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Sodium in PDB 3c7f: Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose.

Enzymatic activity of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose.

All present enzymatic activity of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose.:
3.2.1.55;

Protein crystallography data

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose., PDB code: 3c7f was solved by E.Vandermarliere, T.M.Bourgois, M.D.Winn, S.Van Campenhout, G.Volckaert, S.V.Strelkov, J.A.Delcour, A.Rabijns, C.M.Courtin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.627, 73.662, 106.368, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 3c7f:

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose. also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose. (pdb code 3c7f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose., PDB code: 3c7f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c7f

Go back to Sodium Binding Sites List in 3c7f
Sodium binding site 1 out of 2 in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:15.4
occ:1.00
 OD2 A:ASP393 2.3 15.0 1.0
OE1 A:GLN390 2.3 18.8 1.0
O A:SER388 2.3 14.1 1.0
O A:HOH2194 2.4 19.3 1.0
O A:ARG368 2.4 13.1 1.0
O A:HOH2371 2.6 17.6 1.0
CG A:ASP393 3.2 14.1 1.0
CD A:GLN390 3.3 18.5 1.0
C A:SER388 3.5 14.3 1.0
OD1 A:ASP393 3.6 15.6 1.0
O A:HOH2279 3.6 22.4 1.0
C A:ARG368 3.6 13.1 1.0
NE2 A:GLN390 3.9 19.7 1.0
OG A:SER388 3.9 15.8 1.0
N A:GLN390 4.0 16.3 1.0
O A:HOH2489 4.1 28.3 1.0
CA A:ILE369 4.2 12.2 1.0
CB A:SER388 4.3 14.6 1.0
CG2 A:ILE369 4.3 11.8 1.0
N A:ILE389 4.3 14.2 1.0
CA A:ILE389 4.4 15.2 1.0
N A:ILE369 4.4 12.0 1.0
CA A:SER388 4.5 14.1 1.0
CB A:ASP393 4.5 14.0 1.0
CG A:GLN390 4.5 17.9 1.0
CB A:GLN390 4.5 17.3 1.0
C A:ILE389 4.6 15.6 1.0
O A:HOH2245 4.6 20.0 1.0
CA A:ARG368 4.7 13.4 1.0
N A:ARG368 4.7 13.6 1.0
CA A:GLN390 4.9 16.6 1.0
CB A:ILE369 4.9 11.7 1.0
CB A:ARG368 4.9 13.6 1.0
O A:HOH2504 4.9 37.1 1.0

Sodium binding site 2 out of 2 in 3c7f

Go back to Sodium Binding Sites List in 3c7f
Sodium binding site 2 out of 2 in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotriose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:15.4
occ:1.00
 O A:HOH2085 1.9 12.2 1.0
CE1 A:HIS290 2.2 10.4 1.0
O A:HOH2078 2.3 12.5 1.0
O A:HOH2170 2.3 15.0 1.0
O A:HOH2117 2.3 12.0 1.0
O A:HOH2565 2.7 9.9 1.0
O A:HOH2250 2.8 19.4 1.0
NE2 A:HIS290 3.1 14.0 1.0
ND1 A:HIS290 3.2 14.3 1.0
O A:HOH2204 3.6 19.2 1.0
O A:PRO103 3.9 10.1 1.0
O A:PRO164 4.1 10.6 1.0
OD1 A:ASP226 4.3 9.0 1.0
CD2 A:HIS290 4.3 9.2 1.0
CG A:HIS290 4.3 11.1 1.0
O A:HIS291 4.4 8.3 1.0
O A:PRO25 4.4 9.1 1.0
O A:ALA102 4.4 10.8 1.0
O A:SER227 4.5 8.9 1.0
O A:ASP24 4.5 8.9 1.0
CB A:ALA102 4.6 11.0 1.0
C A:ALA102 4.7 10.3 1.0
CB A:VAL26 4.8 9.2 1.0
C A:PRO103 5.0 10.4 1.0
CA A:ALA102 5.0 10.0 1.0

Reference:

E.Vandermarliere, T.M.Bourgois, M.D.Winn, S.Van Campenhout, G.Volckaert, J.A.Delcour, S.V.Strelkov, A.Rabijns, C.M.Courtin. Structural Analysis of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase in Complex with Xylotetraose Reveals A Different Binding Mechanism Compared with Other Members of the Same Family. Biochem.J. V. 418 39 2009.
ISSN: ISSN 0264-6021
PubMed: 18980579
DOI: 10.1042/BJ20081256
Page generated: Mon Oct 7 06:10:50 2024

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