Calcium in PDB 2uwf: Crystal Structure of Family 10 Xylanase From Bacillus Halodurans

All present enzymatic activity of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans:
3.2.1.8;

The structure of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans, PDB code: 2uwf was solved by G.Mamo, M.Thunnissen, R.Hatti-Kaul, B.Mattiasson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.55 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.602, 53.586, 127.565, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24.1

The structure of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans (pdb code 2uwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans, PDB code: 2uwf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1368 b:20.2 occ:1.00 O A:ARG357 2.3 21.8 1.0 OD1 A:ASP298 2.3 20.0 1.0 O A:HOH2206 2.3 34.0 1.0 O A:HOH2169 2.3 19.2 1.0 O A:HOH2204 2.4 21.5 1.0 OD1 A:ASP360 2.5 29.0 1.0 O A:HOH2208 2.6 16.4 1.0 C A:ARG357 3.4 19.9 1.0 CG A:ASP298 3.5 19.9 1.0 CG A:ASP360 3.5 23.6 1.0 OD2 A:ASP360 3.9 23.2 1.0 O A:HOH2011 4.2 18.7 1.0 CD2 A:HIS362 4.2 29.4 1.0 CB A:ASP298 4.2 20.3 1.0 CA A:ILE358 4.3 18.8 1.0 N A:ILE358 4.3 19.8 1.0 CA A:ARG357 4.3 19.7 1.0 O A:ASP360 4.4 20.4 1.0 CA A:ASP298 4.4 19.7 1.0 OE1 A:GLU302 4.4 18.8 1.0 OD2 A:ASP298 4.4 21.3 1.0 O A:ASP298 4.6 20.6 1.0 CU A:CU1367 4.6 23.4 1.0 CG A:HIS362 4.7 27.4 1.0 O A:HIS362 4.7 22.5 1.0 C A:ILE358 4.7 18.2 1.0 C A:ASP360 4.8 22.0 1.0 CB A:ASP360 4.8 21.8 1.0 CG A:GLU302 4.8 18.9 1.0 N A:ASP360 4.9 20.4 1.0 CD A:GLU302 4.9 19.8 1.0 NE2 A:HIS362 4.9 27.9 1.0 CB A:ARG357 4.9 19.1 1.0 C A:ASP298 4.9 20.7 1.0 CB A:HIS362 4.9 25.2 1.0 O A:ILE358 4.9 17.5 1.0 N A:HIS362 5.0 24.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1369 b:31.0 occ:1.00 O A:GLN28 2.1 19.4 1.0 O A:SER308 2.2 24.4 1.0 O A:HOH2180 2.3 30.7 1.0 O A:HOH2013 2.3 30.3 1.0 O A:ILE311 2.3 18.5 1.0 O A:HOH2015 2.4 26.1 1.0 C A:GLN28 3.3 20.5 1.0 C A:SER308 3.4 25.1 1.0 C A:ILE311 3.4 19.1 1.0 O A:HOH2012 3.6 47.6 1.0 CA A:SER312 4.0 18.4 1.0 CA A:SER308 4.1 25.4 1.0 N A:SER312 4.2 18.7 1.0 CA A:GLN28 4.2 22.1 1.0 CB A:SER308 4.2 25.5 1.0 N A:PHE29 4.2 18.9 1.0 N A:ILE311 4.3 21.0 1.0 N A:ALA309 4.3 24.6 1.0 CA A:PHE29 4.4 18.1 1.0 CB A:PHE29 4.4 17.5 1.0 CA A:ILE311 4.4 19.9 1.0 O A:HOH2178 4.4 38.0 1.0 CA A:ALA309 4.5 24.6 1.0 OG A:SER308 4.5 29.9 1.0 C A:ALA309 4.6 24.4 1.0 CD2 A:PHE29 4.8 18.2 1.0 O A:HOH2181 4.8 23.7 1.0 C A:SER312 4.8 18.4 1.0 O A:ALA309 4.8 24.6 1.0 CB A:ILE311 4.9 19.7 1.0 O A:HOH2016 4.9 25.5 1.0 O A:SER312 5.0 19.3 1.0 O A:GLU27 5.0 26.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1370 b:30.6 occ:1.00 OD1 A:ASP30 2.0 27.2 1.0 OD2 A:ASP30 2.6 24.8 1.0 CG A:ASP30 2.6 19.9 1.0 O A:HOH2077 2.9 41.9 1.0 CG A:GLU91 3.3 24.5 1.0 OE1 A:GLU91 3.4 36.5 1.0 CD A:GLU91 3.6 31.7 1.0 CB A:ASP30 4.1 17.2 1.0 OE2 A:GLU91 4.5 37.9 1.0 O A:HOH2181 4.5 23.7 1.0 CB A:GLU91 4.6 21.5 1.0 O A:HOH2017 4.7 36.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Family 10 Xylanase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Family 10 Xylanase From Bacillus Halodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1371 b:23.8 occ:0.50 OH A:TYR282 2.2 28.4 1.0 O A:ASP321 2.3 18.1 1.0 O A:ASP340 2.4 23.3 1.0 OD2 A:ASP327 2.6 31.5 1.0 OD1 A:ASP327 2.6 30.5 1.0 CG A:ASP327 3.0 29.6 1.0 CZ A:TYR282 3.3 28.2 1.0 C A:ASP321 3.5 19.0 1.0 C A:ASP340 3.6 23.1 1.0 CE1 A:TYR282 3.6 28.3 1.0 OG1 A:THR324 3.8 27.0 1.0 N A:ASP340 3.9 25.0 1.0 CA A:ASP321 4.3 18.5 1.0 CB A:ASP321 4.3 19.2 1.0 CA A:ASP340 4.4 23.5 1.0 CB A:ASP327 4.5 28.8 1.0 CG2 A:VAL339 4.5 29.2 1.0 N A:ASN322 4.5 19.2 1.0 CE2 A:TYR282 4.5 28.1 1.0 CA A:ASN322 4.6 19.6 1.0 N A:ALA341 4.6 21.8 1.0 O A:HOH2189 4.7 33.0 1.0 CB A:THR324 4.7 21.7 1.0 C A:ASN322 4.8 20.4 1.0 CA A:ALA341 4.8 21.1 1.0 C A:VAL339 4.9 26.2 1.0 CG1 A:VAL339 5.0 28.9 1.0 CD1 A:TYR282 5.0 28.1 1.0 CD A:PRO342 5.0 19.1 1.0

G.Mamo, M.Thunnissen, R.Hatti-Kaul, B.Mattiasson. An Alkaline Active Xylanase: Insights Into Mechanisms of High pH Catalytic Adaptation Biochimie V. 91 1187 2009.
ISSN: ISSN 0300-9084
PubMed: 19567261
DOI: 10.1016/J.BIOCHI.2009.06.017