Sodium in PDB 8gkp: Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease

All present enzymatic activity of Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease:
3.4.21.63;

The structure of Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease, PDB code: 8gkp was solved by D.Fernandez, D.D.L.Diec, W.Guo, S.Russi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.20 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.092, 75.218, 87.929, 90, 101.39, 90
R / Rfree (%)	15.3 / 20.7

The binding sites of Sodium atom in the Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease (pdb code 8gkp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease, PDB code: 8gkp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:25.0 occ:1.00 NE2 C:HIS193 2.0 18.8 0.5 OXT I:ASP121 2.2 57.4 1.0 CE1 C:HIS193 3.0 17.3 0.5 CD2 C:HIS193 3.0 19.4 0.5 C I:ASP121 3.5 55.5 1.0 OE1 C:GLU223 3.7 55.2 1.0 O C:HOH731 3.7 41.7 1.0 O I:ASP121 4.0 62.8 1.0 ND1 C:HIS193 4.1 16.9 0.5 CG C:HIS193 4.2 16.7 0.5 ND1 C:HIS193 4.5 15.7 0.5 O I:LEU120 4.6 35.8 1.0 CA I:ASP121 4.6 44.5 1.0 O1 C:PMF501 4.9 38.2 1.0 CD C:GLU223 4.9 51.1 1.0 C I:LEU120 5.0 31.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:23.6 occ:1.00 O2 C:FMT505 2.3 25.4 1.0 O C:ALA300 2.5 18.3 1.0 OD2 C:ASP323 2.6 16.1 1.0 OG1 C:THR302 2.6 14.9 1.0 O C:VAL321 2.7 16.7 1.0 O1 C:FMT505 2.8 33.6 1.0 C C:FMT505 3.0 34.5 1.0 CB C:THR302 3.4 14.7 1.0 CG C:ASP323 3.6 17.6 1.0 C C:ALA300 3.6 16.0 1.0 N C:THR302 3.7 14.7 1.0 O C:PRO298 3.8 39.7 1.0 O C:HOH757 3.8 42.8 1.0 O C:ALA295 3.9 15.4 1.0 C C:VAL321 3.9 16.6 1.0 OD1 C:ASP323 3.9 22.3 1.0 O C:ALA297 4.0 22.5 1.0 CA C:THR302 4.2 13.3 1.0 O C:HOH602 4.3 26.3 1.0 CA C:ALA300 4.4 17.5 1.0 CB C:ALA300 4.4 18.4 1.0 N C:ALA300 4.4 17.6 1.0 N C:LEU301 4.5 14.9 0.5 N C:LEU301 4.5 15.3 0.5 CA C:VAL321 4.6 18.9 1.0 C C:LEU301 4.6 14.7 0.5 CA C:LEU301 4.6 14.6 0.5 C C:LEU301 4.6 15.1 0.5 CA C:LEU301 4.6 15.3 0.5 C C:PRO298 4.6 33.3 1.0 CG2 C:THR302 4.6 14.9 1.0 CB C:VAL321 4.7 19.8 1.0 CB C:ASP323 4.8 15.2 1.0 N C:ASP323 4.9 14.2 1.0 N C:VAL322 4.9 14.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of Aspergillus Fumigatus Alkaline Protease within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:23.8 occ:1.00 O2 D:FMT503 2.4 31.1 1.0 OG1 D:THR302 2.5 17.6 1.0 O D:VAL321 2.5 19.0 1.0 OD2 D:ASP323 2.5 19.9 1.0 O D:ALA300 2.7 19.4 1.0 O1 D:FMT503 2.8 39.1 1.0 C D:FMT503 3.0 37.2 1.0 CB D:THR302 3.2 16.3 1.0 CG D:ASP323 3.5 21.0 1.0 N D:THR302 3.6 15.5 1.0 C D:VAL321 3.7 18.6 1.0 C D:ALA300 3.7 17.9 1.0 O D:HOH673 3.8 39.3 1.0 OD1 D:ASP323 3.8 24.1 1.0 O D:ALA295 3.8 17.5 1.0 CA D:THR302 4.1 15.5 1.0 O D:HOH603 4.1 43.8 1.0 O D:HOH630 4.3 31.7 1.0 O D:ALA297 4.3 19.9 1.0 CA D:VAL321 4.4 21.8 1.0 CB D:ALA300 4.4 18.2 1.0 CG2 D:THR302 4.4 17.4 1.0 CB D:VAL321 4.5 23.0 1.0 CA D:ALA300 4.5 17.7 1.0 C D:LEU301 4.5 15.3 0.5 C D:LEU301 4.5 15.2 0.5 CA D:LEU301 4.6 16.3 0.5 N D:LEU301 4.6 17.0 0.5 N D:LEU301 4.6 16.9 0.5 N D:ALA300 4.6 18.1 1.0 CA D:LEU301 4.7 16.6 0.5 N D:VAL322 4.7 16.6 1.0 CB D:ASP323 4.8 18.3 1.0 N D:ASP323 4.8 16.7 1.0 C D:VAL322 4.9 17.5 1.0 CA D:VAL322 4.9 18.5 1.0

O.N.Pattelli, D.D.L.Diec, W.Guo, S.Russi, D.Fernandez. Targeting Aspergillus Allergen Oryzin with A Chemical Probe at Atomic Precision. Sci Rep V. 13 17926 2023.
ISSN: ESSN 2045-2322
PubMed: 37864071
DOI: 10.1038/S41598-023-45028-Z