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Calcium in PDB 2d0g: Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P5, A Pullulan Model Oligosaccharide

Enzymatic activity of Crystal Structure of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (Tvai) Mutant D356N/E396Q Complexed with P5, 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 P5, 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 P5, A Pullulan Model Oligosaccharide, PDB code: 2d0g 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) 35.00 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.885, 50.698, 108.007, 90.00, 103.43, 90.00
R / Rfree (%) 15 / 19

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 P5, A Pullulan Model Oligosaccharide (pdb code 2d0g). 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 P5, A Pullulan Model Oligosaccharide, PDB code: 2d0g:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2d0g

Go back to Calcium Binding Sites List in 2d0g
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 P5, 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 P5, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:13.3
occ:1.00
 O A:ASN6 2.2 11.2 1.0
OD1 A:ASP42 2.3 15.5 1.0
O A:ALA2 2.3 9.5 1.0
O A:ASP42 2.4 14.3 1.0
OD1 A:ASP4 2.5 12.4 1.0
OD2 A:ASP96 2.5 10.9 1.0
O A:HOH2474 2.6 28.3 1.0
CG A:ASP42 3.2 13.7 1.0
CG A:ASP96 3.3 11.1 1.0
C A:ASN6 3.3 12.7 1.0
C A:ASP42 3.4 13.2 1.0
C A:ALA2 3.6 10.7 1.0
CG A:ASP4 3.6 15.8 1.0
CA A:ASP42 3.8 12.8 1.0
OD1 A:ASP96 3.9 6.9 1.0
OD2 A:ASP42 4.0 12.2 1.0
N A:ASP4 4.0 13.1 1.0
CB A:ASP42 4.1 12.3 1.0
CB A:ASP96 4.1 11.1 1.0
N A:ASN6 4.1 14.4 1.0
CA A:ASN6 4.1 13.5 1.0
N A:ALA2 4.2 12.2 1.0
OD2 A:ASP4 4.2 18.2 1.0
N A:VAL7 4.3 13.9 1.0
CA A:ASN3 4.4 12.8 1.0
CB A:ASN6 4.4 13.9 1.0
N A:ASN3 4.4 11.7 1.0
CA A:VAL7 4.5 13.3 1.0
CA A:ALA2 4.5 11.7 1.0
N A:ILE43 4.6 11.9 1.0
CG A:GLU8 4.7 15.1 1.0
C A:ASN3 4.7 13.1 1.0
OE1 A:GLU8 4.8 15.0 1.0
CB A:ASP4 4.8 14.1 1.0
CA A:ASP4 4.8 13.7 1.0
N A:GLU8 4.9 13.5 1.0
OD1 A:ASN6 4.9 19.4 1.0
CG A:ASN6 5.0 17.2 1.0

Calcium binding site 2 out of 3 in 2d0g

Go back to Calcium Binding Sites List in 2d0g
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 P5, 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 P5, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:22.8
occ:1.00
 OD2 A:ASP189 2.2 10.1 1.0
OD2 A:ASP151 2.4 18.5 1.0
O A:HOH2118 2.4 22.5 1.0
O A:ASP147 2.4 18.8 1.0
OD1 A:ASN150 2.4 20.8 1.0
O A:GLY187 2.6 17.0 1.0
OD1 A:ASN145 2.8 23.7 1.0
CG A:ASP189 3.2 11.8 1.0
CG A:ASN145 3.3 21.7 1.0
C A:ASP147 3.4 17.9 1.0
CG A:ASN150 3.5 19.6 1.0
ND2 A:ASN145 3.6 22.1 1.0
CG A:ASP151 3.6 18.2 1.0
C A:GLY187 3.6 17.9 1.0
CB A:ASP189 3.8 12.0 1.0
CA A:GLY187 4.0 17.0 1.0
ND2 A:ASN150 4.1 18.5 1.0
N A:ASP151 4.1 15.5 1.0
O A:ALA234 4.1 14.2 1.0
N A:SER148 4.2 18.1 1.0
CA A:SER148 4.2 17.7 1.0
N A:ASP147 4.2 17.2 1.0
OD1 A:ASP189 4.2 14.0 1.0
CA A:ASP151 4.3 17.4 1.0
CA A:ASP147 4.3 17.8 1.0
OD1 A:ASP151 4.4 20.2 1.0
CB A:ASN145 4.5 19.2 1.0
C A:ASN150 4.5 16.3 1.0
CA A:ASN145 4.5 18.7 1.0
CB A:ASP151 4.5 17.9 1.0
CB A:ASP147 4.7 18.8 1.0
C A:GLY188 4.7 13.6 1.0
N A:ASP189 4.7 12.7 1.0
C A:SER148 4.7 16.2 1.0
N A:GLY188 4.8 17.9 1.0
N A:ASN150 4.8 14.9 1.0
CB A:ASN150 4.8 17.4 1.0
O A:GLY188 4.8 13.3 1.0
O A:HOH2014 4.9 2.9 1.0
N A:GLY146 4.9 17.5 1.0
CA A:ASP189 4.9 12.0 1.0
CA A:ASN150 4.9 15.8 1.0
O A:ASN150 5.0 15.5 1.0
C A:ASN145 5.0 18.1 1.0

Calcium binding site 3 out of 3 in 2d0g

Go back to Calcium Binding Sites List in 2d0g
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 P5, 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 P5, A Pullulan Model Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:15.0
occ:1.00
 OD2 A:ASP276 2.2 12.9 1.0
OD1 A:ASN279 2.3 19.6 1.0
O A:PHE281 2.4 16.6 1.0
OE1 A:GLU288 2.4 18.5 1.0
O A:HOH2263 2.4 16.9 1.0
OE2 A:GLU288 2.5 19.3 1.0
O A:SER283 2.5 15.4 1.0
CD A:GLU288 2.8 18.7 1.0
CG A:ASN279 3.4 20.0 1.0
CG A:ASP276 3.5 12.8 1.0
C A:PHE281 3.5 14.4 1.0
C A:SER283 3.7 14.9 1.0
CA A:ASN279 3.9 16.9 1.0
CB A:ASN279 4.1 17.7 1.0
O A:HOH2165 4.1 25.3 1.0
C A:SER282 4.2 14.1 1.0
N A:PHE281 4.3 13.6 1.0
CG A:GLU288 4.3 17.4 1.0
CA A:GLN284 4.3 18.6 1.0
OD1 A:ASP276 4.3 14.2 1.0
CB A:ASP276 4.3 12.3 1.0
O A:HOH2090 4.3 8.3 1.0
O A:SER282 4.4 15.2 1.0
N A:SER283 4.4 13.8 1.0
CA A:PHE281 4.4 13.1 1.0
C A:ASN279 4.4 16.6 1.0
N A:GLN284 4.5 15.4 1.0
N A:SER282 4.5 14.5 1.0
ND2 A:ASN279 4.5 19.3 1.0
CA A:SER282 4.5 13.6 1.0
CA A:SER283 4.7 14.7 1.0
N A:GLY285 4.8 18.3 1.0
CB A:PHE281 4.8 11.4 1.0
N A:ASN280 4.8 15.8 1.0
N A:ASN279 5.0 16.4 1.0
O A:ASN279 5.0 16.2 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: Fri Jul 12 09:38:20 2024

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