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Sodium in PDB 7xea: T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking

Enzymatic activity of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking

All present enzymatic activity of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking:
3.2.1.17;

Protein crystallography data

The structure of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking, PDB code: 7xea was solved by T.Tamada, T.Hiromoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.05 / 1.10
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.898, 59.898, 96.77, 90, 90, 120
R / Rfree (%) 15.9 / 18.1

Other elements in 7xea:

The structure of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking (pdb code 7xea). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking, PDB code: 7xea:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7xea

Go back to Sodium Binding Sites List in 7xea
Sodium binding site 1 out of 4 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:21.0
occ:1.00
 O A:ASP20 2.9 12.6 1.0
O A:LYS19 3.2 13.1 1.0
CB A:LYS19 3.7 13.9 1.0
C A:LYS19 3.7 12.6 1.0
C A:ASP20 3.9 11.9 1.0
O A:HOH306 4.1 27.5 1.0
CA A:LYS19 4.3 13.1 1.0
N A:ASP20 4.4 12.0 1.0
CA A:THR21 4.6 11.9 0.1
N A:THR21 4.7 11.7 0.1
CA A:ASP20 4.7 11.8 1.0
N A:THR21 4.7 11.5 0.9
CA A:THR21 4.7 12.5 0.9
CA A:GLY23 4.7 12.6 1.0
N A:GLY23 4.7 11.9 1.0
C A:THR21 4.9 11.6 0.1

Sodium binding site 2 out of 4 in 7xea

Go back to Sodium Binding Sites List in 7xea
Sodium binding site 2 out of 4 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:20.2
occ:1.00
 OE1 A:GLU128 1.8 18.0 0.5
CD A:GLU128 2.7 17.4 0.5
O A:HOH317 3.0 21.0 1.0
OE2 A:GLU128 3.1 18.1 0.5
N A:ASP127 3.2 11.7 1.0
C A:ARG125 3.4 11.3 1.0
N A:TRP126 3.4 11.1 1.0
N A:GLU128 3.5 12.0 1.0
CB A:ASP127 3.5 13.3 1.0
CA A:ARG125 3.6 11.9 1.0
CG A:GLU128 3.8 15.5 0.5
CA A:ASP127 3.8 12.2 1.0
O A:ARG125 3.9 11.7 1.0
CG A:GLU128 4.0 15.4 0.5
CB A:ARG125 4.0 13.6 1.0
C A:TRP126 4.1 11.0 1.0
C A:ASP127 4.1 11.7 1.0
OE2 A:GLU128 4.2 19.8 0.5
CA A:TRP126 4.3 11.2 1.0
CB A:GLU128 4.3 13.6 0.5
CB A:GLU128 4.4 13.6 0.5
CD A:GLU128 4.4 18.1 0.5
CG A:ASP127 4.5 14.0 1.0
CA A:GLU128 4.5 12.4 0.5
CA A:GLU128 4.5 12.4 0.5
O A:HOH429 4.6 14.8 1.0
O A:HOH301 4.6 30.1 1.0
OD1 A:ASP127 4.8 14.9 1.0
CG A:ARG125 4.9 15.8 1.0

Sodium binding site 3 out of 4 in 7xea

Go back to Sodium Binding Sites List in 7xea
Sodium binding site 3 out of 4 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:49.1
occ:1.00
 OE1 A:GLU128 2.2 19.5 0.5
NH1 A:ARG125 3.1 26.2 1.0
CD A:GLU128 3.4 18.1 0.5
O A:HOH438 3.6 24.6 1.0
CD A:ARG125 3.7 17.8 1.0
NH1 A:ARG119 3.9 25.7 0.4
OE2 A:GLU128 4.0 19.8 0.5
O A:HOH562 4.1 47.1 1.0
CZ A:ARG125 4.1 23.9 1.0
CG A:MET120 4.2 14.1 1.0
NE A:ARG125 4.3 20.6 1.0
OE1 A:GLN123 4.4 27.2 1.0
CG A:GLU128 4.4 15.4 0.5
CE A:MET120 4.5 17.2 1.0
CB A:GLU128 4.5 13.6 0.5
CB A:GLU128 4.5 13.6 0.5
CG A:GLU128 4.5 15.5 0.5
NH2 A:ARG119 4.6 26.5 0.4
SD A:MET120 4.6 15.7 1.0
CZ A:ARG119 4.7 25.4 0.4
CG A:ARG125 4.9 15.8 1.0
NH2 A:ARG119 5.0 31.2 0.6

Sodium binding site 4 out of 4 in 7xea

Go back to Sodium Binding Sites List in 7xea
Sodium binding site 4 out of 4 in the T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of T4 Lysozyme Mutant-S44C/C54T/N68C/A93C/C97A/T115C, Dmso 40%, and Then Backsoaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:16.9
occ:1.00
 OD2 A:ASP70 2.7 11.6 1.0
O A:HOH402 2.8 10.9 1.0
O A:ILE29 2.9 10.4 1.0
CA A:PHE67 3.3 10.9 1.0
N A:PHE67 3.5 10.4 1.0
C A:ILE29 3.6 9.9 1.0
CB A:PHE67 3.7 11.4 1.0
CD1 A:PHE67 3.7 12.2 1.0
CB A:HIS31 3.7 11.0 1.0
CG A:ASP70 3.7 10.8 1.0
N A:HIS31 3.8 9.7 1.0
C A:LEU66 3.9 10.2 1.0
CA A:HIS31 3.9 10.1 1.0
CZ A:PHE104 3.9 14.4 1.0
CB A:ASP70 3.9 11.1 1.0
O A:LEU66 4.0 10.8 1.0
CG A:PHE67 4.1 11.9 1.0
CB A:ILE29 4.1 11.5 1.0
C A:GLY30 4.1 10.5 1.0
CA A:ILE29 4.2 10.3 1.0
N A:ILE29 4.2 10.9 1.0
ND1 A:HIS31 4.4 11.4 1.0
CB A:LEU66 4.5 11.4 1.0
CE2 A:PHE104 4.5 13.2 1.0
O A:GLY30 4.5 11.3 1.0
N A:GLY30 4.5 10.5 1.0
C A:PHE67 4.6 11.1 1.0
CG A:HIS31 4.6 10.7 1.0
O A:ALA63 4.6 11.5 1.0
CE1 A:PHE67 4.8 12.8 1.0
O A:PHE67 4.8 11.6 1.0
OD1 A:ASP70 4.8 10.6 1.0
CA A:GLY30 4.8 11.0 1.0
CA A:LEU66 4.9 11.3 1.0
CG2 A:ILE29 4.9 11.8 1.0
C1 A:GOL202 4.9 23.1 0.5
CE1 A:PHE104 5.0 14.5 1.0

Reference:

T.Hiromoto, T.Ikura, E.Honjo, M.Blaber, R.Kuroki, T.Tamada. Creation of Cross-Linked Crystals with Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Front Mol Biosci V. 9 08394 2022.
ISSN: ESSN 2296-889X
PubMed: 35755825
DOI: 10.3389/FMOLB.2022.908394
Page generated: Wed Oct 9 09:40:41 2024

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