Sodium in PDB 1us3: Native XYLANASE10C From Cellvibrio Japonicus

All present enzymatic activity of Native XYLANASE10C From Cellvibrio Japonicus:
3.2.1.8;

The structure of Native XYLANASE10C From Cellvibrio Japonicus, PDB code: 1us3 was solved by G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.175, 78.789, 172.244, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.5

The binding sites of Sodium atom in the Native XYLANASE10C From Cellvibrio Japonicus (pdb code 1us3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Native XYLANASE10C From Cellvibrio Japonicus, PDB code: 1us3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Native XYLANASE10C From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native XYLANASE10C From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1609 b:28.7 occ:1.00 O A:ALA423 2.4 11.8 1.0 O A:HOH2370 2.4 33.1 0.5 OD1 A:ASP369 2.4 13.1 0.5 O A:HOH2132 2.5 30.6 0.5 O A:HOH2449 2.6 42.8 1.0 OE2 A:GLU372 2.7 14.7 0.5 O A:HOH2374 2.8 46.6 1.0 OD1 A:ASP369 2.9 12.9 0.5 CG A:ASP369 3.4 10.6 0.5 C A:ALA423 3.5 11.4 1.0 O A:HOH2371 3.6 33.3 1.0 CD A:GLU372 3.7 14.8 0.5 O A:HOH2368 3.9 31.6 1.0 CG A:ASP369 3.9 10.9 0.5 OE1 A:GLU372 3.9 19.6 0.5 OD2 A:ASP369 4.0 10.6 0.5 O A:HOH2365 4.0 22.9 0.5 CA A:ALA423 4.1 11.3 1.0 CB A:ASP369 4.3 9.5 0.5 CB A:ASP369 4.5 9.4 0.5 CA A:ASP369 4.5 9.6 1.0 N A:ASP424 4.6 9.7 1.0 O A:ALA422 4.7 12.9 1.0 CB A:ALA423 4.8 10.6 1.0 CA A:ASP424 4.9 10.8 1.0 OD2 A:ASP369 4.9 13.9 0.5 O A:HOH2367 4.9 20.1 0.5

Sodium binding site 2 out of 2 in the Native XYLANASE10C From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native XYLANASE10C From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1610 b:49.2 occ:1.00 O A:HOH2316 2.3 39.8 1.0 O A:HOH2046 2.3 29.3 0.5 O A:HOH2045 2.4 34.8 1.0 O A:ASN290 3.0 8.3 1.0 OG1 A:THR328 3.8 10.1 1.0 CG A:ASN290 3.8 11.2 1.0 CB A:ASN290 3.9 9.1 1.0 O A:HOH2319 3.9 18.6 1.0 C A:ASN290 4.0 8.6 1.0 CG2 A:THR328 4.0 10.6 1.0 OD1 A:ASN290 4.1 10.6 1.0 O A:HOH2124 4.1 29.3 0.5 ND2 A:ASN290 4.2 11.4 1.0 N A:THR328 4.3 10.9 1.0 O A:HOH2315 4.4 25.1 0.5 O A:ASN326 4.4 14.5 1.0 CB A:THR328 4.5 10.5 1.0 CA A:ASN290 4.6 9.2 1.0 CA A:MET327 4.9 13.4 1.0 O A:HOH2123 4.9 42.1 1.0

G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, H.J.Gilbert. Structural and Biochemical Analysis of Cellvibrio Japonicus Xylanase 10C: How Variation in Substrate-Binding Cleft Influences the Catalytic Profile of Family Gh-10 Xylanases J.Biol.Chem. V. 279 11777 2004.
ISSN: ISSN 0021-9258
PubMed: 14670951
DOI: 10.1074/JBC.M311947200