Atomistry » Zinc » PDB 3s2l-3sbh » 3sb5
Atomistry »
  Zinc »
    PDB 3s2l-3sbh »
      3sb5 »

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

Go back to Zinc Binding Sites List in 3sb5
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

Go back to Zinc Binding Sites List in 3sb5
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

Go back to Zinc Binding Sites List in 3sb5
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

Go back to Zinc Binding Sites List in 3sb5
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

Go back to Zinc Binding Sites List in 3sb5
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

Go back to Zinc Binding Sites List in 3sb5
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy