Sodium in PDB 7pen: Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus:
1.10.3.2;

The structure of Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus, PDB code: 7pen was solved by A.Gabdulkhakov, S.Tishchenko, I.Kolyadenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.10 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.26, 94.98, 116.27, 90, 91.67, 90
R / Rfree (%)	13.5 / 16.5

The structure of Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus also contains other interesting chemical elements:

Copper

(Cu)

24 atoms

The binding sites of Sodium atom in the Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus (pdb code 7pen). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus, PDB code: 7pen:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:33.6 occ:1.00 O C:HOH531 2.4 23.0 1.0 O C:HOH631 2.5 27.0 1.0 O A:HOH525 2.5 27.9 1.0 O A:HOH681 2.5 26.9 1.0 O B:HOH652 2.5 26.4 1.0 O B:HOH536 2.6 27.8 1.0 O A:HOH720 3.1 39.9 1.0 O A:HOH628 3.7 18.8 1.0 O C:HOH597 3.8 20.6 1.0 O B:HOH594 3.8 20.4 1.0 O C:ASP243 4.2 18.4 1.0 O A:ASP243 4.3 18.5 1.0 O B:ASP243 4.3 16.6 1.0 OG C:SER256 4.6 18.4 1.0 O C:HOH564 4.7 45.9 1.0 O C:HOH680 4.7 51.7 1.0 OG A:SER256 4.8 19.9 1.0 OG B:SER256 4.8 19.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Two-Domain Laccase Mutant Y230A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:37.5 occ:1.00 O E:HOH520 2.4 25.3 1.0 O F:HOH675 2.5 27.1 1.0 O D:HOH658 2.5 24.9 1.0 O E:HOH697 2.5 27.7 1.0 O D:HOH546 2.5 25.8 1.0 O F:HOH555 2.5 28.0 1.0 O D:HOH705 3.2 35.3 1.0 O E:HOH565 3.4 55.7 1.0 O D:HOH601 3.7 20.8 1.0 O E:HOH639 3.7 20.2 1.0 O F:HOH639 3.8 23.1 1.0 O E:ASP243 4.2 18.7 1.0 O D:ASP243 4.2 19.1 1.0 O F:ASP243 4.3 18.3 1.0 OG D:SER256 4.7 19.7 1.0 O D:HOH703 4.8 46.2 1.0 OG F:SER256 4.8 19.3 1.0 OG E:SER256 4.8 16.4 1.0 O E:HOH515 4.9 51.6 1.0

I.Kolyadenko, A.Scherbakova, K.Kovalev, A.Gabdulkhakov, S.Tishchenko. Engineering the Catalytic Properties of Two-Domain Laccase From Streptomyces Griseoflavus Ac-993. Int J Mol Sci V. 23 2021.
ISSN: ESSN 1422-0067
PubMed: 35008493
DOI: 10.3390/IJMS23010065