Sodium in PDB 5x6s: Acetyl Xylan Esterase From Aspergillus Awamori

All present enzymatic activity of Acetyl Xylan Esterase From Aspergillus Awamori:
3.1.1.72;

The structure of Acetyl Xylan Esterase From Aspergillus Awamori, PDB code: 5x6s was solved by D.Komiya, T.Koseki, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.08 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	174.151, 174.151, 50.708, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 18.5

The binding sites of Sodium atom in the Acetyl Xylan Esterase From Aspergillus Awamori (pdb code 5x6s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Acetyl Xylan Esterase From Aspergillus Awamori, PDB code: 5x6s:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Acetyl Xylan Esterase From Aspergillus Awamori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Acetyl Xylan Esterase From Aspergillus Awamori within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:30.9 occ:1.00 O B:HOH433 2.2 24.1 1.0 O A:HOH604 2.4 34.6 1.0 OD1 A:ASN30 2.4 22.9 1.0 O B:HOH588 2.5 36.2 1.0 O A:HOH488 2.5 34.5 1.0 CG A:ASN30 3.5 20.6 1.0 OD2 B:ASP12 3.6 35.8 1.0 O B:HOH454 3.7 32.5 1.0 O A:HOH520 3.9 33.2 1.0 O A:SER29 4.0 22.1 1.0 ND2 A:ASN30 4.0 23.0 1.0 O A:HOH503 4.1 37.2 1.0 O B:HOH615 4.2 32.5 1.0 OD1 B:ASN93 4.4 19.8 1.0 O A:GLY107 4.5 22.0 1.0 ND2 B:ASN93 4.6 16.0 1.0 CG B:ASP12 4.6 28.8 1.0 CB A:ASN30 4.6 20.4 1.0 CB B:ASP12 4.7 25.3 1.0 O B:HOH483 4.8 46.3 1.0 CA A:ASN30 4.9 20.0 1.0 OD1 B:ASN87 4.9 21.6 1.0 C A:SER29 4.9 22.1 1.0 CG B:ASN93 4.9 18.6 1.0

Sodium binding site 2 out of 4 in the Acetyl Xylan Esterase From Aspergillus Awamori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Acetyl Xylan Esterase From Aspergillus Awamori within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:29.1 occ:1.00 O A:HOH607 2.0 39.2 1.0 O B:HOH551 2.4 35.5 1.0 O B:GLU134 2.6 19.7 1.0 O A:GLU134 2.9 18.1 1.0 C B:GLU134 3.8 19.8 1.0 C A:GLU134 4.1 18.4 1.0 CB B:GLU134 4.5 18.6 1.0 CA B:GLU134 4.5 19.3 1.0 O B:HOH609 4.5 34.4 1.0 O B:HOH487 4.7 22.8 1.0 N B:LEU135 4.8 19.0 1.0 CA A:GLU134 4.8 17.6 1.0 O A:HOH452 4.8 21.3 1.0 CB A:GLU134 4.8 18.2 1.0 OG A:SER110 4.8 24.6 1.0 CA B:LEU135 4.9 17.8 1.0 O A:SER110 5.0 19.2 1.0 OG B:SER110 5.0 25.2 1.0

Sodium binding site 3 out of 4 in the Acetyl Xylan Esterase From Aspergillus Awamori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Acetyl Xylan Esterase From Aspergillus Awamori within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:28.8 occ:1.00 OH B:TYR66 2.7 14.6 1.0 O B:TYR48 2.8 14.7 1.0 OG B:SER51 2.8 14.8 1.0 O B:SER51 3.1 15.2 1.0 N B:ALA54 3.1 14.7 1.0 O B:HOH539 3.5 15.7 1.0 CA B:TYR48 3.5 16.3 1.0 C B:TYR48 3.5 16.4 1.0 N B:TYR53 3.6 15.6 1.0 CZ B:TYR66 3.6 14.1 1.0 CB B:ALA54 3.6 15.3 1.0 C B:SER51 3.7 16.2 1.0 CE2 B:TYR66 3.7 16.4 1.0 CA B:ALA54 4.0 15.8 1.0 CA B:TYR53 4.0 15.7 1.0 CD1 B:TYR48 4.0 15.7 1.0 C B:TYR53 4.0 15.0 1.0 CB B:SER51 4.0 16.7 1.0 O B:TYR47 4.0 14.8 1.0 CB B:TYR53 4.0 15.8 1.0 CA B:SER51 4.3 16.5 1.0 C B:PRO52 4.3 16.3 1.0 N B:SER51 4.4 18.8 1.0 CB B:TYR48 4.4 16.0 1.0 N B:PRO52 4.4 16.1 1.0 CG B:TYR48 4.5 18.2 1.0 N B:TYR48 4.6 15.1 1.0 C5 B:MES303 4.6 20.6 0.5 C6 B:MES303 4.7 20.4 0.5 C B:TYR47 4.7 15.3 1.0 CD2 B:TYR53 4.7 16.2 1.0 CA B:PRO52 4.8 16.4 1.0 CE1 B:TYR48 4.8 17.3 1.0 CE1 B:TYR66 4.8 15.7 1.0 N B:GLY49 4.8 16.0 1.0 CG B:TYR53 4.9 15.7 1.0

Sodium binding site 4 out of 4 in the Acetyl Xylan Esterase From Aspergillus Awamori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Acetyl Xylan Esterase From Aspergillus Awamori within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:30.6 occ:1.00 O B:HOH524 2.3 30.6 1.0 OD1 B:ASN30 2.3 21.2 1.0 O A:HOH445 2.4 26.0 1.0 O A:HOH627 2.5 27.1 1.0 O B:HOH575 2.5 31.4 1.0 O A:HOH570 2.6 28.6 1.0 CG B:ASN30 3.5 20.5 1.0 OD2 A:ASP12 3.9 35.3 1.0 O B:HOH425 4.0 35.2 1.0 O B:SER29 4.1 22.2 1.0 ND2 B:ASN30 4.1 21.3 1.0 O A:HOH573 4.2 39.2 1.0 O B:GLY107 4.3 19.0 1.0 CB B:ASN30 4.6 20.2 1.0 OD1 A:ASN93 4.6 17.5 1.0 ND2 A:ASN93 4.6 12.3 1.0 O A:HOH641 4.7 34.5 1.0 OD1 A:ASN87 4.7 21.7 1.0 CA B:ASN30 4.8 18.6 1.0 CG A:ASP12 4.8 28.9 1.0 O A:HOH578 4.8 18.1 1.0 O A:HOH636 4.9 40.5 1.0 C B:SER29 4.9 21.8 1.0 CB A:ASP12 5.0 23.6 1.0 CG A:ASN87 5.0 19.2 1.0 O A:HOH566 5.0 33.2 1.0

D.Komiya, A.Hori, T.Ishida, K.Igarashi, M.Samejima, T.Koseki, S.Fushinobu. Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase From Aspergillus Luchuensis Appl. Environ. Microbiol. V. 83 2017.
ISSN: ESSN 1098-5336
PubMed: 28802264
DOI: 10.1128/AEM.01251-17