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Sodium in PDB 2d3n: Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose

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

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

Protein crystallography data

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose, PDB code: 2d3n 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.630, 82.690, 126.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 2d3n:

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose 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 Maltohexaose (pdb code 2d3n). 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 Maltohexaose, PDB code: 2d3n:

Sodium binding site 1 out of 1 in 2d3n

Go back to Sodium Binding Sites List in 2d3n
Sodium binding site 1 out of 1 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose


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 Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:15.6
occ:1.00
 OD2 A:ASP163 2.3 12.9 1.0
OD2 A:ASP199 2.4 15.0 1.0
OD2 A:ASP205 2.4 16.7 1.0
OD2 A:ASP188 2.4 15.6 1.0
O A:ILE206 2.6 14.1 1.0
OD1 A:ASP199 2.9 15.0 1.0
CG A:ASP199 3.0 14.3 1.0
CG A:ASP188 3.1 16.7 1.0
CG A:ASP163 3.3 13.6 1.0
CG A:ASP205 3.6 13.7 1.0
CB A:ASP163 3.6 13.3 1.0
C A:ILE206 3.6 13.2 1.0
O A:HOH721 3.7 13.7 1.0
OD1 A:ASP188 3.7 17.4 1.0
O A:HOH738 3.7 13.9 1.0
CA A:ASP207 3.9 13.3 1.0
CA A:CA502 4.0 14.3 1.0
CB A:ASP188 4.0 14.8 1.0
N A:ASP207 4.2 13.2 1.0
OD1 A:ASP205 4.2 12.1 1.0
N A:ASP188 4.3 14.9 1.0
N A:MET208 4.3 13.9 1.0
OD1 A:ASP163 4.4 14.2 1.0
CB A:ASP199 4.4 14.5 1.0
CA A:CA501 4.4 14.1 1.0
O A:ASP205 4.6 10.9 1.0
CB A:ASP205 4.6 12.9 1.0
C A:ASP205 4.6 12.4 1.0
C A:ASP207 4.7 14.0 1.0
N A:ILE206 4.7 11.1 1.0
CA A:ILE206 4.8 12.5 1.0
CA A:ASP188 4.8 15.4 1.0
CA A:ASP163 4.9 13.1 1.0
OD1 A:ASP207 4.9 14.6 1.0
CB A:ASP207 4.9 13.0 1.0
N A:ASP163 4.9 13.1 1.0
CE3 A:TRP187 5.0 13.5 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: Tue Dec 15 05:47:13 2020

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