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Magnesium 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:

Chlorine (Cl) 8 atoms
Zinc (Zn) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 3sb5

Go back to Magnesium Binding Sites List in 3sb5
Magnesium binding site 1 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg166

b:34.7
occ:1.00
 O2 B:GOL169 2.9 57.7 1.0
N B:ARG145 3.3 31.0 1.0
CB B:ASN144 3.4 35.4 1.0
N B:ASN144 3.4 33.3 1.0
C2 B:GOL169 3.5 56.9 1.0
C B:THR142 3.5 36.6 1.0
C3 B:GOL169 3.5 57.0 1.0
CA B:THR142 3.6 32.6 1.0
CB B:THR142 3.8 39.5 1.0
O B:THR142 3.8 36.2 1.0
CA B:ASN144 3.8 33.4 1.0
OD1 B:ASN144 3.8 73.7 1.0
N B:PRO143 3.9 33.6 1.0
CG B:ASN144 4.0 65.0 1.0
CB B:ARG145 4.0 27.5 1.0
C B:ASN144 4.0 35.9 1.0
CG2 B:THR142 4.3 28.8 1.0
CA B:ARG145 4.3 30.4 1.0
O3 B:GOL169 4.4 56.7 1.0
C B:PRO143 4.4 37.0 1.0
CD B:PRO143 4.5 35.4 1.0
CA B:PRO143 4.7 32.9 1.0

Magnesium binding site 2 out of 6 in 3sb5

Go back to Magnesium Binding Sites List in 3sb5
Magnesium binding site 2 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg167

b:60.7
occ:1.00
 O B:HOH177 2.9 31.9 1.0
O B:ALA93 3.8 32.1 1.0
OH B:TYR88 4.1 42.2 1.0
CD1 B:ILE100 4.2 36.7 1.0
CB B:ARG96 4.3 25.2 1.0
CA B:ALA93 4.7 28.0 1.0
C B:ALA93 4.7 30.1 1.0
CB B:ALA93 4.7 28.9 1.0
N B:ALA97 4.8 29.0 1.0

Magnesium binding site 3 out of 6 in 3sb5

Go back to Magnesium Binding Sites List in 3sb5
Magnesium binding site 3 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg167

b:36.0
occ:1.00
 N A:ARG145 3.4 27.8 1.0
N A:ASN144 3.5 30.8 1.0
CB A:ASN144 3.6 32.5 1.0
C A:THR142 3.6 41.1 1.0
CA A:THR142 3.7 36.4 1.0
CB A:THR142 3.8 37.1 1.0
CA A:ASN144 3.9 30.2 1.0
N A:PRO143 3.9 36.8 1.0
O A:THR142 4.0 41.8 1.0
ND2 A:ASN144 4.1 48.3 1.0
CB A:ARG145 4.1 23.1 1.0
CG A:ASN144 4.2 57.5 1.0
C A:ASN144 4.2 33.3 1.0
CG2 A:THR142 4.3 26.8 1.0
CD A:PRO143 4.4 38.5 1.0
CA A:ARG145 4.4 26.9 1.0
C A:PRO143 4.5 37.1 1.0
CA A:PRO143 4.8 35.6 1.0

Magnesium binding site 4 out of 6 in 3sb5

Go back to Magnesium Binding Sites List in 3sb5
Magnesium binding site 4 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg171

b:30.0
occ:1.00
 OG A:SER117 2.9 36.7 1.0
OD1 A:ASN132 3.4 40.7 1.0
N A:SER117 3.4 26.5 1.0
CB A:SER117 3.5 29.9 1.0
CA A:PHE114 3.6 28.9 1.0
O A:HOH198 3.7 40.7 1.0
O A:PHE114 3.7 37.6 1.0
C A:PHE114 3.7 35.8 1.0
CB A:ASN116 4.0 30.6 1.0
CB A:PHE114 4.0 29.2 1.0
N A:ASN116 4.1 31.7 1.0
CA A:SER117 4.1 26.2 1.0
CD2 A:PHE114 4.2 30.4 1.0
C A:ASN116 4.3 32.7 1.0
CA A:ASN116 4.3 30.5 1.0
N A:THR115 4.5 33.5 1.0
CG A:ASN132 4.5 43.8 1.0
CG A:PHE114 4.6 29.5 1.0
O A:GLY113 4.8 37.6 1.0
CG A:ASN116 4.9 42.8 1.0
C A:THR115 4.9 37.1 1.0
N A:PHE114 4.9 30.8 1.0
OD1 A:ASN116 5.0 39.3 1.0

Magnesium binding site 5 out of 6 in 3sb5

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Magnesium binding site 5 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg166

b:18.1
occ:1.00
 O3 D:GOL165 2.9 40.7 1.0
O D:HOH193 3.0 27.3 1.0
N D:ARG145 3.4 21.9 1.0
N D:ASN144 3.4 24.5 1.0
CB D:ASN144 3.4 25.7 1.0
C D:THR142 3.5 30.7 1.0
CA D:THR142 3.6 29.7 1.0
CB D:THR142 3.8 27.0 1.0
N D:PRO143 3.8 26.6 1.0
CA D:ASN144 3.8 24.0 1.0
O D:THR142 3.9 29.4 1.0
CB D:ARG145 4.1 19.0 1.0
C D:ASN144 4.1 26.9 1.0
CG D:ASN144 4.2 39.4 1.0
C3 D:GOL165 4.2 41.9 1.0
O2 D:GOL165 4.2 42.5 1.0
CD D:PRO143 4.3 28.7 1.0
CA D:ARG145 4.3 20.8 1.0
C D:PRO143 4.4 29.4 1.0
OD1 D:ASN144 4.4 28.8 1.0
CG2 D:THR142 4.5 18.4 1.0
C2 D:GOL165 4.5 42.0 1.0
O D:HOH225 4.5 33.3 1.0
CA D:PRO143 4.7 26.0 1.0
OG1 D:THR142 4.9 26.8 1.0
ND2 D:ASN144 4.9 35.7 1.0
CG D:PRO143 5.0 32.1 1.0

Magnesium binding site 6 out of 6 in 3sb5

Go back to Magnesium Binding Sites List in 3sb5
Magnesium binding site 6 out of 6 in the Zn-Mediated Trimer of T4 Lysozyme R125C/E128C By Synthetic Symmetrization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg168

b:63.6
occ:1.00
 O D:HOH230 1.7 30.0 1.0
O D:HOH228 1.8 30.0 1.0
O D:HOH226 1.9 30.0 1.0
O D:HOH227 2.0 30.0 1.0
O D:HOH231 2.2 30.0 1.0
O D:HOH229 2.8 30.0 1.0
OE1 D:GLU11 3.6 55.5 1.0
OE2 D:GLU11 4.0 48.6 1.0
CD D:GLU11 4.2 58.8 1.0
O D:HOH202 4.2 39.7 1.0
O D:GLN105 4.4 28.4 1.0
O D:HOH190 4.5 36.6 1.0
O D:PHE104 4.5 28.8 1.0
O D:HOH234 4.5 40.0 1.0
O D:HOH199 4.6 39.8 1.0
CA D:GLN105 4.7 21.9 1.0
OD1 D:ASP20 4.9 37.8 1.0
C D:GLN105 5.0 28.6 1.0
OE2 D:GLU22 5.0 64.0 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: Thu Aug 15 10:50:44 2024

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