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Sodium in PDB 2vgd: Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose

Enzymatic activity of Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose

All present enzymatic activity of Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose, PDB code: 2vgd was solved by M.Vardakou, C.Dumon, J.E.Flint, J.W.Murray, P.Christakopoulos, D.P.Weiner, N.Juge, R.J.Lewis, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.66 / 1.8
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.470, 76.470, 102.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose (pdb code 2vgd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose, PDB code: 2vgd:

Sodium binding site 1 out of 1 in 2vgd

Go back to Sodium Binding Sites List in 2vgd
Sodium binding site 1 out of 1 in the Crystal Structure of Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose


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 Environmental Isolated GH11 in Complex with Xylobiose and Feruloyl-Arabino-Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1196

b:19.2
occ:1.00
 OD2 A:ASP115 2.7 13.6 1.0
NE2 A:HIS159 2.7 12.0 1.0
OH A:TYR119 3.0 12.2 1.0
CZ A:TYR119 3.3 13.3 1.0
CE2 A:TYR119 3.5 13.8 1.0
CD2 A:HIS159 3.7 11.4 1.0
CE1 A:HIS159 3.7 13.7 1.0
CG A:ASP115 3.7 15.2 1.0
CA A:ILE154 3.8 12.9 1.0
CG2 A:ILE154 3.8 12.3 1.0
OG A:SER114 3.9 15.3 1.0
CB A:SER114 3.9 14.0 1.0
CG1 A:ILE154 3.9 12.8 1.0
CB A:ASP115 3.9 15.2 1.0
O A:SER114 4.0 13.9 1.0
CB A:ILE154 4.0 13.0 1.0
O A:THR153 4.1 13.0 1.0
CG1 A:VAL92 4.1 10.1 1.0
N A:THR155 4.2 13.4 1.0
CE1 A:TYR119 4.2 11.5 1.0
C A:SER114 4.3 14.5 1.0
NH2 A:ARG149 4.5 12.6 1.0
C A:ILE154 4.5 12.9 1.0
CD2 A:TYR119 4.5 11.4 1.0
O A:HOH2174 4.5 10.9 1.0
CA A:SER114 4.8 14.9 1.0
N A:ASP115 4.8 14.8 1.0
OD1 A:ASP115 4.8 15.1 1.0
ND1 A:HIS159 4.8 11.1 1.0
N A:ILE154 4.8 12.6 1.0
CG A:HIS159 4.8 11.5 1.0
C A:THR153 4.9 13.3 1.0
OD1 A:ASP94 4.9 12.8 1.0
CA A:ASP115 5.0 15.4 1.0

Reference:

M.Vardakou, C.Dumon, J.W.Murray, P.Christakopoulos, D.P.Weiner, N.Juge, R.J.Lewis, H.J.Gilbert, J.E.Flint. Understanding the Structural Basis For Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases. J.Mol.Biol. V. 375 1293 2008.
ISSN: ISSN 0022-2836
PubMed: 18078955
DOI: 10.1016/J.JMB.2007.11.007
Page generated: Mon Oct 7 04:28:23 2024

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