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:
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 Jul 30 08:54:09 2024
|