Atomistry » Calcium » PDB 2cn6-2dbx » 2d0f
Atomistry »
  Calcium »
    PDB 2cn6-2dbx »
      2d0f »

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: Fri Jul 12 09:37:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy