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Calcium in PDB 2d0h: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide

Enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide

All present enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide, PDB code: 2d0h was solved by A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.450, 92.290, 55.890, 90.00, 91.35, 90.00
R / Rfree (%) 15.6 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide (pdb code 2d0h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide, PDB code: 2d0h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2d0h

Go back to Calcium Binding Sites List in 2d0h
Calcium binding site 1 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:15.4
occ:1.00
 O A:ASN6 2.3 18.6 1.0
O A:ALA2 2.3 17.1 1.0
OD1 A:ASP42 2.3 13.4 1.0
OD2 A:ASP96 2.4 18.2 1.0
O A:HOH2039 2.4 20.2 1.0
O A:ASP42 2.5 14.3 1.0
OD2 A:ASP4 2.6 15.5 1.0
CG A:ASP96 3.3 17.4 1.0
CG A:ASP42 3.3 14.7 1.0
C A:ASN6 3.5 17.5 1.0
C A:ASP42 3.5 14.4 1.0
C A:ALA2 3.5 18.0 1.0
CG A:ASP4 3.6 19.5 1.0
CA A:ASP42 3.7 13.9 1.0
N A:ALA2 3.9 18.5 1.0
N A:ASP4 4.0 18.8 1.0
OD1 A:ASP96 4.0 19.5 1.0
OD1 A:ASP4 4.0 19.1 1.0
CB A:ASP96 4.1 16.7 1.0
CB A:ASP42 4.1 15.6 1.0
OD2 A:ASP42 4.2 14.2 1.0
N A:ASN6 4.2 16.8 1.0
CA A:ASN6 4.3 17.1 1.0
CA A:ALA2 4.3 18.0 1.0
N A:ASN3 4.4 17.3 1.0
N A:VAL7 4.5 16.6 1.0
CA A:ASN3 4.5 17.9 1.0
CB A:ASN6 4.6 16.7 1.0
CA A:VAL7 4.6 15.6 1.0
N A:ILE43 4.7 13.8 1.0
CB A:ASP4 4.8 18.8 1.0
C A:ASN3 4.8 19.2 1.0
CA A:ASP4 4.8 19.1 1.0
OE1 A:GLU8 4.8 22.1 1.0
CG A:GLU8 4.8 21.1 1.0
CB A:ALA1 4.9 16.3 1.0
C A:ALA1 5.0 18.9 1.0
C A:ASP4 5.0 18.3 1.0
O A:GLY41 5.0 19.4 1.0

Calcium binding site 2 out of 3 in 2d0h

Go back to Calcium Binding Sites List in 2d0h
Calcium binding site 2 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:13.8
occ:1.00
 OD2 A:ASP151 2.2 15.1 1.0
OD1 A:ASN150 2.3 11.5 1.0
OD2 A:ASP189 2.3 13.9 1.0
O A:ASP147 2.3 15.5 1.0
O A:HOH2027 2.5 9.5 1.0
OD1 A:ASN145 2.6 14.0 1.0
O A:GLY187 2.6 12.1 1.0
CG A:ASN150 3.4 12.6 1.0
CG A:ASP189 3.4 14.2 1.0
CG A:ASN145 3.4 14.0 1.0
C A:ASP147 3.4 16.3 1.0
CG A:ASP151 3.5 15.3 1.0
C A:GLY187 3.7 12.4 1.0
ND2 A:ASN145 3.9 11.6 1.0
ND2 A:ASN150 3.9 10.4 1.0
CB A:ASP189 4.0 13.5 1.0
N A:ASP151 4.0 12.6 1.0
CA A:GLY187 4.1 10.8 1.0
O A:ALA234 4.2 12.1 1.0
N A:ASP147 4.2 15.6 1.0
OD1 A:ASP151 4.2 17.6 1.0
CA A:ASP151 4.2 13.6 1.0
N A:SER148 4.3 16.8 1.0
CA A:SER148 4.3 18.2 1.0
CA A:ASP147 4.3 16.1 1.0
OD1 A:ASP189 4.4 11.6 1.0
C A:ASN150 4.4 13.2 1.0
CB A:ASP151 4.5 15.9 1.0
CB A:ASN145 4.5 12.1 1.0
CA A:ASN145 4.6 13.3 1.0
CB A:ASP147 4.6 17.8 1.0
CB A:ASN150 4.7 11.4 1.0
N A:ASN150 4.7 14.1 1.0
C A:SER148 4.7 15.8 1.0
C A:GLY188 4.8 12.4 1.0
N A:ASP189 4.8 11.8 1.0
N A:GLY188 4.8 9.9 1.0
CA A:ASN150 4.8 12.7 1.0
O A:GLY188 4.9 13.2 1.0
O A:SER148 4.9 16.0 1.0
N A:GLY146 4.9 13.2 1.0
C A:ASN145 5.0 14.4 1.0
O A:HOH2062 5.0 14.3 1.0

Calcium binding site 3 out of 3 in 2d0h

Go back to Calcium Binding Sites List in 2d0h
Calcium binding site 3 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:40.8
occ:1.00
 O A:HOH2279 2.3 20.3 1.0
O A:PHE281 2.4 27.5 1.0
OE2 A:GLU288 2.7 20.4 1.0
OD1 A:ASN279 2.8 29.5 1.0
O A:SER283 2.9 35.1 1.0
OD2 A:ASP276 3.0 18.3 1.0
OE1 A:GLU288 3.0 20.0 1.0
CD A:GLU288 3.2 20.4 1.0
O A:SER282 3.3 40.6 1.0
C A:PHE281 3.6 30.3 1.0
CG A:ASN279 4.0 28.5 1.0
C A:SER283 4.0 37.1 1.0
C A:SER282 4.0 38.9 1.0
CG A:ASP276 4.1 18.5 1.0
CA A:ASN279 4.2 26.0 1.0
N A:PHE281 4.3 28.5 1.0
O A:HOH2332 4.4 24.2 1.0
CA A:GLN284 4.5 32.2 1.0
CA A:PHE281 4.5 29.3 1.0
N A:SER282 4.6 32.4 1.0
C A:ASN279 4.6 26.3 1.0
CB A:ASN279 4.6 27.3 1.0
CG A:GLU288 4.6 20.1 1.0
CA A:SER282 4.7 37.2 1.0
N A:GLN284 4.7 35.6 1.0
N A:SER283 4.8 39.0 1.0
N A:GLY285 4.8 25.4 1.0
N A:ASN280 4.8 26.2 1.0
CB A:ASP276 4.9 17.5 1.0
OD1 A:ASP276 4.9 17.5 1.0
O A:HOH2382 5.0 34.9 1.0

Reference:

A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, S.Kamitori. Complexes of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 and Pullulan Model Oligossacharides Provide New Insight Into the Mechanism For Recognizing Substrates with Alpha-(1,6) Glycosidic Linkages Febs J. V. 272 6145 2005.
ISSN: ISSN 1742-464X
PubMed: 16302977
DOI: 10.1111/J.1742-4658.2005.05013.X
Page generated: Tue Jul 8 04:56:18 2025

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