Calcium in PDB 1clx: Catalytic Core of Xylanase A

All present enzymatic activity of Catalytic Core of Xylanase A:
3.2.1.8;

The structure of Catalytic Core of Xylanase A, PDB code: 1clx was solved by G.W.Harris, J.A.Jenkins, I.Connerton, R.W.Pickersgill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.110, 97.320, 151.030, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Calcium atom in the Catalytic Core of Xylanase A (pdb code 1clx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Catalytic Core of Xylanase A, PDB code: 1clx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Catalytic Core of Xylanase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Core of Xylanase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca348 b:16.5 occ:1.18 OD1 A:ASN261 2.3 11.1 1.0 O A:ASN258 2.3 17.0 1.0 OD1 A:ASP262 2.4 9.6 1.0 O A:ASN253 2.4 16.7 1.0 OD1 A:ASP256 2.5 10.7 1.0 O A:HOH349 2.5 9.2 1.0 OD2 A:ASP256 2.7 10.3 1.0 CG A:ASP256 3.0 16.6 1.0 CG A:ASP262 3.4 16.6 1.0 CG A:ASN261 3.5 15.0 1.0 C A:ASN258 3.5 16.2 1.0 C A:ASN253 3.6 16.7 1.0 OD2 A:ASP262 3.7 13.5 1.0 ND2 A:ASN261 3.8 16.3 1.0 CA A:ASN253 4.4 11.2 1.0 CA A:ASN258 4.4 10.8 1.0 N A:SER259 4.4 21.2 1.0 CB A:ASN258 4.4 7.3 1.0 N A:ASN253 4.4 11.5 1.0 CB A:ASP256 4.5 6.8 1.0 N A:ASN258 4.5 9.3 1.0 N A:PRO254 4.5 7.7 1.0 CA A:PRO254 4.5 18.7 1.0 CA A:SER259 4.5 10.3 1.0 CB A:ASN253 4.5 8.8 1.0 N A:ASP262 4.6 10.3 1.0 C A:ASN261 4.7 14.8 1.0 O B:HOH740 4.7 13.8 1.0 CB A:ASP262 4.7 6.8 1.0 CB A:ASN261 4.8 15.2 1.0 CA A:ASP262 4.8 7.3 1.0 O A:ASN261 4.9 21.1 1.0 N A:ASP256 4.9 12.9 1.0 N A:ASN261 4.9 8.4 1.0

Calcium binding site 2 out of 4 in the Catalytic Core of Xylanase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Core of Xylanase A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca348 b:16.3 occ:1.09 OD1 B:ASP262 2.3 14.8 1.0 OD1 B:ASN261 2.4 19.3 1.0 O B:ASN253 2.4 13.6 1.0 OD1 B:ASP256 2.6 13.7 1.0 O B:ASN258 2.6 20.8 1.0 O B:HOH626 2.7 17.3 1.0 OD2 B:ASP256 2.8 15.6 1.0 CG B:ASP256 3.1 14.8 1.0 CG B:ASP262 3.4 23.3 1.0 CG B:ASN261 3.5 21.7 1.0 C B:ASN253 3.6 5.5 1.0 OD2 B:ASP262 3.6 24.2 1.0 C B:ASN258 3.7 21.2 1.0 ND2 B:ASN261 3.8 21.3 1.0 CA B:PRO254 4.3 18.3 1.0 CA B:ASN253 4.3 15.6 1.0 N B:ASN253 4.4 9.5 1.0 N B:PRO254 4.5 10.8 1.0 CB B:ASN253 4.5 22.6 1.0 CA B:ASN258 4.5 15.6 1.0 N B:ASP262 4.5 15.1 1.0 CB B:ASN258 4.5 10.3 1.0 N B:ASN258 4.5 14.6 1.0 CB B:ASP256 4.5 28.4 1.0 O A:HOH463 4.6 15.4 1.0 C B:ASN261 4.6 21.9 1.0 N B:SER259 4.6 14.4 1.0 CB B:ASP262 4.7 15.9 1.0 CA B:SER259 4.7 26.1 1.0 N B:ASP256 4.8 14.1 1.0 CA B:ASP262 4.8 19.8 1.0 CB B:ASN261 4.8 17.0 1.0 O B:ASN261 4.9 25.7 1.0 C B:PRO254 5.0 19.4 1.0

Calcium binding site 3 out of 4 in the Catalytic Core of Xylanase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Core of Xylanase A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca348 b:19.8 occ:1.10 OD1 C:ASP262 2.3 13.9 1.0 O C:ASN253 2.4 11.1 1.0 OD1 C:ASN261 2.5 20.7 1.0 O C:ASN258 2.5 19.8 1.0 OD1 C:ASP256 2.6 22.0 1.0 O C:HOH903 2.6 16.1 1.0 OD2 C:ASP256 2.6 22.8 1.0 CG C:ASP256 3.0 21.2 1.0 CG C:ASP262 3.3 19.6 1.0 C C:ASN253 3.5 31.3 1.0 OD2 C:ASP262 3.6 20.0 1.0 CG C:ASN261 3.6 26.7 1.0 C C:ASN258 3.6 21.3 1.0 ND2 C:ASN261 4.1 34.7 1.0 CA C:ASN253 4.3 23.0 1.0 N C:ASN253 4.3 15.4 1.0 CA C:PRO254 4.4 14.0 1.0 CB C:ASP256 4.5 28.9 1.0 N C:PRO254 4.5 14.2 1.0 CA C:ASN258 4.5 25.5 1.0 N C:ASN258 4.5 22.4 1.0 CB C:ASN258 4.5 23.4 1.0 N C:SER259 4.5 16.7 1.0 CA C:SER259 4.5 14.0 1.0 N C:ASP262 4.5 21.2 1.0 CB C:ASN253 4.6 15.1 1.0 CB C:ASP262 4.6 20.8 1.0 C C:ASN261 4.6 46.2 1.0 O D:HOH1294 4.7 20.0 1.0 CA C:ASP262 4.8 11.9 1.0 N C:ASN261 4.9 18.6 1.0 CB C:ASN261 4.9 26.8 1.0 N C:ASP256 4.9 23.2 1.0 O C:ASN261 5.0 27.2 1.0 CA C:ASN261 5.0 24.9 1.0 C C:PRO254 5.0 24.9 1.0

Calcium binding site 4 out of 4 in the Catalytic Core of Xylanase A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catalytic Core of Xylanase A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca348 b:12.4 occ:1.09 OD1 D:ASN261 2.2 15.6 1.0 O D:ASN258 2.3 9.7 1.0 OD1 D:ASP262 2.4 9.1 1.0 O D:ASN253 2.5 7.0 1.0 OD1 D:ASP256 2.5 9.7 1.0 O D:HOH1180 2.5 14.7 1.0 OD2 D:ASP256 2.7 13.7 1.0 CG D:ASP256 2.9 10.0 1.0 CG D:ASN261 3.3 4.5 1.0 CG D:ASP262 3.4 17.1 1.0 C D:ASN258 3.5 9.9 1.0 C D:ASN253 3.6 9.5 1.0 OD2 D:ASP262 3.7 15.0 1.0 ND2 D:ASN261 3.7 14.5 1.0 CA D:ASN258 4.4 11.3 1.0 N D:SER259 4.4 11.6 1.0 CB D:ASP256 4.4 10.7 1.0 CA D:PRO254 4.5 11.8 1.0 N D:ASP262 4.5 7.5 1.0 N D:PRO254 4.5 8.8 1.0 CA D:ASN253 4.5 7.1 1.0 N D:ASN258 4.5 9.1 1.0 C D:ASN261 4.5 17.4 1.0 N D:ASN253 4.5 9.5 1.0 CB D:ASN258 4.5 10.6 1.0 CB D:ASN253 4.5 11.8 1.0 CA D:SER259 4.6 7.3 1.0 CB D:ASN261 4.7 8.1 1.0 CB D:ASP262 4.7 14.8 1.0 N D:ASN261 4.8 11.4 1.0 N D:ASP256 4.9 9.9 1.0 CA D:ASN261 4.9 11.4 1.0 O D:ASN261 4.9 22.5 1.0 CA D:ASP262 4.9 12.5 1.0 O C:HOH1017 4.9 16.1 1.0

G.W.Harris, J.A.Jenkins, I.Connerton, R.W.Pickersgill. Refined Crystal Structure of the Catalytic Domain of Xylanase A From Pseudomonas Fluorescens at 1.8 A Resolution. Acta Crystallogr.,Sect.D V. 52 393 1996.
ISSN: ISSN 0907-4449
PubMed: 15299710
DOI: 10.1107/S0907444995013540