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Calcium in PDB 2d0f: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N Complexed with P2, A Pullulan Model Oligosaccharide

Enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N 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 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 Complexed with P2, A Pullulan Model Oligosaccharide, PDB code: 2d0f 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) 46.00 / 2.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.532, 50.429, 107.834, 90.00, 104.30, 90.00
R / Rfree (%) 15.4 / 18.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N Complexed with P2, A Pullulan Model Oligosaccharide (pdb code 2d0f). 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 Complexed with P2, A Pullulan Model Oligosaccharide, PDB code: 2d0f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2d0f

Go back to Calcium Binding Sites List in 2d0f
Calcium binding site 1 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N 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 Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:11.5
occ:1.00
 O A:ASN6 2.3 8.5 1.0
O A:ALA2 2.3 11.3 1.0
OD1 A:ASP42 2.3 9.9 1.0
O A:HOH2019 2.4 11.5 1.0
OD1 A:ASP4 2.5 7.7 1.0
OD2 A:ASP96 2.5 14.8 1.0
O A:ASP42 2.6 11.0 1.0
CG A:ASP42 3.3 12.2 1.0
CG A:ASP96 3.3 12.8 1.0
C A:ASN6 3.5 10.0 1.0
CG A:ASP4 3.5 10.4 1.0
C A:ASP42 3.5 11.0 1.0
C A:ALA2 3.5 13.0 1.0
CA A:ASP42 3.8 10.9 1.0
OD2 A:ASP4 3.9 12.5 1.0
N A:ASP4 3.9 11.8 1.0
OD1 A:ASP96 4.0 12.4 1.0
OD2 A:ASP42 4.1 11.3 1.0
N A:ALA2 4.1 13.0 1.0
N A:ASN6 4.1 10.4 1.0
CB A:ASP42 4.1 10.1 1.0
CB A:ASP96 4.2 8.9 1.0
CA A:ASN6 4.2 10.9 1.0
CA A:ASN3 4.4 12.4 1.0
N A:ASN3 4.4 11.2 1.0
N A:VAL7 4.5 9.2 1.0
CA A:ALA2 4.5 13.8 1.0
CB A:ASN6 4.6 13.2 1.0
CG A:GLU8 4.6 7.3 1.0
CA A:VAL7 4.7 9.7 1.0
CB A:ASP4 4.7 8.9 1.0
C A:ASN3 4.7 12.2 1.0
OE1 A:GLU8 4.7 12.0 1.0
CA A:ASP4 4.8 9.8 1.0
N A:ILE43 4.8 10.1 1.0
N A:GLU8 4.9 8.0 1.0
C A:ASP4 4.9 10.5 1.0

Calcium binding site 2 out of 3 in 2d0f

Go back to Calcium Binding Sites List in 2d0f
Calcium binding site 2 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N 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 Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:11.7
occ:1.00
 OD2 A:ASP151 2.2 12.9 1.0
OD1 A:ASN150 2.3 8.6 1.0
OD2 A:ASP189 2.3 10.6 1.0
O A:ASP147 2.4 13.2 1.0
O A:HOH2037 2.4 7.3 1.0
OD1 A:ASN145 2.5 15.7 1.0
O A:GLY187 2.6 7.7 1.0
CG A:ASN145 3.4 13.0 1.0
C A:ASP147 3.4 14.0 1.0
CG A:ASP189 3.4 12.3 1.0
CG A:ASN150 3.4 9.5 1.0
CG A:ASP151 3.5 14.9 1.0
C A:GLY187 3.6 11.1 1.0
ND2 A:ASN145 3.9 9.3 1.0
CB A:ASP189 3.9 10.6 1.0
ND2 A:ASN150 4.0 8.9 1.0
N A:ASP151 4.0 13.3 1.0
CA A:GLY187 4.1 10.2 1.0
N A:SER148 4.1 14.1 1.0
CA A:SER148 4.1 15.0 1.0
N A:ASP147 4.2 14.5 1.0
O A:ALA234 4.2 11.0 1.0
CA A:ASP151 4.2 13.3 1.0
OD1 A:ASP151 4.3 13.3 1.0
CA A:ASP147 4.3 13.3 1.0
C A:ASN150 4.4 13.4 1.0
OD1 A:ASP189 4.4 11.4 1.0
CB A:ASN145 4.5 12.2 1.0
CB A:ASP151 4.5 13.8 1.0
CA A:ASN145 4.6 10.9 1.0
C A:SER148 4.7 15.3 1.0
N A:ASN150 4.7 13.1 1.0
CB A:ASP147 4.7 13.6 1.0
CB A:ASN150 4.7 11.5 1.0
C A:GLY188 4.7 9.9 1.0
N A:ASP189 4.8 9.5 1.0
N A:GLY188 4.8 10.4 1.0
O A:GLY188 4.8 10.8 1.0
CA A:ASN150 4.8 13.3 1.0
O A:ASN150 4.9 13.6 1.0
O A:HOH2014 4.9 11.2 1.0
C A:ASN145 4.9 11.6 1.0
N A:GLY146 4.9 11.8 1.0
CA A:ASP189 5.0 10.1 1.0

Calcium binding site 3 out of 3 in 2d0f

Go back to Calcium Binding Sites List in 2d0f
Calcium binding site 3 out of 3 in the Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N 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 Complexed with P2, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:13.7
occ:1.00
 O A:PHE281 2.3 18.3 1.0
OD1 A:ASN279 2.3 17.5 1.0
OD2 A:ASP276 2.4 11.2 1.0
OE1 A:GLU288 2.4 11.8 1.0
O A:SER283 2.4 13.4 1.0
OE2 A:GLU288 2.4 10.8 1.0
O A:HOH2013 2.5 11.0 1.0
CD A:GLU288 2.7 11.6 1.0
CG A:ASN279 3.5 17.2 1.0
C A:PHE281 3.5 17.3 1.0
CG A:ASP276 3.5 11.5 1.0
C A:SER283 3.6 14.3 1.0
CA A:ASN279 3.9 16.8 1.0
CB A:ASN279 4.1 16.2 1.0
C A:SER282 4.1 17.3 1.0
N A:PHE281 4.2 18.0 1.0
O A:SER282 4.2 16.5 1.0
CA A:GLN284 4.2 12.7 1.0
CG A:GLU288 4.3 13.4 1.0
CB A:ASP276 4.3 10.3 1.0
O A:HOH2220 4.3 13.1 1.0
N A:SER283 4.3 16.8 1.0
CA A:PHE281 4.3 17.9 1.0
N A:GLN284 4.4 13.7 1.0
C A:ASN279 4.4 18.0 1.0
N A:SER282 4.4 17.1 1.0
OD1 A:ASP276 4.5 10.0 1.0
CA A:SER282 4.5 17.8 1.0
ND2 A:ASN279 4.5 19.1 1.0
N A:GLY285 4.6 10.3 1.0
CA A:SER283 4.6 14.9 1.0
CB A:PHE281 4.7 18.0 1.0
N A:ASN280 4.8 18.1 1.0
O A:ASN279 4.9 19.1 1.0
O A:ASP276 5.0 10.7 1.0
C A:GLN284 5.0 12.1 1.0
N A:ASN279 5.0 15.7 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: Sat Dec 12 03:34:34 2020

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