Atomistry » Sodium » PDB 3b2n-3biu » 3bcd
Atomistry »
  Sodium »
    PDB 3b2n-3biu »
      3bcd »

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: Mon Oct 7 06:02:28 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy