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Zinc 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
Chlorine (Cl) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization, PDB code: 3sb5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn163

b:27.1
occ:0.33
 SG B:CYS128 2.3 31.4 1.0
CL B:CL170 2.4 30.0 0.3
CB B:CYS128 3.0 27.3 1.0
ZN B:ZN164 3.7 27.9 1.0
CA B:CYS128 4.3 26.5 1.0
SG B:CYS125 4.5 26.3 1.0

Zinc binding site 2 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn164

b:27.9
occ:1.00
 SG B:CYS125 2.2 26.3 1.0
CL B:CL165 2.3 28.1 1.0
CB B:CYS125 3.4 22.8 1.0
ZN B:ZN163 3.7 27.1 0.3
SG B:CYS128 4.4 31.4 1.0
CB B:CYS128 4.7 27.3 1.0
CA B:CYS125 4.8 23.2 1.0

Zinc binding site 3 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn163

b:27.4
occ:1.00
 CL A:CL166 2.2 25.4 1.0
SG A:CYS125 2.4 27.2 1.0
SG A:CYS128 2.4 29.3 1.0
CB A:CYS125 3.4 23.4 1.0
CB A:CYS128 3.4 25.3 1.0
ZN A:ZN164 3.8 28.1 0.3
CA A:CYS125 3.8 22.9 1.0
N A:CYS128 4.2 25.4 1.0
CA A:CYS128 4.4 24.9 1.0
C A:CYS125 4.4 27.8 1.0
O A:CYS125 4.7 29.3 1.0

Zinc binding site 4 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn164

b:28.1
occ:0.33
 SG A:CYS128 2.3 29.3 1.0
CL A:CL169 2.3 30.0 0.3
CB A:CYS128 3.0 25.3 1.0
ZN A:ZN163 3.8 27.4 1.0
CA A:CYS128 4.3 24.9 1.0
SG A:CYS125 4.5 27.2 1.0
CE A:MET120 4.9 27.6 1.0

Zinc binding site 5 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn163

b:33.4
occ:1.00
 CL C:CL165 2.2 32.6 1.0
SG C:CYS128 2.3 39.3 1.0
SG C:CYS125 2.4 37.1 1.0
CB C:CYS125 3.5 32.1 1.0
CB C:CYS128 3.5 35.8 1.0
ZN C:ZN164 3.9 38.4 0.3
CA C:CYS125 3.9 30.7 1.0
N C:CYS128 4.2 35.8 1.0
CA C:CYS128 4.4 35.7 1.0
C C:CYS125 4.5 34.9 1.0
O C:CYS125 4.7 34.4 1.0

Zinc binding site 6 out of 8 in 3sb5

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Zinc 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 Zinc with other atoms in the Zn 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:Zn164

b:38.4
occ:0.33
 CL C:CL167 2.2 30.0 0.3
SG C:CYS128 2.3 39.3 1.0
CB C:CYS128 3.0 35.8 1.0
ZN C:ZN163 3.9 33.4 1.0
CA C:CYS128 4.2 35.7 1.0
SG C:CYS125 4.7 37.1 1.0
CE C:MET120 4.9 38.2 1.0

Zinc binding site 7 out of 8 in 3sb5

Go back to Zinc Binding Sites List in 3sb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn163

b:23.8
occ:1.00
 SG D:CYS125 2.3 25.4 1.0
CL D:CL167 2.3 24.2 1.0
CB D:CYS125 3.4 21.5 1.0
ZN D:ZN164 3.9 30.4 0.3
SG D:CYS128 4.4 26.0 1.0
CB D:CYS128 4.7 22.9 1.0
CA D:CYS125 4.8 21.3 1.0

Zinc binding site 8 out of 8 in 3sb5

Go back to Zinc Binding Sites List in 3sb5
Zinc 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 Zinc with other atoms in the Zn 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:Zn164

b:30.4
occ:0.33
 CL D:CL171 2.1 30.0 0.3
SG D:CYS128 2.3 26.0 1.0
CB D:CYS128 3.0 22.9 1.0
ZN D:ZN163 3.9 23.8 1.0
CA D:CYS128 4.3 23.5 1.0
SG D:CYS125 4.6 25.4 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: Wed Dec 16 04:49:41 2020

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