Atomistry » Calcium » PDB 3b1u-3biw » 3bcd
Atomistry »
  Calcium »
    PDB 3b1u-3biw »
      3bcd »

Calcium 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:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium where determined in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin, PDB code: 3bcd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 1 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca701

b:8.2
occ:1.00
OD1 A:ASP305 2.3 8.2 1.0
O A:SER303 2.3 7.0 1.0
OD1 A:ASP321 2.3 7.8 1.0
OE1 A:GLU323 2.3 6.3 1.0
OD1 A:ASP283 2.4 6.0 1.0
O A:HOH1240 2.5 11.7 1.0
OD2 A:ASP283 2.6 4.0 1.0
CG A:ASP283 2.9 4.1 1.0
CG A:ASP321 3.2 9.2 1.0
CG A:ASP305 3.3 6.7 1.0
CD A:GLU323 3.4 6.4 1.0
C A:SER303 3.5 7.2 1.0
OD2 A:ASP305 3.8 7.0 1.0
OD2 A:ASP321 3.8 13.0 1.0
CB A:GLU323 4.0 7.3 1.0
CG A:GLU323 4.0 6.7 1.0
N A:SER303 4.1 8.8 1.0
CB A:ASP321 4.1 6.8 1.0
N A:ASP305 4.3 4.5 1.0
C A:TRP304 4.3 4.0 1.0
CA A:ASP321 4.3 5.8 1.0
OE2 A:GLU323 4.3 3.3 1.0
CA A:SER303 4.4 7.7 1.0
N A:GLU323 4.4 6.7 1.0
CB A:ASP283 4.4 4.5 1.0
NA A:NA704 4.4 6.1 1.0
N A:TRP304 4.5 4.6 1.0
CB A:ASP305 4.6 4.3 1.0
CA A:TRP304 4.6 4.1 1.0
CA A:ASP305 4.6 3.7 1.0
OG A:SER303 4.7 11.7 1.0
O A:TRP304 4.7 3.8 1.0
N A:TYR322 4.7 4.8 1.0
C A:ASP321 4.8 5.6 1.0
CA A:GLU323 4.8 7.2 1.0
O A:HOH1108 4.9 14.5 1.0
O A:HOH1049 5.0 8.2 1.0

Calcium binding site 2 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 2 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:9.1
occ:1.00
OD1 A:ASN232 2.3 2.0 1.0
O A:ASP313 2.3 10.9 1.0
OD1 A:ASP313 2.3 10.4 1.0
OD1 A:ASP319 2.3 6.8 1.0
O A:HIS354 2.3 2.6 1.0
O A:HOH1016 2.4 7.8 1.0
CG A:ASP319 3.2 6.0 1.0
C A:ASP313 3.3 9.0 1.0
CG A:ASP313 3.3 7.7 1.0
OD2 A:ASP319 3.5 7.0 1.0
CG A:ASN232 3.5 3.3 1.0
C A:HIS354 3.6 2.0 1.0
CA A:ASP313 3.7 7.4 1.0
O A:HOH1007 4.0 3.9 1.0
CB A:HIS354 4.1 2.0 1.0
CB A:ASP313 4.1 7.9 1.0
O A:ASN232 4.1 4.2 1.0
O A:HOH1006 4.1 2.0 1.0
OD2 A:ASP313 4.2 6.6 1.0
ND2 A:ASN232 4.3 5.8 1.0
N A:TYR314 4.4 8.7 1.0
CA A:HIS354 4.4 2.0 1.0
N A:ILE355 4.5 2.8 1.0
NA A:NA704 4.5 6.1 1.0
CB A:ASN232 4.6 3.2 1.0
CB A:ASP319 4.6 3.8 1.0
CA A:ILE355 4.6 2.4 1.0
CA A:TYR314 4.7 8.5 1.0
CA A:ASN232 4.8 3.0 1.0
C A:ASN232 4.8 3.5 1.0
CG1 A:ILE355 4.8 3.4 1.0
O A:GLU312 5.0 2.3 1.0

Calcium binding site 3 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 3 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:8.4
occ:1.00
O A:HOH1050 2.1 2.0 1.0
O A:ALA517 2.3 4.9 1.0
O A:ALA419 2.3 9.5 1.0
OD1 A:ASP518 2.3 6.3 1.0
OD1 A:ASP541 2.3 7.7 1.0
OD2 A:ASP541 2.4 9.1 1.0
CG A:ASP541 2.7 7.1 1.0
C A:ALA517 3.2 2.4 1.0
CG A:ASP518 3.5 3.7 1.0
C A:ALA419 3.5 7.1 1.0
CA A:ASP518 3.7 3.0 1.0
N A:ASP518 3.8 2.9 1.0
N A:ALA419 4.0 6.7 1.0
CB A:ASP518 4.0 2.4 1.0
CA A:ALA517 4.2 2.4 1.0
CG A:MET421 4.2 3.5 1.0
CB A:ASP541 4.2 7.7 1.0
CB A:ALA517 4.3 2.0 1.0
CA A:ALA419 4.4 6.6 1.0
N A:TYR420 4.5 7.2 1.0
OD2 A:ASP518 4.5 7.1 1.0
N A:MET421 4.5 6.5 1.0
CA A:TYR420 4.6 6.2 1.0
C A:GLY418 4.7 7.0 1.0
CA A:GLY418 4.8 6.5 1.0
C A:ASP518 4.8 2.6 1.0

Calcium binding site 4 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 4 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:29.8
occ:1.00
OD1 A:ASP533 2.3 22.4 1.0
O A:PHE527 2.3 22.6 1.0
O A:VAL530 2.5 17.4 1.0
CG A:ASP533 3.4 15.1 1.0
C A:PHE527 3.5 19.5 1.0
C A:VAL530 3.7 17.0 1.0
N A:PHE527 3.8 16.9 1.0
OD2 A:ASP533 3.9 16.2 1.0
C A:GLY526 4.0 15.1 1.0
CA A:GLY526 4.1 14.0 1.0
CA A:PHE527 4.2 17.8 1.0
N A:VAL530 4.3 18.8 1.0
N A:ASP533 4.4 11.7 1.0
CA A:PRO528 4.4 20.8 1.0
N A:PRO528 4.4 20.1 1.0
CA A:VAL530 4.5 17.6 1.0
O A:ASP533 4.5 10.4 1.0
C A:PRO528 4.6 21.1 1.0
N A:GLY532 4.6 13.6 1.0
O A:GLY526 4.6 16.0 1.0
N A:ALA531 4.6 15.2 1.0
O A:SER525 4.7 13.0 1.0
CB A:ASP533 4.7 11.6 1.0
CA A:ALA531 4.7 14.6 1.0
CB A:VAL530 4.8 17.2 1.0
C A:ASP533 4.8 10.1 1.0
CA A:ASP533 4.8 11.6 1.0
O A:PRO528 4.8 21.2 1.0
CB A:PHE527 4.8 18.1 1.0
C A:ALA531 4.9 14.2 1.0
OE1 A:GLN556 4.9 20.4 1.0
N A:ASP529 5.0 21.4 1.0

Calcium binding site 5 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 5 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca706

b:18.9
occ:1.00
O A:HOH1135 2.3 13.0 1.0
O A:HOH1168 2.4 16.7 1.0
O A:HOH1125 2.4 14.1 1.0
O A:LYS31 2.4 9.8 1.0
O A:HOH1065 2.4 13.5 1.0
O A:HOH1252 2.6 19.6 1.0
C A:LYS31 3.5 8.0 1.0
O A:LEU33 3.9 11.8 1.0
CA A:ASN32 4.0 7.8 1.0
N A:LEU80 4.0 9.9 1.0
O A:HOH1048 4.0 6.7 1.0
N A:ASN32 4.2 8.2 1.0
CA A:SER79 4.2 7.4 1.0
C A:ASN32 4.3 8.1 1.0
O A:PHE78 4.4 6.1 1.0
NZ A:LYS31 4.4 13.7 1.0
OG A:SER79 4.5 7.2 1.0
O A:LEU80 4.5 10.4 1.0
C A:SER79 4.6 9.4 1.0
O A:ASN32 4.6 8.0 1.0
CA A:LYS31 4.7 7.5 1.0
N A:LEU33 4.8 9.6 1.0
CE A:LYS31 4.8 16.9 1.0
CB A:SER79 4.8 7.2 1.0
C A:LEU33 4.9 10.3 1.0
CB A:LEU80 4.9 8.1 1.0
CA A:LEU80 4.9 9.0 1.0
CB A:LYS31 5.0 8.1 1.0

Calcium binding site 6 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 6 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca707

b:17.8
occ:1.00
OD1 A:ASN417 2.3 12.9 1.0
OD1 A:ASP414 2.3 13.2 1.0
O A:ASP414 2.3 8.2 1.0
O A:HOH1076 2.4 13.3 1.0
O A:GLY418 2.4 9.3 1.0
O A:HOH1166 2.7 12.6 1.0
C A:ASP414 3.2 5.8 1.0
C A:GLY418 3.4 7.0 1.0
CG A:ASP414 3.4 9.8 1.0
CG A:ASN417 3.5 8.5 1.0
CA A:ASP414 3.5 6.5 1.0
O A:HOH1096 3.8 12.2 1.0
N A:GLY418 4.0 5.4 1.0
CB A:ASP414 4.0 6.6 1.0
ND2 A:ASN417 4.1 8.2 1.0
C A:ASN417 4.2 6.1 1.0
N A:ALA419 4.2 6.7 1.0
CA A:GLY418 4.3 6.5 1.0
N A:MET415 4.3 5.0 1.0
N A:ASN417 4.4 5.3 1.0
OD2 A:ASP414 4.4 14.1 1.0
CA A:ALA419 4.5 6.6 1.0
O A:ASN417 4.6 5.6 1.0
CA A:ASN417 4.6 6.1 1.0
CB A:ASN417 4.6 6.1 1.0
CA A:MET415 4.8 4.0 1.0
CB A:ALA419 4.8 5.4 1.0
N A:ASP414 4.9 5.5 1.0
O A:VAL413 4.9 5.1 1.0
C A:MET415 5.0 3.0 1.0

Calcium binding site 7 out of 7 in 3bcd

Go back to Calcium Binding Sites List in 3bcd
Calcium binding site 7 out of 7 in the Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Alpha-Amylase B in Complex with Maltotetraose and Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca708

b:21.9
occ:1.00
O A:SER371 2.3 16.5 1.0
O A:GLN368 2.3 10.8 1.0
O A:ARG373 2.3 18.3 1.0
O A:HOH1183 2.3 22.9 1.0
O A:HOH1181 2.4 23.1 1.0
OE1 A:GLN368 2.4 15.7 1.0
C A:GLN368 3.3 7.9 1.0
C A:SER371 3.4 15.2 1.0
CD A:GLN368 3.4 6.8 1.0
C A:ARG373 3.5 15.5 1.0
CA A:GLN368 3.7 7.8 1.0
CG A:GLN368 3.8 7.8 1.0
C A:ASN372 4.0 14.8 1.0
N A:ARG373 4.0 14.8 1.0
N A:SER371 4.1 13.0 1.0
CA A:SER371 4.2 15.2 1.0
N A:ASN372 4.2 14.4 1.0
CA A:ASN372 4.3 14.8 1.0
OG A:SER371 4.3 21.0 1.0
CB A:GLN368 4.3 7.0 1.0
N A:VAL375 4.4 8.9 1.0
O A:ASN372 4.4 14.6 1.0
CG2 A:VAL375 4.4 7.1 1.0
N A:ASP374 4.4 13.7 1.0
N A:ASN369 4.4 8.1 1.0
CA A:ASP374 4.4 12.5 1.0
CA A:ARG373 4.4 15.9 1.0
CB A:SER371 4.6 15.8 1.0
O A:VAL367 4.7 8.6 1.0
NE2 A:GLN368 4.7 3.5 1.0
CA A:ASN369 4.9 7.6 1.0
C A:ASP374 5.0 11.0 1.0
N A:GLN368 5.0 7.5 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: Sat Jul 13 08:14:41 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy