Calcium in PDB 1w2v: The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus

All present enzymatic activity of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus:
3.2.1.8;

The structure of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w2v was solved by S.Andrews, E.J.Taylor, G.N.Pell, F.Vincent, V.M.A.Ducros, G.J.Davies, J.H.Lakey, H.J.Glbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.609, 95.609, 150.315, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.6

The binding sites of Calcium atom in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus (pdb code 1w2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w2v:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1347 b:15.2 occ:0.50 CA A:CA1347 0.0 15.2 0.5 CA A:CA1347 0.6 19.8 0.5 OD1 A:ASP256 1.8 22.0 0.5 OE1 A:GLU262 2.1 23.7 0.5 O A:ASN253 2.1 15.8 0.5 OD2 A:ASP256 2.3 21.2 0.5 O A:ASN258 2.4 17.1 0.5 CG A:ASP256 2.4 21.8 0.5 OD1 A:ASN261 2.4 19.3 0.5 O A:HOH2266 2.4 22.5 1.0 OD2 A:ASP256 2.4 18.8 0.5 O A:ASN258 2.5 20.3 0.5 O A:ASN253 2.6 19.5 0.5 OE1 A:GLU262 2.7 15.0 0.5 OD1 A:ASP256 2.7 19.1 0.5 O A:HOH2265 2.8 21.7 1.0 CD A:GLU262 2.9 22.3 0.5 CG A:ASP256 2.9 19.0 0.5 OD1 A:ASN261 3.0 19.3 0.5 OE2 A:GLU262 3.1 23.7 0.5 C A:ASN253 3.3 15.2 0.5 C A:ASN258 3.5 19.4 0.5 CG A:ASN261 3.5 20.6 0.5 C A:ASN258 3.5 16.9 0.5 C A:ASN253 3.8 19.6 0.5 CD A:GLU262 3.8 17.8 0.5 CB A:ASP256 3.8 21.9 0.5 CG A:ASN261 3.9 20.5 0.5 ND2 A:ASN261 3.9 20.3 0.5 ND2 A:ASN261 4.0 21.3 0.5 N A:ASN258 4.0 19.9 0.5 CA A:ASN258 4.1 19.8 0.5 CG A:GLU262 4.2 21.3 0.5 O A:HOH2267 4.2 30.1 1.0 N A:ASP256 4.2 22.1 0.5 OE2 A:GLU262 4.2 19.7 0.5 N A:PRO254 4.2 15.2 0.5 CA A:PRO254 4.3 15.8 0.5 CB A:ASN258 4.3 19.3 0.5 CA A:ASN253 4.3 14.5 0.5 N A:SER259 4.3 16.7 0.5 CA A:ASN258 4.3 17.4 0.5 CA A:SER259 4.4 16.9 0.5 CB A:ASP256 4.4 18.6 0.5 N A:SER259 4.4 19.6 0.5 CB A:ASN253 4.4 14.8 0.5 N A:ASN258 4.4 18.0 0.5 CA A:ASP256 4.4 21.9 0.5 N A:ASN253 4.5 14.2 0.5 CB A:ASN258 4.5 17.8 0.5 CA A:ASN253 4.7 18.6 0.5 CA A:SER259 4.7 19.6 0.5 O A:HOH2256 4.7 16.8 0.5 N A:PRO254 4.7 20.2 0.5 CA A:PRO254 4.7 20.8 0.5 C A:ASP256 4.7 21.6 0.5 N A:ASP256 4.7 19.3 0.5 C A:PRO254 4.7 16.8 0.5 C A:ASN261 4.7 19.8 0.5 N A:ASN261 4.7 20.0 0.5 N A:ASN253 4.8 18.2 0.5 CB A:ASN261 4.8 20.1 0.5 CB A:ASN253 4.8 18.8 0.5 C A:PRO254 4.8 21.0 0.5 N A:TYR255 4.8 21.5 0.5 N A:GLY257 4.8 21.2 0.5 O A:ASN261 4.9 20.1 0.5 N A:GLU262 4.9 19.3 0.5 C A:SER259 5.0 17.7 0.5 CG A:ASN253 5.0 15.9 0.5 CA A:ASN261 5.0 19.9 0.5 O A:HOH2257 5.0 34.0 1.0 CG A:GLU262 5.0 18.4 0.5

Calcium binding site 2 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1347 b:19.8 occ:0.50 CA A:CA1347 0.0 19.8 0.5 CA A:CA1347 0.6 15.2 0.5 OE1 A:GLU262 1.7 23.7 0.5 OD1 A:ASN261 2.1 19.3 0.5 OE1 A:GLU262 2.1 15.0 0.5 CD A:GLU262 2.3 22.3 0.5 O A:ASN253 2.3 15.8 0.5 O A:ASN258 2.4 20.3 0.5 O A:HOH2265 2.4 21.7 1.0 OD1 A:ASP256 2.4 22.0 0.5 O A:ASN258 2.5 17.1 0.5 OE2 A:GLU262 2.5 23.7 0.5 OD1 A:ASN261 2.5 19.3 0.5 O A:HOH2266 2.6 22.5 1.0 OD2 A:ASP256 2.7 21.2 0.5 O A:ASN253 2.8 19.5 0.5 CG A:ASP256 2.9 21.8 0.5 OD2 A:ASP256 3.0 18.8 0.5 OD1 A:ASP256 3.1 19.1 0.5 CD A:GLU262 3.2 17.8 0.5 CG A:ASN261 3.3 20.6 0.5 C A:ASN253 3.5 15.2 0.5 CG A:ASP256 3.5 19.0 0.5 C A:ASN258 3.5 19.4 0.5 CG A:ASN261 3.5 20.5 0.5 CG A:GLU262 3.6 21.3 0.5 OE2 A:GLU262 3.6 19.7 0.5 C A:ASN258 3.7 16.9 0.5 ND2 A:ASN261 3.9 21.3 0.5 C A:ASN253 3.9 19.6 0.5 ND2 A:ASN261 3.9 20.3 0.5 O A:HOH2267 4.0 30.1 1.0 C A:ASN261 4.2 19.8 0.5 CA A:SER259 4.3 16.9 0.5 N A:ASN253 4.3 14.2 0.5 O A:ASN261 4.3 20.1 0.5 N A:GLU262 4.3 19.3 0.5 CA A:ASN253 4.4 14.5 0.5 N A:PRO254 4.4 15.2 0.5 CA A:ASN258 4.4 19.8 0.5 N A:ASN261 4.4 20.0 0.5 CB A:ASP256 4.4 21.9 0.5 N A:SER259 4.4 19.6 0.5 CA A:PRO254 4.4 15.8 0.5 CG A:GLU262 4.4 18.4 0.5 N A:ASN258 4.4 19.9 0.5 N A:SER259 4.4 16.7 0.5 CA A:SER259 4.5 19.6 0.5 CB A:ASN258 4.5 19.3 0.5 CB A:ASN261 4.5 20.1 0.5 CA A:ASN261 4.6 19.9 0.5 CB A:ASN253 4.6 14.8 0.5 N A:ASN253 4.6 18.2 0.5 CB A:GLU262 4.7 19.1 0.5 CA A:ASN258 4.7 17.4 0.5 CA A:ASN253 4.7 18.6 0.5 C A:SER259 4.7 17.7 0.5 CA A:GLU262 4.8 18.9 0.5 N A:PRO254 4.8 20.2 0.5 N A:ASP256 4.8 22.1 0.5 CA A:PRO254 4.8 20.8 0.5 CB A:ASN258 4.9 17.8 0.5 CB A:ASN261 4.9 20.2 0.5 N A:ASN258 4.9 18.0 0.5 CB A:ASN253 5.0 18.8 0.5 CB A:ASP256 5.0 18.6 0.5 N A:SER260 5.0 19.0 0.5

Calcium binding site 3 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1347 b:14.1 occ:1.00 OE1 B:GLU262 2.1 20.0 0.5 OD1 B:ASN261 2.3 15.8 0.5 OE2 B:GLU262 2.3 20.4 0.5 OD1 B:ASP256 2.4 16.3 1.0 O B:ASN258 2.4 15.4 1.0 O B:HOH2280 2.4 11.7 0.5 O B:ASN253 2.4 14.1 1.0 O B:HOH2282 2.7 23.2 1.0 OD2 B:ASP256 2.7 18.9 1.0 O B:HOH2267 2.7 17.7 0.5 CG B:ASP256 2.9 16.3 1.0 CD B:GLU262 3.0 19.4 0.5 OD1 B:ASN261 3.1 26.6 0.5 OE2 B:GLU262 3.3 20.9 0.5 CG B:ASN261 3.4 18.7 0.5 C B:ASN258 3.5 14.7 1.0 CD B:GLU262 3.5 21.2 0.5 C B:ASN253 3.6 13.9 1.0 ND2 B:ASN261 3.9 19.4 0.5 CG B:ASN261 3.9 24.6 0.5 ND2 B:ASN261 4.1 28.8 0.5 OE1 B:GLU262 4.3 23.6 0.5 N B:ASN258 4.3 13.8 1.0 CA B:ASN258 4.3 14.4 1.0 CB B:ASP256 4.4 15.1 1.0 N B:SER259 4.4 14.7 1.0 CG B:GLU262 4.4 19.5 0.5 CA B:SER259 4.4 15.3 1.0 N B:PRO254 4.4 14.1 0.5 CA B:ASN253 4.4 13.4 1.0 N B:PRO254 4.4 14.0 0.5 CG B:GLU262 4.5 21.1 0.5 CA B:PRO254 4.5 15.0 0.5 CA B:PRO254 4.5 14.9 0.5 N B:ASN253 4.5 13.3 1.0 CB B:ASN258 4.5 14.7 1.0 CB B:ASN253 4.6 14.2 1.0 N B:ASP256 4.7 14.6 1.0 CB B:ASN261 4.8 17.9 0.5 C B:PRO254 4.8 14.8 0.5 C B:ASN261 4.8 17.1 0.5 N B:ASN261 4.8 17.4 0.5 O B:HOH2266 4.9 17.2 0.5 N B:GLU262 4.9 16.6 0.5 CA B:ASN261 5.0 17.7 0.5 C B:PRO254 5.0 14.7 0.5 CA B:ASP256 5.0 15.2 1.0

S.Andrews, E.J.Taylor, G.N.Pell, F.Vincent, V.M.A.Ducros, G.J.Davies, J.H.Lakey, H.J.Gilbert. The Use of Forced Protein Evolution to Investigate and Improve Stability of Family 10 Xylanases: the Production of CA2+-Independent Stable Xylanases J.Biol.Chem. V. 279 54369 2004.
ISSN: ISSN 0021-9258
PubMed: 15452124
DOI: 10.1074/JBC.M409044200