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Sodium in PDB 3c7e: Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis.

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

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

Protein crystallography data

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis., PDB code: 3c7e 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) 28.61 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.710, 74.430, 106.990, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.3

Other elements in 3c7e:

The structure of Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis. 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. (pdb code 3c7e). 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., PDB code: 3c7e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3c7e

Go back to Sodium Binding Sites List in 3c7e
Sodium binding site 1 out of 2 in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis.


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

b:22.9
occ:1.00
 O A:SER388 2.3 15.4 1.0
O A:ARG368 2.3 16.5 1.0
O A:HOH2361 2.4 16.7 1.0
OE1 A:GLN390 2.5 20.1 1.0
OD2 A:ASP393 2.5 15.8 1.0
CG A:ASP393 3.3 15.4 1.0
CD A:GLN390 3.4 19.9 1.0
C A:SER388 3.5 16.0 1.0
C A:ARG368 3.5 17.3 1.0
OD1 A:ASP393 3.6 16.6 1.0
OG A:SER388 3.7 18.0 1.0
NE2 A:GLN390 3.8 19.5 1.0
N A:GLN390 4.1 16.6 1.0
CA A:ILE369 4.2 15.5 1.0
N A:ILE369 4.3 16.0 1.0
N A:ILE389 4.3 15.0 1.0
CA A:ILE389 4.4 15.1 1.0
CG2 A:ILE369 4.4 15.1 1.0
CB A:SER388 4.4 17.0 1.0
CA A:SER388 4.5 15.8 1.0
CG A:GLN390 4.5 19.8 1.0
CB A:GLN390 4.5 17.4 1.0
CB A:ASP393 4.6 15.8 1.0
C A:ILE389 4.6 15.6 1.0
CA A:ARG368 4.6 17.5 1.0
CB A:ARG368 4.7 18.2 1.0
CB A:ILE369 4.9 15.1 1.0
CA A:GLN390 5.0 17.9 1.0

Sodium binding site 2 out of 2 in 3c7e

Go back to Sodium Binding Sites List in 3c7e
Sodium binding site 2 out of 2 in the Crystal Structure of A Glycoside Hydrolase Family 43 Arabinoxylan Arabinofuranohydrolase From Bacillus Subtilis.


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

b:24.7
occ:1.00
 O A:HOH2068 2.1 13.3 1.0
O A:HOH2128 2.3 13.3 1.0
O A:HOH2358 2.3 16.0 1.0
O A:HOH2067 2.4 7.6 1.0
CE1 A:HIS290 2.5 12.7 1.0
O A:HOH2184 2.5 21.8 1.0
O A:HOH2171 2.6 13.0 1.0
NE2 A:HIS290 3.1 13.9 1.0
ND1 A:HIS290 3.5 13.7 1.0
O A:HOH2311 3.8 24.3 1.0
O A:PRO164 3.8 12.9 1.0
O A:PRO103 3.9 10.5 1.0
O A:PRO25 4.3 8.1 1.0
O A:SER227 4.3 9.5 1.0
OD1 A:ASP226 4.4 7.5 1.0
O A:HIS291 4.4 9.2 1.0
CD2 A:HIS290 4.4 10.0 1.0
O A:ALA102 4.5 10.7 1.0
CG A:HIS290 4.6 11.3 1.0
CB A:VAL26 4.7 9.8 1.0
O A:ASP24 4.7 10.7 1.0
CB A:ALA102 4.7 11.0 1.0
C A:ALA102 4.8 10.9 1.0
CG2 A:VAL26 4.9 9.0 1.0
C A:PRO103 4.9 11.2 1.0
C A:PRO164 5.0 12.6 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 06:10:47 2024

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