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Chlorine in PDB 3sb5: Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization

Enzymatic activity of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization

All present enzymatic activity of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization:
3.2.1.17;

Protein crystallography data

The structure of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization, PDB code: 3sb5 was solved by A.Laganowsky, A.B.Soriaga, M.Zhao, M.R.Sawaya, D.Cascio, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.50 / 2.46
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 128.970, 128.970, 295.140, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 23

Other elements in 3sb5:

The structure of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Zinc (Zn) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization (pdb code 3sb5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization, PDB code: 3sb5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3sb5

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Chlorine binding site 1 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl165

b:28.1
occ:1.00
 ZN B:ZN164 2.3 27.9 1.0
CG B:GLN123 3.8 34.0 1.0
SG B:CYS125 3.8 26.3 1.0
CB B:GLN123 3.8 26.5 1.0
CB B:CYS125 4.3 22.8 1.0
CG B:MET120 4.6 26.3 1.0
CA B:MET120 4.7 22.6 1.0
CB B:MET120 5.0 23.7 1.0

Chlorine binding site 2 out of 8 in 3sb5

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Chlorine binding site 2 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl170

b:30.0
occ:0.33
 ZN B:ZN163 2.4 27.1 0.3
SG B:CYS128 3.9 31.4 1.0
CB B:CYS128 4.0 27.3 1.0
CE B:MET120 4.6 26.0 1.0
CA B:CYS128 4.7 26.5 1.0

Chlorine binding site 3 out of 8 in 3sb5

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Chlorine binding site 3 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl166

b:25.4
occ:1.00
 ZN A:ZN163 2.2 27.4 1.0
N A:CYS128 3.5 25.4 1.0
N A:ASP127 3.6 28.3 1.0
SG A:CYS128 3.6 29.3 1.0
CA A:CYS125 3.7 22.9 1.0
C A:CYS125 3.8 27.8 1.0
SG A:CYS125 3.8 27.2 1.0
CB A:ASP127 3.9 29.3 1.0
CA A:ASP127 4.0 27.8 1.0
N A:TRP126 4.0 23.4 1.0
CB A:CYS125 4.1 23.4 1.0
C A:ASP127 4.2 30.1 1.0
CB A:CYS128 4.2 25.3 1.0
O A:CYS125 4.3 29.3 1.0
CA A:CYS128 4.5 24.9 1.0
C A:TRP126 4.6 31.0 1.0
OD2 A:ASP127 4.7 46.5 1.0
CA A:TRP126 4.8 24.0 1.0
CG A:ASP127 4.9 38.5 1.0
O A:LYS124 4.9 25.8 1.0

Chlorine binding site 4 out of 8 in 3sb5

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Chlorine binding site 4 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl169

b:30.0
occ:0.33
 ZN A:ZN164 2.3 28.1 0.3
SG A:CYS128 3.8 29.3 1.0
CB A:CYS128 4.0 25.3 1.0
CE A:MET120 4.5 27.6 1.0
CA A:CYS128 4.8 24.9 1.0

Chlorine binding site 5 out of 8 in 3sb5

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Chlorine binding site 5 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl165

b:32.6
occ:1.00
 ZN C:ZN163 2.2 33.4 1.0
N C:ASP127 3.5 35.5 1.0
N C:CYS128 3.5 35.8 1.0
SG C:CYS128 3.6 39.3 1.0
CA C:CYS125 3.6 30.7 1.0
C C:CYS125 3.6 34.9 1.0
CB C:ASP127 3.7 37.8 1.0
SG C:CYS125 3.8 37.1 1.0
N C:TRP126 3.8 31.9 1.0
CA C:ASP127 3.9 35.8 1.0
CB C:CYS125 4.0 32.1 1.0
C C:ASP127 4.1 39.9 1.0
O C:CYS125 4.1 34.4 1.0
CB C:CYS128 4.3 35.8 1.0
OD2 C:ASP127 4.4 57.6 1.0
C C:TRP126 4.5 36.5 1.0
CA C:CYS128 4.5 35.7 1.0
CG C:ASP127 4.6 50.3 1.0
CA C:TRP126 4.7 31.8 1.0
O C:LYS124 4.8 28.9 1.0
N C:CYS125 4.9 30.1 1.0

Chlorine binding site 6 out of 8 in 3sb5

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Chlorine binding site 6 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl167

b:30.0
occ:0.33
 ZN C:ZN164 2.2 38.4 0.3
SG C:CYS128 3.7 39.3 1.0
CB C:CYS128 3.8 35.8 1.0
CE C:MET120 4.5 38.2 1.0
CA C:CYS128 4.6 35.7 1.0

Chlorine binding site 7 out of 8 in 3sb5

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Chlorine binding site 7 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl167

b:24.2
occ:1.00
 ZN D:ZN163 2.3 23.8 1.0
CG D:GLN123 3.7 26.4 1.0
CB D:GLN123 3.7 24.2 1.0
SG D:CYS125 3.8 25.4 1.0
CB D:CYS125 4.3 21.5 1.0
CA D:MET120 4.6 21.8 1.0
CG D:MET120 4.7 25.6 1.0
CB D:MET120 4.9 23.3 1.0
CD D:GLN123 4.9 42.2 1.0
O D:MET120 5.0 23.8 1.0

Chlorine binding site 8 out of 8 in 3sb5

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Chlorine binding site 8 out of 8 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl171

b:30.0
occ:0.33
 ZN D:ZN164 2.1 30.4 0.3
SG D:CYS128 3.6 26.0 1.0
CB D:CYS128 3.8 22.9 1.0
CA D:CYS128 4.6 23.5 1.0
O D:HOH207 4.7 46.9 0.3
CE D:MET120 4.9 26.1 1.0

Reference:

A.Laganowsky, M.Zhao, A.B.Soriaga, M.R.Sawaya, D.Cascio, T.O.Yeates. An Approach to Crystallizing Proteins By Metal-Mediated Synthetic Symmetrization. Protein Sci. V. 20 1876 2011.
ISSN: ISSN 0961-8368
PubMed: 21898649
DOI: 10.1002/PRO.727
Page generated: Sun Jul 21 04:17:13 2024

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