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Sodium in PDB 2d3l: Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.

Enzymatic activity of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.

All present enzymatic activity of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.:
3.2.1.98;

Protein crystallography data

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose., PDB code: 2d3l was solved by R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.450, 82.460, 126.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.3

Other elements in 2d3l:

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose. also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose. (pdb code 2d3l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose., PDB code: 2d3l:

Sodium binding site 1 out of 1 in 2d3l

Go back to Sodium Binding Sites List in 2d3l
Sodium binding site 1 out of 1 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.


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 Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:27.7
occ:1.00
 OD2 A:ASP163 2.3 23.2 1.0
OD2 A:ASP205 2.3 20.3 1.0
O A:ILE206 2.4 18.8 1.0
OD2 A:ASP199 2.4 20.4 1.0
OD2 A:ASP188 2.6 18.6 1.0
OD1 A:ASP199 2.8 19.7 1.0
CG A:ASP199 3.0 18.8 1.0
CG A:ASP163 3.3 19.0 1.0
CG A:ASP188 3.3 21.5 1.0
CG A:ASP205 3.4 19.2 1.0
C A:ILE206 3.4 18.8 1.0
O A:HOH884 3.6 14.4 1.0
CB A:ASP163 3.6 18.3 1.0
O A:HOH724 3.7 23.5 1.0
CA A:ASP207 3.8 17.4 1.0
CA A:CA502 3.9 22.3 1.0
OD1 A:ASP205 3.9 17.9 1.0
OD1 A:ASP188 4.0 18.4 1.0
N A:ASP207 4.0 17.7 1.0
CB A:ASP188 4.1 21.1 1.0
O A:ASP205 4.3 19.1 1.0
N A:MET208 4.3 18.2 1.0
N A:ASP188 4.4 22.6 1.0
C A:ASP205 4.4 18.8 1.0
OD1 A:ASP163 4.4 19.4 1.0
CB A:ASP199 4.5 17.9 1.0
N A:ILE206 4.5 20.4 1.0
CB A:ASP205 4.5 18.0 1.0
CA A:CA501 4.5 22.2 1.0
CA A:ILE206 4.6 19.9 1.0
C A:ASP207 4.6 18.9 1.0
N A:ASP163 4.8 20.2 1.0
CB A:ASP207 4.8 17.3 1.0
CA A:ASP163 4.8 19.0 1.0
OD1 A:ASP207 4.9 18.0 1.0
CA A:ASP188 4.9 21.2 1.0
CE3 A:TRP187 4.9 26.1 1.0

Reference:

R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata. Role of TRP140 at Subsite -6 on the Maltohexaose Production of Maltohexaose-Producing Amylase From Alkalophilic Bacillus Sp.707 Protein Sci. V. 15 468 2006.
ISSN: ISSN 0961-8368
PubMed: 16452622
DOI: 10.1110/PS.051877006
Page generated: Mon Oct 7 02:11:03 2024

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