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Chlorine in PDB 4ii8: Lysozyme with Benzyl Alcohol

Enzymatic activity of Lysozyme with Benzyl Alcohol

All present enzymatic activity of Lysozyme with Benzyl Alcohol:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme with Benzyl Alcohol, PDB code: 4ii8 was solved by P.Sharma, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.97 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.198, 78.198, 37.174, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.5

Other elements in 4ii8:

The structure of Lysozyme with Benzyl Alcohol also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme with Benzyl Alcohol (pdb code 4ii8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Lysozyme with Benzyl Alcohol, PDB code: 4ii8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 1 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:28.2
occ:1.00
 OH A:TYR23 3.0 20.5 1.0
O A:HOH322 3.5 26.1 1.0
CZ A:TYR23 3.7 20.7 1.0
CE2 A:TYR23 3.7 22.4 1.0
CA A:GLY104 4.1 21.4 1.0
O A:ARG21 4.6 25.4 1.0
N A:GLY104 4.7 21.2 1.0
CE1 A:TYR23 4.9 18.6 1.0
O A:HOH310 4.9 27.5 1.0
CD2 A:TYR23 5.0 21.4 1.0

Chlorine binding site 2 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 2 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:31.4
occ:1.00
 OG A:SER24 3.1 24.6 1.0
N A:GLY26 3.1 22.4 1.0
CB A:SER24 3.5 25.2 1.0
CA A:GLY26 3.5 21.7 1.0
CA A:GLN121 3.6 26.8 1.0
CD1 A:ILE124 3.9 28.5 1.0
N A:GLN121 4.0 27.5 1.0
CB A:GLN121 4.0 31.0 1.0
N A:LEU25 4.1 22.9 1.0
CG A:GLN121 4.2 35.5 1.0
CG1 A:ILE124 4.2 27.2 1.0
C A:SER24 4.3 25.7 1.0
CG2 A:VAL120 4.3 23.7 1.0
C A:LEU25 4.3 20.5 1.0
C A:VAL120 4.4 25.4 1.0
O A:VAL120 4.4 25.2 1.0
CA A:SER24 4.5 24.0 1.0
C A:GLY26 4.6 23.4 1.0
CA A:LEU25 4.7 22.9 1.0
N A:ASN27 4.7 21.9 1.0
O A:SER24 4.8 23.4 1.0
C A:GLN121 4.8 27.2 1.0
CB A:LEU25 4.9 26.0 1.0

Chlorine binding site 3 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 3 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:42.9
occ:1.00
 CE2 A:PHE38 3.6 27.2 1.0
NZ A:LYS33 3.7 25.6 1.0
CZ3 A:TRP123 3.9 25.2 1.0
CE A:LYS33 4.1 28.9 1.0
CB A:ARG5 4.2 27.0 1.0
CD A:ARG5 4.2 27.3 1.0
CZ A:PHE38 4.4 20.9 1.0
CD A:LYS33 4.4 22.7 1.0
CD2 A:PHE38 4.6 24.3 1.0
CG A:ARG5 4.6 27.9 1.0
CE3 A:TRP123 4.7 26.4 1.0
CH2 A:TRP123 4.7 27.8 1.0
NE A:ARG5 4.8 34.0 1.0

Chlorine binding site 4 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 4 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:40.6
occ:1.00
 ND2 A:ASN65 3.1 32.0 1.0
O A:HOH355 3.1 28.7 1.0
CB A:PRO79 3.7 18.0 1.0
CA A:PRO79 3.8 21.4 1.0
CB A:ASN65 4.0 24.7 1.0
CG A:ASN65 4.0 22.7 1.0
N A:PRO79 4.1 23.4 1.0
CD A:PRO79 4.4 25.8 1.0
O A:ASN65 4.4 20.7 1.0
CG A:PRO79 4.5 26.4 1.0
C A:ILE78 4.7 23.9 1.0
O A:ILE78 4.9 22.9 1.0
O A:HOH307 5.0 22.6 1.0
ND2 A:ASN74 5.0 27.1 1.0

Chlorine binding site 5 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 5 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:41.1
occ:1.00
 N A:ILE88 3.3 23.4 1.0
O A:HOH365 3.3 41.5 1.0
O A:HOH334 3.6 33.1 1.0
CG1 A:ILE88 3.7 22.1 1.0
CA A:ASP87 3.7 26.8 1.0
CE1 A:HIS15 3.9 29.0 1.0
C A:ASP87 4.0 22.2 1.0
CG A:ASP87 4.0 37.7 1.0
OD2 A:ASP87 4.0 31.7 1.0
O A:SER86 4.1 30.3 1.0
OD1 A:ASP87 4.2 44.8 1.0
CA A:ILE88 4.3 23.6 1.0
CB A:ILE88 4.3 20.3 1.0
CG2 A:ILE88 4.4 23.1 1.0
CB A:ALA11 4.4 25.3 1.0
CB A:ASP87 4.4 29.9 1.0
CZ A:PHE3 4.5 28.4 1.0
CD1 A:ILE88 4.6 23.1 1.0
NH1 A:ARG14 4.6 41.7 1.0
ND1 A:HIS15 4.7 31.8 1.0
NE2 A:HIS15 4.8 32.8 1.0
N A:ASP87 4.8 25.4 1.0
C A:SER86 4.9 26.1 1.0
N A:THR89 4.9 25.5 1.0
CE2 A:PHE3 5.0 29.8 1.0
C A:ILE88 5.0 25.3 1.0

Chlorine binding site 6 out of 6 in 4ii8

Go back to Chlorine Binding Sites List in 4ii8
Chlorine binding site 6 out of 6 in the Lysozyme with Benzyl Alcohol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lysozyme with Benzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:44.7
occ:0.50
 N A:GLY71 2.9 30.3 1.0
CA A:GLY71 3.7 37.5 1.0
CA A:PRO70 3.8 29.9 1.0
C A:PRO70 3.8 32.8 1.0
N A:SER72 4.3 37.6 1.0
O A:THR69 4.4 26.5 1.0
C A:GLY71 4.5 36.5 1.0
CB A:PRO70 4.8 34.9 1.0
N A:PRO70 4.8 29.0 1.0
NA A:NA207 4.9 24.0 1.0
C A:THR69 5.0 26.6 1.0
O A:PRO70 5.0 35.2 1.0

Reference:

P.Sharma, Ashish. Crystal Structure of Lysozyme with Benzyl Alcohol To Be Published.
Page generated: Sun Jul 21 16:41:47 2024

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