Sodium in PDB 3akr: Crystal Structure of Xylanase From Trichoderma Longibrachiatum

All present enzymatic activity of Crystal Structure of Xylanase From Trichoderma Longibrachiatum:
3.2.1.8;

The structure of Crystal Structure of Xylanase From Trichoderma Longibrachiatum, PDB code: 3akr was solved by M.Sugahara, N.Kunishima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.02 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.755, 38.904, 40.214, 90.00, 110.48, 90.00
R / Rfree (%)	18.2 / 18.4

The binding sites of Sodium atom in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum (pdb code 3akr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum, PDB code: 3akr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


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 Xylanase From Trichoderma Longibrachiatum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na192 b:21.1 occ:1.00 OE1 A:GLN125 2.4 21.4 1.0 O A:HOH273 2.4 20.2 1.0 O A:HOH309 2.4 14.4 1.0 O A:HOH370 2.4 30.2 1.0 O A:HOH395 2.5 18.9 1.0 O A:ASN124 2.5 14.3 1.0 CD A:GLN125 3.1 18.3 1.0 C A:ASN124 3.6 12.5 1.0 NE2 A:GLN125 3.7 20.8 1.0 O A:VAL123 3.8 12.2 1.0 O A:HOH373 4.0 24.2 1.0 CG A:GLN125 4.0 16.9 1.0 CA A:GLN125 4.1 12.4 1.0 N A:GLN125 4.3 11.7 1.0 ND2 A:ASN124 4.3 15.7 1.0 O A:HOH455 4.3 29.2 1.0 CB A:ASN124 4.4 13.3 1.0 O A:HOH416 4.6 29.7 1.0 CA A:ASN124 4.6 12.2 1.0 CB A:GLN125 4.7 13.3 1.0 C A:VAL123 4.9 11.4 1.0 CG A:ASN124 4.9 15.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


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 Xylanase From Trichoderma Longibrachiatum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na193 b:16.7 occ:1.00 O A:HOH224 2.2 25.4 1.0 OD1 A:ASN92 2.3 8.3 1.0 O A:HOH231 2.4 28.1 1.0 O A:HOH270 2.5 25.1 1.0 O A:PHE93 2.6 8.8 1.0 ND1 A:HIS144 2.6 13.9 1.0 CE1 A:HIS144 3.5 13.3 1.0 CG A:ASN92 3.5 6.3 1.0 CG A:HIS144 3.6 11.4 1.0 C A:PHE93 3.7 7.9 1.0 N A:PHE93 3.8 6.3 1.0 CB A:HIS144 3.9 10.4 1.0 ND2 A:ASN92 4.1 7.6 1.0 O A:HOH400 4.3 22.4 1.0 CA A:PHE93 4.4 7.0 1.0 O A:HOH406 4.6 27.4 1.0 NE2 A:HIS144 4.6 13.9 1.0 CB A:ASN92 4.7 6.2 1.0 C A:ASN92 4.7 5.6 1.0 N A:GLY94 4.7 8.1 1.0 CD2 A:HIS144 4.7 12.4 1.0 CA A:ASN92 4.8 5.6 1.0 CE2 A:TYR66 4.9 5.7 1.0 CA A:GLY94 4.9 9.8 1.0

M.Sugahara, Y.Kageyama-Morikawa, N.Kunishima. Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite As A Heteroepitaxic Nucleant Cryst.Growth Des. V. 11 110 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG100987G