

Enzymatic activity of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa

All present enzymatic activity of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa, PDB code: 6b7v was solved by M.A.B.Morais, A.F.Z.Nascimento, C.Y.Tominaga, M.Cristianini, A.A.L.Tribst, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.44 / 1.48
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.144, 78.144, 36.999, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.3

Other elements in 6b7v:

The structure of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa (pdb code 6b7v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa, PDB code: 6b7v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 1 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:30.4
occ:1.00
 O A:HOH393 2.9 24.4 1.0
ND2 A:ASN83 3.2 25.5 1.0
CB A:PRO97 3.7 14.1 1.0
CA A:PRO97 3.8 15.4 1.0
CB A:ASN83 3.9 15.6 1.0
N A:PRO97 4.0 17.1 1.0
CG A:ASN83 4.0 14.7 1.0
CD A:PRO97 4.3 16.6 1.0
O A:ASN83 4.4 13.7 1.0
CG A:PRO97 4.4 17.3 1.0
C A:ILE96 4.5 16.5 1.0
O A:ILE96 4.7 14.5 1.0
ND2 A:ASN92 4.9 16.8 1.0
C A:ASN83 5.0 12.1 1.0
CA A:ASN83 5.0 12.7 1.0

Chlorine binding site 2 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 2 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:18.6
occ:1.00
 OH A:TYR41 3.0 14.6 1.0
O A:HOH345 3.3 17.8 1.0
O A:HOH339 3.7 36.2 1.0
CZ A:TYR41 3.7 12.5 1.0
CE2 A:TYR41 3.7 11.9 1.0
CA A:GLY122 4.1 12.9 1.0
O A:ARG39 4.5 16.7 1.0
N A:GLY122 4.7 12.9 1.0
CE1 A:TYR41 4.9 10.6 1.0
CD2 A:TYR41 4.9 11.5 1.0

Chlorine binding site 3 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 3 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:22.1
occ:1.00
 OG A:SER42 3.0 18.2 1.0
N A:GLY44 3.1 14.0 1.0
CA A:GLY44 3.5 12.5 1.0
CB A:SER42 3.5 16.9 1.0
CA A:GLN139 3.6 18.5 1.0
N A:GLN139 4.0 18.1 1.0
CD1 A:ILE142 4.0 31.1 1.0
CB A:GLN139 4.0 22.1 1.0
N A:LEU43 4.1 14.7 1.0
C A:SER42 4.3 16.3 1.0
CG2 A:VAL138 4.3 20.8 1.0
C A:LEU43 4.3 14.7 1.0
C A:VAL138 4.3 17.9 1.0
CG A:GLN139 4.3 32.4 1.0
O A:VAL138 4.3 15.3 1.0
CG1 A:ILE142 4.4 22.1 1.0
CA A:SER42 4.5 14.7 1.0
C A:GLY44 4.5 13.9 1.0
N A:ASN45 4.6 12.5 1.0
CA A:LEU43 4.7 14.0 1.0
O A:SER42 4.7 14.9 1.0
C A:GLN139 4.8 16.1 1.0
CB A:LEU43 5.0 15.7 1.0
O A:HOH404 5.0 31.0 1.0

Chlorine binding site 4 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 4 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:33.6
occ:1.00
 N A:ILE106 3.3 14.3 1.0
CG1 A:ILE106 3.6 16.5 1.0
O A:HOH318 3.7 32.1 1.0
NH2 A:ARG32 3.7 36.4 1.0
CE1 A:HIS33 3.9 26.4 1.0
CA A:ASP105 3.9 18.6 1.0
O A:SER104 4.0 20.5 1.0
OD1 A:ASP105 4.0 22.3 1.0
C A:ASP105 4.1 17.3 1.0
CB A:ILE106 4.2 15.7 1.0
CG2 A:ILE106 4.3 17.7 1.0
CA A:ILE106 4.3 14.9 1.0
CB A:ALA29 4.3 19.3 1.0
CZ A:PHE21 4.3 18.7 1.0
CD1 A:ILE106 4.5 17.1 1.0
ND1 A:HIS33 4.7 27.4 1.0
CG A:ASP105 4.7 30.0 1.0
NE2 A:HIS33 4.8 29.9 1.0
CB A:ASP105 4.8 21.0 1.0
N A:ASP105 4.9 15.4 1.0
C A:SER104 4.9 17.9 1.0
CE2 A:PHE21 4.9 16.3 1.0
N A:THR107 5.0 16.7 1.0

Chlorine binding site 5 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 5 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:23.2
occ:1.00
 N A:THR87 3.1 14.1 1.0
O A:HOH360 3.2 14.1 1.0
O A:THR87 3.2 18.6 1.0
O A:HOH407 3.2 29.5 1.0
N A:ARG86 3.4 14.3 1.0
C A:GLY85 3.5 17.4 1.0
CA A:GLY85 3.6 15.1 1.0
C A:THR87 3.6 14.0 1.0
N A:GLY85 3.7 14.3 1.0
OD1 A:ASN83 3.7 16.8 1.0
OG A:SER90 3.7 21.4 1.0
CA A:THR87 3.8 13.2 1.0
O A:HOH302 3.9 20.7 1.0
C A:ARG86 4.1 17.7 1.0
CB A:THR87 4.1 15.5 1.0
O A:GLY85 4.1 19.8 1.0
CA A:ARG86 4.2 14.1 1.0
OD1 A:ASP84 4.2 13.1 1.0
N A:PRO88 4.6 20.5 1.0
NA A:NA207 4.6 19.7 1.0
OG1 A:THR87 4.7 14.9 1.0
C A:ASP84 4.7 14.8 1.0
N A:ASP84 4.8 11.1 1.0
OXT A:ACT211 4.8 38.6 1.0
CG A:ASN83 4.9 14.7 1.0
CH3 A:ACT211 4.9 36.9 1.0
O A:HOH348 5.0 20.7 0.5
CB A:SER90 5.0 21.0 1.0

Chlorine binding site 6 out of 6 in 6b7v

Go back to Chlorine Binding Sites List in 6b7v
Chlorine binding site 6 out of 6 in the Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Hen Egg-White Lysozyme Pre-Treated with High-Pressure Homogenization at 120 Mpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:32.4
occ:1.00
 NZ A:LYS51 3.5 20.8 1.0
CE2 A:PHE56 3.7 14.3 1.0
CE A:LYS51 4.0 22.1 1.0
CZ3 A:TRP141 4.0 17.2 1.0
O A:HOH379 4.0 33.8 1.0
CD A:LYS51 4.2 18.0 1.0
CZ A:PHE56 4.4 15.5 1.0
CB A:ARG23 4.4 18.3 1.0
CD A:ARG23 4.4 18.3 1.0
CD2 A:PHE56 4.6 15.1 1.0
O3 A:GOL209 4.6 40.5 1.0
O A:HOH362 4.8 35.1 1.0
CH2 A:TRP141 4.8 21.3 1.0
CE3 A:TRP141 4.8 17.5 1.0
CG A:ARG23 4.8 19.7 1.0

Reference:

M.A.B.Morais, A.F.Z.Nascimento, C.Y.Tominaga, M.Cristianini, A.A.L.Tribst, M.T.Murakami. How High Pressure Pre-Treatments Affect the Function and Structure of Hen Egg-White Lysozyme Innov Food Sci Emerg Technol V. 47 195 2018.
DOI: 10.1016/J.IFSET.2018.02.008
Page generated: Fri Jul 26 22:35:15 2024

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