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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

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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

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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

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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

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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

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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

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