Sodium in PDB 1bg4: Xylanase From Penicillium Simplicissimum

All present enzymatic activity of Xylanase From Penicillium Simplicissimum:
3.2.1.8;

The structure of Xylanase From Penicillium Simplicissimum, PDB code: 1bg4 was solved by A.Schmidt, C.Kratky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.020, 81.020, 113.400, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.9

The binding sites of Sodium atom in the Xylanase From Penicillium Simplicissimum (pdb code 1bg4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Xylanase From Penicillium Simplicissimum, PDB code: 1bg4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na619 b:14.6 occ:1.00 OG1 A:THR231 2.7 7.2 1.0 O A:LEU226 2.8 8.2 1.0 N A:THR231 3.0 6.8 1.0 O A:ALA227 3.1 10.0 1.0 N A:GLY230 3.3 9.5 1.0 NZ A:LYS261 3.4 7.7 1.0 C A:ALA227 3.5 9.4 1.0 CA A:ALA227 3.5 8.0 1.0 O A:THR231 3.6 7.8 1.0 CB A:THR231 3.6 5.4 1.0 CA A:THR231 3.7 7.0 1.0 C A:LEU226 3.8 7.7 1.0 CB A:ALA229 3.8 8.9 1.0 N A:ALA229 3.8 9.3 1.0 CD A:LYS261 3.9 4.2 1.0 C A:GLY230 3.9 7.7 1.0 C A:ALA229 4.0 9.2 1.0 CA A:GLY230 4.0 8.7 1.0 CG2 A:ILE234 4.0 3.8 1.0 C A:THR231 4.0 7.0 1.0 CA A:ALA229 4.1 7.9 1.0 N A:ALA227 4.1 8.2 1.0 CG2 A:THR231 4.2 4.6 1.0 CE A:LYS261 4.2 5.1 1.0 N A:SER228 4.4 9.0 1.0 CD1 A:ILE205 4.5 8.9 1.0 C A:SER228 4.7 10.3 1.0 CB A:ALA227 4.8 7.4 1.0 O A:GLU233 4.8 5.1 1.0 O A:GLY230 5.0 8.7 1.0 O A:ALA229 5.0 7.7 1.0

Sodium binding site 2 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na620 b:15.6 occ:1.00 O A:ASP165 2.7 7.5 1.0 O A:ALA168 2.7 8.1 1.0 NH1 A:ARG162 2.8 8.6 1.0 CA A:PRO166 3.5 12.2 1.0 CG A:LEU170 3.5 6.8 1.0 CD2 A:LEU170 3.6 7.4 1.0 C A:ASP165 3.6 9.2 1.0 CA A:ARG162 3.6 6.9 1.0 C A:PRO166 3.7 11.9 1.0 CD A:ARG162 3.7 8.6 1.0 O A:PRO166 3.7 12.0 1.0 CD1 A:LEU170 3.8 5.2 1.0 C A:ALA168 3.8 8.5 1.0 CZ A:ARG162 3.9 8.1 1.0 N A:PRO166 4.0 10.9 1.0 N A:ALA168 4.0 7.5 1.0 O A:ARG162 4.0 8.0 1.0 O A:ALA161 4.2 3.1 1.0 NE A:ARG162 4.3 9.0 1.0 CA A:ALA168 4.3 8.3 1.0 C A:ARG162 4.3 6.4 1.0 N A:ARG162 4.3 4.9 1.0 CB A:ARG162 4.4 8.3 1.0 N A:ASN167 4.4 10.6 1.0 O A:HOH445 4.5 33.8 1.0 CB A:ALA168 4.5 6.7 1.0 C A:ALA161 4.5 4.0 1.0 CG A:ARG162 4.6 8.8 1.0 OD2 A:ASP203 4.6 7.2 1.0 CB A:PRO166 4.8 11.7 1.0 C A:ASN167 4.8 9.6 1.0 O A:HOH565 4.9 33.6 1.0 CA A:ASP165 4.9 9.0 1.0 N A:LYS169 4.9 8.6 1.0 CB A:LEU170 5.0 5.4 1.0

Sodium binding site 3 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na621 b:14.6 occ:1.00 OG1 A:THR266 2.6 4.9 1.0 OH A:TYR17 2.7 7.0 1.0 O A:ILE236 2.8 5.8 1.0 CD A:ARG82 3.4 6.2 1.0 CE1 A:TYR17 3.5 6.1 1.0 CB A:THR266 3.5 5.9 1.0 CZ A:TYR17 3.5 7.5 1.0 CA A:THR237 3.6 6.4 1.0 N A:THR266 3.6 6.0 1.0 C A:ILE236 3.7 6.0 1.0 NE A:ARG82 3.8 5.7 1.0 CG2 A:THR237 3.9 6.8 1.0 CB A:ALA235 3.9 5.6 1.0 N A:THR237 4.0 6.5 1.0 C A:ILE265 4.0 5.9 1.0 CA A:THR266 4.1 6.7 1.0 O A:GLY264 4.2 5.9 1.0 CB A:THR237 4.3 5.6 1.0 CA A:ILE265 4.3 6.8 1.0 O A:HOH346 4.4 8.8 1.0 C A:GLY264 4.4 7.0 1.0 CZ A:ARG82 4.4 7.1 1.0 N A:ILE236 4.4 4.3 1.0 N A:ILE265 4.5 7.8 1.0 O A:THR237 4.5 8.0 1.0 C A:THR237 4.5 6.9 1.0 O A:HOH330 4.6 5.9 1.0 O A:ILE265 4.6 6.2 1.0 OE1 A:GLN43 4.7 8.8 1.0 C A:ALA235 4.7 5.3 1.0 NH1 A:ARG82 4.8 5.4 1.0 CG A:ARG82 4.8 5.9 1.0 CG2 A:THR266 4.8 8.2 1.0 CD1 A:TYR17 4.8 6.2 1.0 CA A:ILE236 4.8 5.3 1.0 CE2 A:TYR17 4.9 6.2 1.0 CA A:ALA235 4.9 5.0 1.0

Sodium binding site 4 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na622 b:15.6 occ:1.00 O A:HOH550 2.6 8.9 1.0 OG A:SER143 2.7 7.2 1.0 OH A:TYR153 2.8 4.6 1.0 CB A:SER143 3.4 10.1 1.0 CZ A:TYR153 3.6 5.2 1.0 CD2 A:PHE145 3.8 6.8 1.0 CG2 A:ILE133 3.8 7.1 1.0 CE1 A:TYR153 3.9 4.8 1.0 CB A:PHE145 4.2 7.9 1.0 O A:HOH323 4.2 10.5 1.0 CB A:ILE133 4.2 6.3 1.0 CG A:PHE145 4.4 8.1 1.0 CA A:ILE133 4.5 5.3 1.0 CE2 A:TYR153 4.6 4.9 1.0 N A:HIS89 4.7 5.6 1.0 CE2 A:PHE145 4.7 7.4 1.0 CB A:HIS89 4.8 7.3 1.0 CA A:SER143 4.8 9.9 1.0 CG1 A:VAL87 4.8 7.0 1.0 O A:ASN131 4.9 4.2 1.0

Sodium binding site 5 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na623 b:14.5 occ:1.00 O A:HOH561 2.4 42.0 1.0 O A:SER49 2.8 6.7 1.0 O A:THR63 2.9 7.1 1.0 O A:ALA54 3.2 6.6 1.0 N A:SER67 3.3 6.3 1.0 OG A:SER67 3.4 6.8 1.0 O A:HOH467 3.7 4.2 1.0 N A:GLY66 3.8 3.2 1.0 CB A:SER67 3.8 5.1 1.0 CA A:PHE64 3.8 6.7 1.0 C A:SER49 3.9 7.7 1.0 C A:THR63 3.9 6.9 1.0 C A:PHE64 4.0 6.5 1.0 C A:ALA54 4.0 5.2 1.0 CG2 A:THR55 4.1 3.4 1.0 CA A:GLY66 4.1 5.2 1.0 C A:GLY66 4.2 4.8 1.0 CA A:SER67 4.2 8.2 1.0 CB A:SER49 4.2 7.3 1.0 N A:SER65 4.3 6.2 1.0 CA A:SER49 4.3 5.5 1.0 O A:PHE64 4.3 6.0 1.0 N A:PHE64 4.3 6.8 1.0 CB A:ALA54 4.4 5.0 1.0 CA A:THR55 4.6 4.6 1.0 N A:THR55 4.6 2.9 1.0 C A:SER65 4.7 4.6 1.0 O3 A:GOL627 4.7 39.3 1.0 CA A:ALA54 4.8 5.4 1.0 OG1 A:THR63 4.9 5.4 1.0 CB A:THR55 5.0 3.6 1.0

Sodium binding site 6 out of 6 in the Xylanase From Penicillium Simplicissimum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Xylanase From Penicillium Simplicissimum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na624 b:13.8 occ:1.00 O A:HIS84 2.6 7.3 1.0 O A:PRO46 2.7 6.6 1.0 N A:MET50 3.1 6.4 1.0 C A:ASN48 3.2 5.3 1.0 CA A:ASN48 3.3 5.9 1.0 N A:ASN48 3.3 5.6 1.0 O A:ASN48 3.5 6.2 1.0 N A:SER49 3.5 6.8 1.0 C A:PRO46 3.5 5.9 1.0 CG A:PRO46 3.6 6.7 1.0 CG A:LYS51 3.6 3.0 1.0 N A:LYS51 3.7 4.1 1.0 C A:GLU47 3.7 5.6 1.0 CA A:MET50 3.7 6.9 1.0 C A:HIS84 3.8 5.8 1.0 CB A:MET50 3.8 7.6 1.0 CB A:PRO46 3.8 6.1 1.0 O A:GLU47 3.9 5.3 1.0 C A:MET50 4.0 6.3 1.0 CD2 A:HIS84 4.0 10.2 1.0 CE A:LYS51 4.0 5.4 1.0 C A:SER49 4.2 7.7 1.0 CD A:LYS51 4.2 4.2 1.0 CA A:PRO46 4.3 6.2 1.0 N A:GLU47 4.3 5.9 1.0 CA A:SER49 4.3 5.5 1.0 N A:THR85 4.5 8.2 1.0 CB A:HIS84 4.5 5.9 1.0 CA A:GLU47 4.5 5.2 1.0 CB A:LYS51 4.6 4.7 1.0 CG A:HIS84 4.6 9.1 1.0 CA A:LYS51 4.6 3.9 1.0 CA A:HIS84 4.7 5.8 1.0 CD A:PRO46 4.8 4.0 1.0 CB A:ASN48 4.8 6.4 1.0 CG A:MET50 4.8 8.2 1.0 N A:PRO46 4.9 6.3 1.0 OG A:SER49 4.9 6.9 1.0 O A:MET50 4.9 6.3 1.0

A.Schmidt, A.Schlacher, W.Steiner, H.Schwab, C.Kratky. Structure of the Xylanase From Penicillium Simplicissimum. Protein Sci. V. 7 2081 1998.
ISSN: ISSN 0961-8368
PubMed: 9792094