Sodium in PDB 8b8e: Wild-Type GH11 From Blastobotrys Mokoenaii

All present enzymatic activity of Wild-Type GH11 From Blastobotrys Mokoenaii:
3.2.1.8;

The structure of Wild-Type GH11 From Blastobotrys Mokoenaii, PDB code: 8b8e was solved by T.Coleman, J.L.Ravn, J.Larsbrink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.11 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.039, 37.86, 142.609, 90, 104.27, 90
R / Rfree (%)	19.3 / 22.5

The binding sites of Sodium atom in the Wild-Type GH11 From Blastobotrys Mokoenaii (pdb code 8b8e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Wild-Type GH11 From Blastobotrys Mokoenaii, PDB code: 8b8e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Wild-Type GH11 From Blastobotrys Mokoenaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild-Type GH11 From Blastobotrys Mokoenaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:32.5 occ:1.00 H A:ASN109 2.2 27.7 1.0 OE2 A:GLU156 2.6 40.2 1.0 HB2 A:LEU111 2.9 23.8 1.0 N A:ASN109 3.1 23.1 1.0 HB A:THR108 3.1 27.3 1.0 OE1 A:GLU156 3.2 37.0 1.0 CD A:GLU156 3.3 35.2 1.0 HA A:THR108 3.3 25.9 1.0 H A:LEU111 3.4 23.7 1.0 HA A:ASN109 3.6 29.6 1.0 N A:LEU111 3.8 19.8 1.0 O A:HOH474 3.8 33.2 1.0 CB A:THR108 3.8 22.8 1.0 CB A:LEU111 3.8 19.9 1.0 CA A:THR108 3.9 21.6 1.0 CA A:ASN109 3.9 24.6 1.0 C A:THR108 3.9 21.5 1.0 HB2 A:ASN109 3.9 34.9 1.0 HD13 A:LEU111 3.9 23.6 1.0 HG22 A:THR108 4.0 26.2 1.0 HA A:LEU111 4.1 22.8 1.0 CA A:LEU111 4.1 19.0 1.0 HA A:PRO110 4.1 25.2 1.0 HB3 A:LEU111 4.3 23.8 1.0 C A:PRO110 4.4 19.8 1.0 CG2 A:THR108 4.4 21.9 1.0 CB A:ASN109 4.5 29.0 1.0 HD22 A:LEU111 4.6 24.9 1.0 CG A:GLU156 4.7 30.5 1.0 CD1 A:LEU111 4.7 19.6 1.0 CA A:PRO110 4.8 21.0 1.0 HG23 A:THR108 4.8 26.2 1.0 CG A:LEU111 4.8 19.1 1.0 HG3 A:GLU156 4.8 36.6 1.0 HD12 A:LEU111 5.0 23.6 1.0 OG1 A:THR108 5.0 21.4 1.0 O A:HOH497 5.0 41.2 1.0

Sodium binding site 2 out of 5 in the Wild-Type GH11 From Blastobotrys Mokoenaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild-Type GH11 From Blastobotrys Mokoenaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na311 b:31.6 occ:1.00 H B:PHE93 2.3 21.2 1.0 HA B:SER92 2.8 22.1 1.0 HG22 B:THR173 3.0 23.4 1.0 N B:PHE93 3.1 17.6 1.0 HB2 B:SER92 3.2 27.8 1.0 O B:PHE93 3.4 19.0 1.0 CA B:SER92 3.5 18.4 1.0 HD22 B:ASN94 3.5 30.0 0.5 CB B:SER92 3.7 23.1 1.0 C B:SER92 3.8 18.3 1.0 OD1 B:ASN94 3.8 23.8 0.5 HB3 B:SER92 3.8 27.8 1.0 OG1 B:THR173 3.8 22.6 1.0 CG2 B:THR173 3.9 19.5 1.0 C B:PHE93 4.0 19.1 1.0 ND2 B:ASN94 4.0 25.0 0.5 O B:HOH434 4.1 33.1 1.0 CA B:PHE93 4.1 17.5 1.0 HG23 B:THR173 4.1 23.4 1.0 CG B:ASN94 4.2 22.6 0.5 HB3 B:PHE93 4.2 17.4 1.0 CB B:THR173 4.3 20.4 1.0 HB B:THR173 4.3 24.5 1.0 HG1 B:THR173 4.3 27.2 1.0 O B:GLY91 4.6 17.4 1.0 HD21 B:ASN94 4.6 30.0 0.5 HG21 B:THR173 4.6 23.4 1.0 HB2 B:ASN94 4.6 25.3 0.5 CB B:PHE93 4.7 14.5 1.0 N B:SER92 4.7 17.5 1.0 HA B:PHE93 4.9 21.0 1.0 N B:ASN94 4.9 19.2 1.0

Sodium binding site 3 out of 5 in the Wild-Type GH11 From Blastobotrys Mokoenaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Wild-Type GH11 From Blastobotrys Mokoenaii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:45.8 occ:1.00 HB2 D:ALA187 3.7 22.1 1.0 HB3 D:ALA187 3.8 22.1 1.0 HE22 D:GLN188 4.1 21.6 1.0 NE2 D:GLN188 4.2 18.0 1.0 CB D:ALA187 4.2 18.4 1.0 HE21 D:GLN188 4.4 21.6 1.0 HD21 D:ASN184 4.5 23.4 0.9 CD D:GLN188 4.5 18.6 1.0 OE1 D:GLN188 4.6 18.8 1.0 ND2 D:ASN184 4.7 19.5 0.9 HG2 D:GLN188 4.7 19.7 1.0 HA D:ASN184 4.8 27.0 1.0 HB1 D:ALA187 4.8 22.1 1.0 HD22 D:ASN184 4.9 23.4 0.9 HA D:GLN188 4.9 19.7 1.0

Sodium binding site 4 out of 5 in the Wild-Type GH11 From Blastobotrys Mokoenaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Wild-Type GH11 From Blastobotrys Mokoenaii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:29.4 occ:1.00 O D:HOH446 2.6 31.5 1.0 HB3 D:ASN69 3.1 19.9 1.0 HD22 D:ASN69 3.1 20.6 1.0 HB2 D:ASN69 3.2 19.9 1.0 ND2 D:ASN69 3.5 17.1 1.0 CB D:ASN69 3.5 16.6 1.0 CG D:ASN69 3.7 17.3 1.0 HD21 D:ASN69 4.0 20.6 1.0 OD1 D:ASN69 4.6 19.5 1.0 O D:ASN69 4.7 17.3 1.0 HA2 D:GLY51 4.7 25.3 1.0 CA D:ASN69 4.9 16.3 1.0

Sodium binding site 5 out of 5 in the Wild-Type GH11 From Blastobotrys Mokoenaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Wild-Type GH11 From Blastobotrys Mokoenaii within 5.0Å range: probe atom residue distance (Å) B Occ E:Na306 b:39.8 occ:1.00 HG1 E:THR31 2.3 24.6 1.0 HG23 E:THR31 3.0 24.0 1.0 OG1 E:THR31 3.1 20.5 1.0 O E:TYR55 3.3 15.7 1.0 HG22 E:THR54 3.4 27.3 1.0 CG2 E:THR31 3.6 20.0 1.0 HG21 E:THR31 3.7 24.0 1.0 CB E:THR31 3.9 19.7 1.0 HA E:THR31 3.9 25.2 1.0 H E:TYR55 3.9 22.2 1.0 HA E:THR54 4.1 25.9 1.0 CG2 E:THR54 4.3 22.8 1.0 C E:TYR55 4.4 18.2 1.0 HD2 E:PRO32 4.4 22.1 1.0 HG21 E:THR54 4.4 27.3 1.0 CA E:THR31 4.4 21.0 1.0 N E:TYR55 4.4 18.5 1.0 HG22 E:THR31 4.5 24.0 1.0 HB E:THR31 4.7 23.6 1.0 HG23 E:THR54 4.8 27.3 1.0 OG1 E:THR56 4.8 20.8 1.0 HA E:THR56 4.8 22.1 1.0 O E:HOH489 4.8 34.0 1.0 CA E:THR54 4.9 21.6 1.0 H E:THR31 5.0 26.9 1.0

J.L.Ravn, A.S.Ristinmaa, T.Coleman, J.Larsbrink, C.Geijer. Yeasts Have Evolved Divergent Enzyme Strategies to Deconstruct and Metabolize Xylan. Microbiol Spectr 24523 2023.
ISSN: ISSN 2165-0497
PubMed: 37098941
DOI: 10.1128/SPECTRUM.00245-23