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Sodium in PDB 3c7o: Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Cellotetraose.

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

All present enzymatic activity of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Cellotetraose.:
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 Cellotetraose., PDB code: 3c7o 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) 29.59 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.990, 73.080, 105.690, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 3c7o:

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Cellotetraose. 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 Cellotetraose. (pdb code 3c7o). 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 Cellotetraose., PDB code: 3c7o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c7o

Go back to Sodium Binding Sites List in 3c7o
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 Cellotetraose.


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 Cellotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na489

b:14.6
occ:1.00
 O A:SER388 2.3 14.8 1.0
O A:HOH2192 2.3 20.6 1.0
OD2 A:ASP393 2.3 16.3 1.0
OE1 A:GLN390 2.3 19.3 1.0
O A:ARG368 2.4 13.4 1.0
O A:HOH2156 2.7 19.7 1.0
CG A:ASP393 3.2 15.0 1.0
CD A:GLN390 3.3 19.1 1.0
C A:SER388 3.5 14.3 1.0
OD1 A:ASP393 3.6 16.1 1.0
O A:HOH2262 3.6 32.2 1.0
C A:ARG368 3.6 13.1 1.0
OG A:SER388 3.8 16.9 1.0
NE2 A:GLN390 3.9 19.4 1.0
N A:GLN390 4.0 15.7 1.0
CA A:ILE369 4.2 12.6 1.0
CB A:SER388 4.2 14.8 1.0
O A:HOH2316 4.3 40.1 1.0
N A:ILE389 4.3 14.4 1.0
N A:ILE369 4.4 12.5 1.0
CA A:ILE389 4.4 14.7 1.0
CG2 A:ILE369 4.4 11.6 1.0
CA A:SER388 4.4 14.5 1.0
CB A:ASP393 4.5 12.5 1.0
CG A:GLN390 4.5 18.4 1.0
CB A:GLN390 4.6 16.5 1.0
C A:ILE389 4.6 15.7 1.0
CA A:ARG368 4.7 13.4 1.0
N A:ARG368 4.7 14.1 1.0
OG1 A:THR2 4.8 36.9 1.0
CB A:ARG368 4.9 13.4 1.0
CA A:GLN390 4.9 16.4 1.0
CB A:ILE369 4.9 11.8 1.0

Sodium binding site 2 out of 2 in 3c7o

Go back to Sodium Binding Sites List in 3c7o
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 Cellotetraose.


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 Cellotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na490

b:32.0
occ:1.00
 O A:HOH2148 2.0 17.1 1.0
O A:HOH2088 2.3 13.7 1.0
O A:HOH2100 2.3 12.9 1.0
O A:HOH2076 2.4 10.7 1.0
NE2 A:HIS290 2.4 11.2 1.0
O A:HOH2304 2.6 12.8 1.0
O A:HOH2252 2.7 19.2 1.0
CD2 A:HIS290 3.3 11.2 1.0
CE1 A:HIS290 3.4 10.5 1.0
O A:HOH2326 3.5 27.6 1.0
O A:PRO103 3.8 10.7 1.0
O A:PRO164 4.0 12.6 1.0
OD1 A:ASP226 4.4 11.2 1.0
O A:SER227 4.4 11.1 1.0
O A:HIS291 4.4 8.8 1.0
O A:PRO25 4.4 10.7 1.0
ND1 A:HIS290 4.4 11.6 1.0
CG A:HIS290 4.4 9.8 1.0
O A:ALA102 4.5 11.6 1.0
O A:ASP24 4.6 8.8 1.0
CB A:ALA102 4.7 10.8 1.0
C A:ALA102 4.7 11.2 1.0
CB A:VAL26 4.8 9.4 1.0
C A:PRO103 4.9 10.8 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: Sun Aug 17 12:57:20 2025

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