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Chlorine in PDB 4d9z: Lysozyme at 318K

Enzymatic activity of Lysozyme at 318K

All present enzymatic activity of Lysozyme at 318K:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme at 318K, PDB code: 4d9z 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) 21.36 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.010, 55.954, 72.484, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.8

Other elements in 4d9z:

The structure of Lysozyme at 318K also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme at 318K (pdb code 4d9z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Lysozyme at 318K, PDB code: 4d9z:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4d9z

Go back to Chlorine Binding Sites List in 4d9z
Chlorine binding site 1 out of 4 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme at 318K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:18.4
occ:1.00
 N A:SER81 3.2 12.9 1.0
O A:ASN65 3.6 14.7 1.0
CA A:ASP66 3.7 11.7 1.0
N A:CYS80 3.7 13.9 1.0
CB A:SER81 3.7 16.7 1.0
CB A:CYS80 3.9 12.2 1.0
CB A:ASP66 3.9 14.8 1.0
CA A:SER81 4.0 12.6 1.0
OG A:SER81 4.0 19.7 1.0
C A:CYS80 4.1 10.5 1.0
CA A:CYS80 4.1 13.9 1.0
O A:HOH340 4.3 32.8 1.0
C A:ASP66 4.4 19.1 1.0
O A:ASP66 4.4 17.5 1.0
C A:PRO79 4.4 14.1 1.0
C A:ASN65 4.5 18.8 1.0
N A:ASP66 4.6 14.3 1.0
O A:HOH387 4.6 30.0 1.0
CB A:PRO79 4.6 15.7 1.0
CA A:PRO79 4.8 10.7 1.0

Chlorine binding site 2 out of 4 in 4d9z

Go back to Chlorine Binding Sites List in 4d9z
Chlorine binding site 2 out of 4 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme at 318K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:19.1
occ:1.00
 N A:GLY26 3.1 11.5 1.0
OG A:SER24 3.2 18.2 1.0
CB A:SER24 3.5 17.4 1.0
O A:HOH415 3.6 24.6 1.0
CA A:GLY26 3.6 11.1 1.0
CA A:GLN121 3.6 18.4 1.0
CD1 A:ILE124 3.8 22.4 1.0
N A:LEU25 4.0 12.2 1.0
N A:GLN121 4.0 15.0 1.0
CB A:GLN121 4.0 18.3 1.0
C A:SER24 4.1 10.7 1.0
O A:VAL120 4.2 12.8 1.0
C A:LEU25 4.2 12.6 1.0
CG A:GLN121 4.3 23.6 1.0
C A:VAL120 4.3 15.1 1.0
CG1 A:ILE124 4.3 19.5 1.0
CA A:SER24 4.4 14.9 1.0
CG2 A:VAL120 4.5 13.8 1.0
CA A:LEU25 4.5 10.2 1.0
O A:SER24 4.6 13.1 1.0
C A:GLY26 4.7 10.5 1.0
C A:GLN121 4.7 14.3 1.0
N A:ASN27 4.8 11.2 1.0
CB A:LEU25 4.8 12.3 1.0
O A:GLN121 4.9 16.1 1.0
CG2 A:ILE124 5.0 16.3 1.0

Chlorine binding site 3 out of 4 in 4d9z

Go back to Chlorine Binding Sites List in 4d9z
Chlorine binding site 3 out of 4 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme at 318K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:21.0
occ:1.00
 O A:HOH390 2.9 34.1 1.0
O A:HOH360 3.1 29.4 1.0
O A:HOH326 3.1 23.1 1.0
N A:ILE88 3.3 13.7 1.0
CG1 A:ILE88 3.7 14.5 1.0
CA A:ASP87 3.8 11.6 1.0
C A:ASP87 4.1 12.2 1.0
CZ A:PHE3 4.1 17.8 1.0
CE1 A:HIS15 4.2 16.8 1.0
CG2 A:ILE88 4.2 10.4 1.0
O A:SER86 4.2 14.9 1.0
CB A:ILE88 4.3 10.1 1.0
CG A:ASP87 4.3 17.1 1.0
O A:HOH337 4.3 25.2 1.0
CA A:ILE88 4.4 11.7 1.0
CB A:ALA11 4.4 12.6 1.0
OD2 A:ASP87 4.4 19.4 1.0
O A:HOH400 4.5 37.0 1.0
CD1 A:ILE88 4.5 12.7 1.0
CB A:ASP87 4.6 15.6 1.0
OD1 A:ASP87 4.6 16.6 1.0
O A:HOH367 4.7 25.7 1.0
CE2 A:PHE3 4.7 13.4 1.0
NE2 A:HIS15 4.8 18.4 1.0
N A:ASP87 4.9 13.1 1.0
C A:SER86 5.0 13.1 1.0

Chlorine binding site 4 out of 4 in 4d9z

Go back to Chlorine Binding Sites List in 4d9z
Chlorine binding site 4 out of 4 in the Lysozyme at 318K


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme at 318K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:21.8
occ:1.00
 ND2 A:ASN93 3.2 16.6 1.0
O A:HOH432 3.2 13.7 1.0
O A:HOH431 3.2 30.4 1.0
CA A:ALA90 3.7 12.9 1.0
O A:HOH430 4.0 33.4 1.0
CB A:ALA90 4.0 13.2 1.0
CB A:ASN93 4.0 10.3 1.0
CG A:ASN93 4.1 15.4 1.0
CD1 A:ILE78 4.4 13.8 1.0
N A:ALA90 4.5 11.6 1.0
O A:ALA90 4.6 10.0 1.0
C A:ALA90 4.7 11.8 1.0
O A:THR89 4.7 11.2 1.0
O A:HOH433 4.8 15.1 1.0
C A:THR89 4.8 10.2 1.0
O A:HOH355 4.9 29.7 1.0

Reference:

P.Sharma, N.Verma, P.K.Singh, S.Korpole, Ashish. Characterization of Heat Induced Spherulites of Lysozyme Reveals New Insight on Amyloid Initiation Sci Rep V. 6 22475 2016.
ISSN: ESSN 2045-2322
PubMed: 26926993
DOI: 10.1038/SREP22475
Page generated: Fri Jul 11 14:17:05 2025

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