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Sodium in PDB 7pes: Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus

Enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus, PDB code: 7pes 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) 47.18 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.175, 94.355, 119.795, 90, 91.14, 90
R / Rfree (%) 16.6 / 20.1

Other elements in 7pes:

The structure of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus also contains other interesting chemical elements:

Copper (Cu) 24 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus (pdb code 7pes). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus, PDB code: 7pes:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7pes

Go back to Sodium Binding Sites List in 7pes
Sodium binding site 1 out of 4 in the Crystal Structure of Two-Domain Laccase Mutant M199G 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 M199G From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:50.9
occ:1.00
 O A:HOH565 2.4 43.8 1.0
O B:HOH563 2.4 43.2 1.0
O C:HOH519 2.4 44.1 1.0
O B:HOH626 2.8 40.6 1.0
O A:HOH665 2.9 40.2 1.0
O C:HOH635 2.9 39.5 1.0
O A:HOH631 3.6 40.8 1.0
O C:HOH568 3.8 37.9 1.0
O B:HOH558 3.8 39.2 1.0
O C:HOH503 3.9 46.7 1.0
O A:HOH664 3.9 48.0 1.0
O A:HOH558 4.0 44.4 1.0
O B:HOH528 4.0 50.7 1.0
O A:HOH527 4.3 43.0 1.0
O C:HOH538 4.4 47.0 1.0
O B:HOH535 4.4 47.9 1.0
OD2 B:ASP243 4.5 32.5 1.0
OD2 A:ASP243 4.5 32.6 1.0
OD2 C:ASP243 4.5 35.1 1.0
NZ C:LYS262 4.7 36.6 1.0
NZ A:LYS262 4.8 36.2 1.0
NZ B:LYS262 4.8 33.0 1.0

Sodium binding site 2 out of 4 in 7pes

Go back to Sodium Binding Sites List in 7pes
Sodium binding site 2 out of 4 in the Crystal Structure of Two-Domain Laccase Mutant M199G 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 M199G From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:48.3
occ:1.00
 O B:HOH531 2.4 37.6 1.0
O A:HOH655 2.4 37.4 1.0
O B:HOH553 2.5 35.6 1.0
O A:HOH531 2.6 39.3 1.0
O C:HOH552 2.6 37.7 1.0
O C:HOH612 2.6 37.6 1.0
O A:HOH664 3.4 48.0 1.0
O C:HOH575 3.7 38.1 1.0
O B:HOH560 3.7 31.5 1.0
O A:HOH630 3.8 35.5 1.0
O B:ASP243 4.2 32.9 1.0
O A:ASP243 4.3 30.4 1.0
O C:ASP243 4.4 35.0 1.0
OG B:SER256 4.5 34.3 1.0
O B:HOH528 4.7 50.7 1.0
OG C:SER256 4.8 34.0 1.0
OG A:SER256 4.8 33.8 1.0
O A:HOH558 4.9 44.4 1.0
CB B:SER256 4.9 32.0 1.0
CA B:SER256 5.0 28.9 1.0

Sodium binding site 3 out of 4 in 7pes

Go back to Sodium Binding Sites List in 7pes
Sodium binding site 3 out of 4 in the Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:49.1
occ:1.00
 O E:HOH603 2.4 37.0 1.0
O E:HOH530 2.4 38.2 1.0
O F:HOH632 2.5 37.3 1.0
O D:HOH568 2.5 35.8 1.0
O F:HOH544 2.6 38.1 1.0
O D:HOH527 2.6 38.2 1.0
O F:HOH654 3.4 49.5 1.0
O E:HOH575 3.7 39.9 1.0
O F:HOH577 3.8 35.6 1.0
O D:HOH562 3.8 38.6 1.0
O E:ASP243 4.2 33.2 1.0
O D:ASP243 4.3 35.9 1.0
O F:ASP243 4.5 31.2 1.0
OG D:SER256 4.6 31.9 1.0
OG E:SER256 4.7 34.0 1.0
OG F:SER256 4.8 31.4 1.0
O E:HOH549 4.8 47.4 1.0
O D:HOH565 4.9 45.9 1.0

Sodium binding site 4 out of 4 in 7pes

Go back to Sodium Binding Sites List in 7pes
Sodium binding site 4 out of 4 in the Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Two-Domain Laccase Mutant M199G From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na406

b:50.2
occ:1.00
 O F:HOH556 2.5 50.6 1.0
O D:HOH633 2.6 40.2 1.0
O F:HOH560 2.7 40.3 1.0
O E:HOH584 2.8 39.2 1.0
O F:HOH622 3.1 34.6 1.0
O E:HOH548 3.5 44.0 1.0
O F:HOH552 3.6 45.6 1.0
O F:HOH653 3.9 47.6 1.0
O D:HOH629 4.0 46.6 1.0
CG2 F:ILE263 4.2 34.2 1.0
O E:HOH594 4.3 45.3 1.0
O F:HOH532 4.3 44.8 1.0
NZ E:LYS262 4.3 41.6 1.0
OD2 F:ASP243 4.4 29.3 1.0
O F:HOH508 4.4 38.0 1.0
NZ F:LYS262 4.5 36.5 1.0
O F:HOH513 4.5 52.2 1.0
CG F:LYS262 4.8 31.8 1.0
O D:HOH543 4.9 50.7 1.0
O F:ILE263 5.0 31.0 1.0

Reference:

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
Page generated: Fri Apr 7 15:38:42 2023

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