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Sodium in PDB 3c7g: Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotetraose.

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

All present enzymatic activity of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotetraose.:
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 Xylotetraose., PDB code: 3c7g 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) 31.96 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.523, 72.401, 106.869, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 18.7

Other elements in 3c7g:

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Xylotetraose. 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 Xylotetraose. (pdb code 3c7g). 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 Xylotetraose., PDB code: 3c7g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c7g

Go back to Sodium Binding Sites List in 3c7g
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 Xylotetraose.


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 Xylotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1142

b:16.6
occ:1.00
 OD2 A:ASP393 2.3 13.2 1.0
OE1 A:GLN390 2.3 18.2 1.0
O A:ARG368 2.3 9.8 1.0
O A:SER388 2.3 10.5 1.0
O A:HOH1927 2.6 18.9 1.0
O A:HOH1973 2.7 17.2 1.0
CG A:ASP393 3.1 11.1 1.0
CD A:GLN390 3.3 17.0 1.0
OD1 A:ASP393 3.4 15.4 1.0
O A:HOH2136 3.5 30.8 1.0
C A:SER388 3.5 10.8 1.0
C A:ARG368 3.5 9.7 1.0
NE2 A:GLN390 3.8 18.1 1.0
OG A:SER388 3.8 12.2 1.0
N A:GLN390 3.9 13.1 1.0
CA A:ILE369 4.1 8.0 1.0
CG2 A:ILE369 4.3 7.3 1.0
N A:ILE369 4.3 8.8 1.0
CB A:ASP393 4.3 10.9 1.0
N A:ILE389 4.4 11.2 1.0
CB A:SER388 4.4 9.9 1.0
CA A:ILE389 4.4 12.2 1.0
CB A:GLN390 4.4 14.1 1.0
O A:HOH1990 4.4 24.5 1.0
CG A:GLN390 4.4 15.7 1.0
N A:ARG368 4.5 11.1 1.0
CA A:SER388 4.5 10.6 1.0
C A:ILE389 4.5 13.1 1.0
CA A:ARG368 4.6 10.3 1.0
CB A:ARG368 4.8 10.7 1.0
CA A:GLN390 4.8 13.9 1.0
CB A:ILE369 4.8 8.4 1.0

Sodium binding site 2 out of 2 in 3c7g

Go back to Sodium Binding Sites List in 3c7g
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 Xylotetraose.


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 Xylotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1143

b:42.1
occ:1.00
 O A:HOH1777 2.0 14.1 1.0
O A:HOH1735 2.2 6.5 1.0
O A:HOH2167 2.4 6.8 1.0
O A:HOH2168 2.4 9.0 1.0
NE2 A:HIS290 2.5 7.8 1.0
O A:HOH2169 2.7 7.2 1.0
O A:HOH1913 2.8 11.8 1.0
CE1 A:HIS290 3.4 7.5 1.0
CD2 A:HIS290 3.4 9.5 1.0
O A:HOH1801 3.6 14.6 1.0
O A:PRO103 3.8 6.9 1.0
O A:PRO164 3.9 7.8 1.0
O A:PRO25 4.3 6.6 1.0
O A:ALA102 4.3 7.2 1.0
O A:ASP24 4.3 7.3 1.0
O A:HIS291 4.4 7.4 1.0
OD1 A:ASP226 4.5 6.6 1.0
O A:SER227 4.5 9.5 1.0
ND1 A:HIS290 4.5 7.7 1.0
C A:ALA102 4.5 6.6 1.0
CB A:ALA102 4.6 4.4 1.0
CG A:HIS290 4.6 9.2 1.0
CB A:VAL26 4.7 5.6 1.0
CA A:ALA102 4.8 6.3 1.0
C A:PRO103 4.9 7.1 1.0
C A:ASP24 4.9 7.1 1.0
CG2 A:VAL26 4.9 5.4 1.0
C A:PRO25 5.0 6.8 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: Mon Oct 7 06:11:00 2024

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