Chlorine in PDB 8dyz: Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset

Enzymatic activity of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset

All present enzymatic activity of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset:
3.2.1.17;

Protein crystallography data

The structure of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset, PDB code: 8dyz was solved by S.P.Meisburger, N.Ando, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.82 / 1.27
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.632, 79.632, 38.296, 90, 90, 90
R / Rfree (%) 11.5 / 13.3

Other elements in 8dyz:

The structure of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset (pdb code 8dyz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset, PDB code: 8dyz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8dyz

Go back to Chlorine Binding Sites List in 8dyz
Chlorine binding site 1 out of 3 in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:24.3
occ:1.00
 HD22 A:ASN113 2.5 18.6 1.0
HB2 A:ASN113 2.9 16.6 1.0
HA A:ALA110 3.0 16.0 1.0
HG11 A:VAL109 3.1 23.8 0.5
HG21 A:VAL109 3.3 22.5 0.5
O A:HOH353 3.4 25.8 1.0
ND2 A:ASN113 3.4 18.9 1.0
CB A:ASN113 3.6 16.4 1.0
HD2 A:ARG114 3.7 19.0 1.0
HB3 A:ASN113 3.7 16.4 1.0
HG3 A:ARG114 3.8 18.9 1.0
HG13 A:VAL109 3.9 21.6 0.5
CG1 A:VAL109 3.9 23.9 0.5
CA A:ALA110 4.0 16.2 1.0
HD21 A:ASN113 4.0 18.4 1.0
CG A:ASN113 4.0 17.6 1.0
HG13 A:VAL109 4.0 23.5 0.5
O A:VAL109 4.1 16.8 1.0
HB2 A:ALA110 4.2 18.8 1.0
CG2 A:VAL109 4.3 23.5 0.5
C A:VAL109 4.3 14.8 1.0
N A:ALA110 4.3 15.3 1.0
HG12 A:VAL109 4.4 23.6 0.5
CD A:ARG114 4.4 19.0 1.0
HD3 A:ARG114 4.5 18.8 1.0
CB A:ALA110 4.5 19.2 1.0
CG A:ARG114 4.6 19.3 1.0
HG22 A:VAL109 4.6 22.9 0.5
HB1 A:ALA110 4.6 18.4 1.0
CG1 A:VAL109 4.7 21.8 0.5
H A:ASN113 4.7 15.0 1.0
HG23 A:VAL109 4.8 23.4 0.5
HH11 A:ARG114 4.9 20.9 1.0
H A:ALA110 4.9 15.2 1.0
HG2 A:ARG114 4.9 19.1 1.0
CA A:ASN113 4.9 15.6 1.0
CB A:VAL109 5.0 20.1 0.5

Chlorine binding site 2 out of 3 in 8dyz

Go back to Chlorine Binding Sites List in 8dyz
Chlorine binding site 2 out of 3 in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:54.1
occ:1.00
 H A:ILE88 2.4 18.9 1.0
HG12 A:ILE88 2.7 22.1 1.0
HA A:ASP87 3.0 21.8 1.0
HE1 A:HIS15 3.2 32.0 1.0
N A:ILE88 3.3 19.1 1.0
HB1 A:ALA11 3.6 21.4 1.0
CG1 A:ILE88 3.6 21.8 1.0
HZ A:PHE3 3.7 21.3 1.0
O A:HOH314 3.7 39.7 1.0
HG23 A:ILE88 3.8 22.7 1.0
CA A:ASP87 3.9 21.9 1.0
HG13 A:ILE88 3.9 22.3 1.0
OD1 A:ASP87 4.0 30.6 1.0
CE1 A:HIS15 4.0 30.7 1.0
C A:ASP87 4.1 20.3 1.0
HH21 A:ARG14 4.1 56.4 1.0
O A:SER86 4.2 26.6 1.0
CB A:ILE88 4.3 19.6 1.0
CA A:ILE88 4.3 18.0 1.0
HB2 A:ALA11 4.4 21.5 1.0
CB A:ALA11 4.4 21.8 1.0
H A:THR89 4.4 18.0 1.0
CG2 A:ILE88 4.5 23.5 1.0
CG A:ASP87 4.5 31.3 1.0
CZ A:PHE3 4.6 22.2 1.0
HD12 A:ILE88 4.6 25.2 1.0
CD1 A:ILE88 4.6 25.5 1.0
HD1 A:HIS15 4.6 30.3 0.0
HE2 A:PHE3 4.6 20.2 1.0
HD13 A:ILE88 4.7 24.6 1.0
CB A:ASP87 4.7 26.7 1.0
ND1 A:HIS15 4.7 30.5 1.0
NH2 A:ARG14 4.8 61.8 1.0
HH22 A:ARG14 4.9 57.2 1.0
N A:ASP87 4.9 20.5 1.0
HB3 A:ALA11 4.9 21.7 1.0
N A:THR89 4.9 18.1 1.0
HG22 A:ILE88 4.9 22.7 1.0
HB2 A:ASP87 5.0 26.8 1.0
C A:SER86 5.0 20.7 1.0

Chlorine binding site 3 out of 3 in 8dyz

Go back to Chlorine Binding Sites List in 8dyz
Chlorine binding site 3 out of 3 in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:64.9
occ:1.00
 HE2 A:PHE38 2.9 18.4 1.0
HZ3 A:LYS33 3.2 38.4 1.0
HZ3 A:TRP123 3.3 24.6 1.0
HD3 A:ARG5 3.3 25.1 1.0
HB2 A:ARG5 3.4 22.3 1.0
HD3 A:LYS33 3.6 25.4 1.0
CE2 A:PHE38 3.7 19.5 1.0
NZ A:LYS33 4.0 39.6 1.0
HE2 A:LYS33 4.1 32.7 1.0
HZ A:PHE38 4.2 16.9 1.0
CZ3 A:TRP123 4.2 26.1 1.0
CD A:ARG5 4.2 25.4 1.0
CB A:ARG5 4.3 22.4 1.0
HZ2 A:LYS33 4.4 38.8 1.0
CD A:LYS33 4.4 25.5 1.0
CE A:LYS33 4.4 34.4 1.0
CZ A:PHE38 4.4 17.1 1.0
HE A:ARG5 4.4 26.7 1.0
HZ1 A:LYS33 4.6 37.7 1.0
HB3 A:ARG5 4.6 22.5 1.0
HG3 A:ARG5 4.6 22.2 1.0
CG A:ARG5 4.6 21.9 1.0
HD2 A:PHE38 4.7 17.6 1.0
CD2 A:PHE38 4.7 18.8 1.0
HE3 A:TRP123 4.7 21.6 1.0
HD2 A:ARG5 4.8 24.9 1.0
NE A:ARG5 4.8 27.0 1.0
HH2 A:TRP123 4.9 25.9 1.0
CE3 A:TRP123 4.9 21.4 1.0
HD2 A:LYS33 5.0 25.9 1.0

Reference:

S.P.Meisburger, D.A.Case, N.Ando. Robust Total X-Ray Scattering Workflow to Study Correlated Motion of Proteins in Crystals Biorxiv 2022.
DOI: 10.1101/2022.08.22.504832
Page generated: Tue Apr 4 22:48:01 2023

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