Calcium in PDB 1w2p: The 3-Dimensional Structure of A Xylanase (XYN10A) From Cellvibrio Japonicus

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

The structure of The 3-Dimensional Structure of A Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w2p was solved by E.J.Taylor, F.Vincent, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.653, 95.653, 150.205, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.2

The binding sites of Calcium atom in the The 3-Dimensional Structure of A Xylanase (XYN10A) From Cellvibrio Japonicus (pdb code 1w2p). 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 Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w2p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The 3-Dimensional Structure 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 Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1348 b:9.8 occ:0.50 CA A:CA1348 0.0 9.8 0.5 CA A:CA1348 0.4 11.2 0.5 OD1 A:ASP256 2.0 15.1 0.5 O A:ASN253 2.3 7.3 0.5 OD2 A:ASP256 2.3 13.9 0.5 O A:ASN258 2.4 11.8 0.5 OD1 A:ASN261 2.4 11.3 0.5 OD2 A:ASP256 2.4 10.1 0.5 OD1 A:ASP262 2.4 9.1 0.5 O A:ASN258 2.4 13.8 0.5 O A:ASN253 2.5 14.9 0.5 CG A:ASP256 2.5 14.3 0.5 O A:HOH2352 2.5 13.2 1.0 OD1 A:ASP256 2.5 11.0 0.5 OD1 A:ASN261 2.7 12.6 0.5 O A:HOH2353 2.7 12.5 1.0 OD1 A:ASP262 2.8 14.3 0.5 CG A:ASP256 2.8 10.1 0.5 CG A:ASN261 3.4 9.9 0.5 CG A:ASP262 3.4 10.3 0.5 C A:ASN253 3.5 7.5 0.5 C A:ASN258 3.5 11.4 0.5 C A:ASN258 3.5 13.1 0.5 CG A:ASN261 3.7 14.2 0.5 C A:ASN253 3.7 15.3 0.5 OD2 A:ASP262 3.7 11.5 0.5 ND2 A:ASN261 3.9 10.7 0.5 CG A:ASP262 3.9 14.2 0.5 ND2 A:ASN261 3.9 14.0 0.5 CB A:ASP256 4.0 14.6 0.5 OD2 A:ASP262 4.1 13.3 0.5 N A:ASN258 4.2 13.0 0.5 CA A:ASN258 4.2 12.9 0.5 CB A:ASN258 4.3 12.3 0.5 CB A:ASN258 4.3 11.6 0.5 CA A:ASN258 4.3 11.6 0.5 CB A:ASP256 4.3 10.7 0.5 CA A:ASN253 4.4 7.3 0.5 N A:PRO254 4.4 8.4 0.5 CA A:PRO254 4.4 8.6 0.5 O A:ASN261 4.4 9.7 0.5 C A:ASN261 4.4 9.9 0.5 N A:ASN258 4.4 12.1 0.5 N A:ASN253 4.4 6.5 0.5 N A:ASP256 4.4 15.4 0.5 CB A:ASN253 4.5 7.7 0.5 N A:SER259 4.6 12.1 0.5 CA A:ASN253 4.6 15.2 0.5 N A:SER259 4.6 13.9 0.5 N A:PRO254 4.6 15.6 0.5 N A:ASP262 4.6 10.1 0.5 CA A:PRO254 4.6 15.9 0.5 N A:ASN253 4.7 14.5 0.5 CB A:ASN253 4.7 15.5 0.5 CA A:ASP256 4.7 14.6 0.5 CA A:SER259 4.7 11.8 0.5 CB A:ASN261 4.7 10.5 0.5 O A:HOH2351 4.7 14.1 0.5 CB A:ASP262 4.8 9.4 0.5 CA A:SER259 4.8 14.4 0.5 N A:ASN261 4.8 11.1 0.5 N A:ASP256 4.9 10.7 0.5 C A:PRO254 4.9 9.3 0.5 CA A:ASN261 4.9 10.3 0.5 N A:TYR255 4.9 16.4 0.5 O A:HOH2340 4.9 20.9 1.0 CA A:ASP262 5.0 9.6 0.5 CG A:ASN258 5.0 12.2 0.5 C A:ASP256 5.0 14.1 0.5

Calcium binding site 2 out of 3 in the The 3-Dimensional Structure 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 Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1348 b:11.2 occ:0.50 CA A:CA1348 0.0 11.2 0.5 CA A:CA1348 0.4 9.8 0.5 OD1 A:ASP262 2.0 9.1 0.5 OD1 A:ASN261 2.3 11.3 0.5 O A:ASN253 2.4 7.3 0.5 OD1 A:ASP262 2.4 14.3 0.5 OD1 A:ASP256 2.5 15.1 0.5 O A:ASN258 2.5 13.8 0.5 O A:ASN258 2.5 11.8 0.5 O A:HOH2353 2.5 12.5 1.0 O A:HOH2352 2.5 13.2 1.0 OD1 A:ASN261 2.5 12.6 0.5 O A:ASN253 2.6 14.9 0.5 OD2 A:ASP256 2.6 13.9 0.5 OD2 A:ASP256 2.8 10.1 0.5 OD1 A:ASP256 2.9 11.0 0.5 CG A:ASP256 2.9 14.3 0.5 CG A:ASP262 3.1 10.3 0.5 CG A:ASP256 3.2 10.1 0.5 CG A:ASN261 3.4 9.9 0.5 OD2 A:ASP262 3.4 11.5 0.5 CG A:ASP262 3.5 14.2 0.5 C A:ASN253 3.5 7.5 0.5 CG A:ASN261 3.6 14.2 0.5 C A:ASN258 3.6 13.1 0.5 C A:ASN258 3.7 11.4 0.5 C A:ASN253 3.7 15.3 0.5 OD2 A:ASP262 3.8 13.3 0.5 ND2 A:ASN261 4.0 10.7 0.5 ND2 A:ASN261 4.0 14.0 0.5 O A:ASN261 4.1 9.7 0.5 C A:ASN261 4.1 9.9 0.5 N A:ASP262 4.3 10.1 0.5 N A:ASN253 4.3 6.5 0.5 CB A:ASP262 4.4 9.4 0.5 CA A:ASN253 4.4 7.3 0.5 N A:PRO254 4.4 8.4 0.5 CB A:ASP256 4.4 14.6 0.5 CA A:ASN258 4.4 12.9 0.5 CA A:PRO254 4.4 8.6 0.5 CB A:ASN258 4.5 12.3 0.5 N A:ASN258 4.5 13.0 0.5 CB A:ASN258 4.5 11.6 0.5 CA A:ASN258 4.5 11.6 0.5 N A:ASN253 4.6 14.5 0.5 CA A:ASP262 4.6 9.6 0.5 CA A:ASN253 4.6 15.2 0.5 CB A:ASN253 4.6 7.7 0.5 N A:SER259 4.6 13.9 0.5 N A:PRO254 4.6 15.6 0.5 N A:SER259 4.6 12.1 0.5 CA A:SER259 4.6 11.8 0.5 CB A:ASN261 4.6 10.5 0.5 CA A:PRO254 4.6 15.9 0.5 N A:ASN261 4.7 11.1 0.5 CA A:SER259 4.7 14.4 0.5 C A:ASN261 4.7 14.6 0.5 N A:ASP262 4.7 14.3 0.5 CB A:ASP256 4.7 10.7 0.5 CA A:ASN261 4.7 10.3 0.5 O A:HOH2351 4.7 14.1 0.5 N A:ASN258 4.7 12.1 0.5 CB A:ASN253 4.8 15.5 0.5 CB A:ASP262 4.8 13.8 0.5 N A:ASP256 4.8 15.4 0.5 CB A:ASN261 4.9 14.4 0.5 O A:ASN261 4.9 15.8 0.5 CA A:ASP262 5.0 13.6 0.5 N A:ASN261 5.0 14.4 0.5

Calcium binding site 3 out of 3 in the The 3-Dimensional Structure 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 Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1348 b:9.2 occ:1.00 OD1 B:ASP262 2.4 10.2 1.0 O B:ASN253 2.4 9.5 1.0 O B:ASN258 2.4 11.6 1.0 OD1 B:ASN261 2.4 10.9 1.0 OD1 B:ASP256 2.5 9.5 1.0 O B:HOH2351 2.5 6.6 0.5 O B:HOH2349 2.5 16.8 0.5 O B:HOH2350 2.6 10.8 1.0 OD2 B:ASP256 2.6 10.8 1.0 CG B:ASP256 2.9 9.7 1.0 CG B:ASP262 3.4 11.4 1.0 CG B:ASN261 3.5 11.5 1.0 C B:ASN253 3.6 9.5 1.0 C B:ASN258 3.6 10.5 1.0 OD2 B:ASP262 3.8 9.7 1.0 ND2 B:ASN261 3.9 15.2 1.0 CB B:ASP256 4.4 9.1 1.0 CA B:ASN258 4.4 10.4 1.0 CA B:ASN253 4.4 9.7 1.0 CB B:ASN258 4.4 10.7 1.0 N B:ASN258 4.4 10.3 1.0 N B:ASN253 4.5 9.9 1.0 N B:PRO254 4.5 10.5 0.5 N B:PRO254 4.5 9.7 0.5 CA B:PRO254 4.5 9.9 0.5 C B:ASN261 4.5 10.9 1.0 O B:ASN261 4.5 14.4 1.0 CA B:PRO254 4.5 10.8 0.5 N B:SER259 4.6 10.9 1.0 CB B:ASN253 4.6 10.3 1.0 N B:ASP262 4.6 10.5 1.0 CA B:SER259 4.7 11.7 1.0 O B:HOH2348 4.7 15.0 0.5 CB B:ASP262 4.7 10.3 1.0 CB B:ASN261 4.8 11.3 1.0 N B:ASP256 4.9 9.6 1.0 N B:ASN261 4.9 12.0 1.0 C B:PRO254 4.9 11.0 0.5 CA B:ASP262 4.9 10.3 1.0 O B:HOH2332 5.0 21.7 0.5 CA B:ASN261 5.0 11.7 1.0

S.Andrews, E.J.Taylor, G.Pell, F.Vincent, V.Ducros, G.J.Davies, J.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