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Sodium in PDB 3bcd: Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin

Enzymatic activity of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin

All present enzymatic activity of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin:
3.2.1.1;

Protein crystallography data

The structure of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin, PDB code: 3bcd was solved by T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.700, 78.050, 50.640, 90.00, 98.90, 90.00
R / Rfree (%) 19.6 / 24

Other elements in 3bcd:

The structure of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin (pdb code 3bcd). 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 Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin, PDB code: 3bcd:

Sodium binding site 1 out of 1 in 3bcd

Go back to Sodium Binding Sites List in 3bcd
Sodium binding site 1 out of 1 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:6.1
occ:1.00
 OD2 A:ASP283 2.2 4.0 1.0
OD2 A:ASP313 2.3 6.6 1.0
OD2 A:ASP305 2.3 7.0 1.0
OD2 A:ASP319 2.3 7.0 1.0
O A:VAL320 2.5 4.8 1.0
CG A:ASP313 3.0 7.7 1.0
OD1 A:ASP313 3.1 10.4 1.0
CG A:ASP305 3.1 6.7 1.0
CG A:ASP283 3.3 4.1 1.0
CG A:ASP319 3.6 6.0 1.0
C A:VAL320 3.6 4.6 1.0
O A:HOH1006 3.7 2.0 1.0
OD1 A:ASP305 3.7 8.2 1.0
CB A:ASP283 3.8 4.5 1.0
CA A:ASP321 4.0 5.8 1.0
CB A:ASP305 4.0 4.3 1.0
O A:HOH1016 4.1 7.8 1.0
N A:ASP305 4.1 4.5 1.0
N A:ASP321 4.2 4.5 1.0
OD1 A:ASP283 4.3 6.0 1.0
OD1 A:ASP319 4.3 6.8 1.0
CA A:CA701 4.4 8.2 1.0
N A:TYR322 4.5 4.8 1.0
CB A:ASP313 4.5 7.9 1.0
CA A:CA702 4.5 9.1 1.0
CE3 A:TRP304 4.6 6.9 1.0
N A:VAL320 4.6 4.9 1.0
CB A:ASP319 4.7 3.8 1.0
CA A:VAL320 4.7 4.5 1.0
C A:ASP319 4.7 4.4 1.0
CA A:ASP305 4.7 3.7 1.0
C A:ASP321 4.8 5.6 1.0
O A:ASP319 4.8 5.8 1.0
CA A:TRP304 4.9 4.1 1.0
O A:SER303 4.9 7.0 1.0
CB A:ASP321 5.0 6.8 1.0
C A:TRP304 5.0 4.0 1.0
OD1 A:ASP321 5.0 7.8 1.0

Reference:

T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne. Crystal Structure of the Polyextremophilic Alpha-Amylase Amyb From Halothermothrix Orenii: Details of A Productive Enzyme-Substrate Complex and An N Domain with A Role in Binding Raw Starch J.Mol.Biol. V. 378 850 2008.
ISSN: ISSN 0022-2836
PubMed: 18387632
DOI: 10.1016/J.JMB.2008.02.041
Page generated: Tue Dec 15 06:03:23 2020

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