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Sodium in PDB 3c7h: Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5.

Enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5.

All present enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5.:
3.2.1.55;

Protein crystallography data

The structure of Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5., PDB code: 3c7h 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) 28.65 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.770, 74.230, 107.340, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 19

Other elements in 3c7h:

The structure of Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5. also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5. (pdb code 3c7h). 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 Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5., PDB code: 3c7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c7h

Go back to Sodium Binding Sites List in 3c7h
Sodium binding site 1 out of 2 in the Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5.


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 Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:20.6
occ:1.00
 O A:SER388 2.2 13.0 1.0
O A:ARG368 2.3 12.3 1.0
OD2 A:ASP393 2.4 11.8 1.0
OE1 A:GLN390 2.5 20.1 1.0
O A:HOH2320 2.5 21.1 1.0
O A:HOH2262 2.9 25.0 1.0
CG A:ASP393 3.3 11.2 1.0
CD A:GLN390 3.3 19.7 1.0
C A:SER388 3.4 13.3 1.0
O A:HOH2373 3.5 23.1 1.0
C A:ARG368 3.6 11.9 1.0
OG A:SER388 3.6 14.8 1.0
OD1 A:ASP393 3.7 14.7 1.0
NE2 A:GLN390 3.8 19.6 1.0
N A:GLN390 4.1 15.4 1.0
CA A:ILE369 4.2 9.8 1.0
CB A:SER388 4.2 14.3 1.0
N A:ILE369 4.3 11.0 1.0
N A:ILE389 4.3 13.3 1.0
CG2 A:ILE369 4.3 9.3 1.0
CA A:ILE389 4.4 13.6 1.0
CA A:SER388 4.4 13.2 1.0
CB A:ASP393 4.5 12.1 1.0
CG A:GLN390 4.5 18.4 1.0
CB A:GLN390 4.5 16.3 1.0
C A:ILE389 4.6 13.9 1.0
N A:ARG368 4.6 13.6 1.0
CA A:ARG368 4.6 12.0 1.0
O A:HOH2315 4.6 29.9 1.0
CB A:ARG368 4.8 12.4 1.0
CB A:ILE369 4.9 10.1 1.0
CA A:GLN390 5.0 16.1 1.0

Sodium binding site 2 out of 2 in 3c7h

Go back to Sodium Binding Sites List in 3c7h
Sodium binding site 2 out of 2 in the Crystal Structure of Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5.


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 Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis in Complex with Axos-4- 0.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:24.4
occ:1.00
 O A:HOH2080 2.1 13.3 1.0
O A:HOH2079 2.3 7.8 1.0
NE2 A:HIS290 2.3 12.1 1.0
O A:HOH2077 2.4 10.5 1.0
O A:HOH2446 2.5 13.1 1.0
O A:HOH2107 2.7 9.9 1.0
O A:HOH2202 2.9 21.5 1.0
CE1 A:HIS290 3.2 12.4 1.0
CD2 A:HIS290 3.3 9.3 1.0
O A:PRO103 3.8 8.2 1.0
O A:HOH2238 3.8 17.8 1.0
O A:PRO164 4.0 8.9 1.0
ND1 A:HIS290 4.3 10.0 1.0
O A:PRO25 4.3 6.7 1.0
O A:ALA102 4.3 9.6 1.0
OD1 A:ASP226 4.4 6.5 1.0
CG A:HIS290 4.4 9.2 1.0
O A:HIS291 4.5 6.9 1.0
O A:ASP24 4.5 7.1 1.0
O A:SER227 4.5 7.3 1.0
C A:ALA102 4.6 9.6 1.0
CB A:ALA102 4.7 8.8 1.0
CB A:VAL26 4.7 4.2 1.0
C A:PRO103 4.9 9.5 1.0
CA A:ALA102 5.0 9.0 1.0
C A:ASP24 5.0 6.5 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 06:11:06 2024

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