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Calcium in PDB 1ji1: Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1

Enzymatic activity of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1

All present enzymatic activity of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1, PDB code: 1ji1 was solved by S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.46 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.570, 50.840, 107.800, 90.00, 104.20, 90.00
R / Rfree (%) 18.2 / 20.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 (pdb code 1ji1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1, PDB code: 1ji1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ji1

Go back to Calcium Binding Sites List in 1ji1
Calcium binding site 1 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:7.6
occ:1.00
 O A:ALA2 2.3 9.9 1.0
OD1 A:ASP42 2.3 6.0 1.0
OD2 A:ASP96 2.3 7.0 1.0
O A:ASN6 2.4 6.9 1.0
OD1 A:ASP4 2.4 7.5 1.0
O A:HOH2487 2.5 6.6 1.0
O A:ASP42 2.5 5.5 1.0
CG A:ASP96 3.3 8.4 1.0
CG A:ASP42 3.3 7.4 1.0
C A:ASP42 3.5 5.7 1.0
C A:ASN6 3.5 8.0 1.0
CG A:ASP4 3.5 9.5 1.0
C A:ALA2 3.5 12.0 1.0
CA A:ASP42 3.8 6.1 1.0
N A:ASP4 3.9 9.1 1.0
OD2 A:ASP4 4.0 10.3 1.0
OD1 A:ASP96 4.0 7.4 1.0
OD2 A:ASP42 4.1 7.0 1.0
CB A:ASP96 4.1 9.2 1.0
CB A:ASP42 4.1 6.5 1.0
N A:ASN6 4.1 6.9 1.0
N A:ALA2 4.1 11.6 1.0
CA A:ASN6 4.2 7.7 1.0
CA A:ASN3 4.4 11.7 1.0
N A:ASN3 4.4 11.8 1.0
O A:HOH2726 4.4 27.5 1.0
N A:VAL7 4.5 7.5 1.0
CA A:ALA2 4.5 11.8 1.0
CB A:ASN6 4.6 9.7 1.0
CB A:ASP4 4.6 8.4 1.0
CA A:VAL7 4.6 6.2 1.0
CG A:GLU8 4.7 7.5 1.0
C A:ASN3 4.7 11.2 1.0
CA A:ASP4 4.7 8.8 1.0
N A:ILE43 4.7 6.6 1.0
OE1 A:GLU8 4.8 8.1 1.0
C A:ASP4 4.9 8.0 1.0
N A:GLU8 4.9 5.1 1.0

Calcium binding site 2 out of 6 in 1ji1

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Calcium binding site 2 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:12.6
occ:1.00
 OD2 A:ASP151 2.2 14.3 1.0
OD2 A:ASP189 2.3 13.5 1.0
OD1 A:ASN150 2.4 12.2 1.0
O A:HOH2145 2.4 10.2 1.0
OD1 A:ASN145 2.5 10.6 1.0
O A:ASP147 2.5 13.3 1.0
O A:GLY187 2.5 11.0 1.0
CG A:ASN145 3.3 12.7 1.0
CG A:ASP189 3.4 13.0 1.0
C A:ASP147 3.4 13.7 1.0
CG A:ASP151 3.5 15.2 1.0
CG A:ASN150 3.5 11.3 1.0
C A:GLY187 3.6 11.3 1.0
ND2 A:ASN145 3.7 12.8 1.0
CB A:ASP189 4.0 11.8 1.0
CA A:GLY187 4.0 12.3 1.0
ND2 A:ASN150 4.1 12.2 1.0
N A:ASP151 4.1 13.4 1.0
OD1 A:ASP151 4.2 16.8 1.0
N A:SER148 4.2 13.6 1.0
CA A:SER148 4.2 14.3 1.0
N A:ASP147 4.2 12.7 1.0
O A:ALA234 4.3 11.9 1.0
CA A:ASP151 4.3 13.5 1.0
CA A:ASP147 4.4 13.4 1.0
OD1 A:ASP189 4.4 11.6 1.0
CB A:ASN145 4.4 13.6 1.0
C A:ASN150 4.5 13.1 1.0
CB A:ASP151 4.5 14.4 1.0
CA A:ASN145 4.5 14.1 1.0
C A:SER148 4.7 14.0 1.0
C A:GLY188 4.7 11.8 1.0
N A:ASN150 4.7 14.6 1.0
N A:GLY188 4.7 11.9 1.0
CB A:ASN150 4.8 12.7 1.0
CB A:ASP147 4.8 13.8 1.0
N A:ASP189 4.8 11.0 1.0
O A:GLY188 4.8 12.8 1.0
CA A:ASN150 4.9 13.2 1.0
C A:ASN145 4.9 13.6 1.0
N A:GLY146 4.9 12.5 1.0
O A:SER148 5.0 14.3 1.0
O A:ASN150 5.0 13.7 1.0
O A:HOH2012 5.0 13.4 1.0

Calcium binding site 3 out of 6 in 1ji1

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Calcium binding site 3 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:12.3
occ:1.00
 OD2 A:ASP276 2.3 11.1 1.0
O A:PHE281 2.3 13.5 1.0
OD1 A:ASN279 2.4 15.6 1.0
OE2 A:GLU288 2.4 14.2 1.0
O A:SER283 2.4 14.1 1.0
O A:HOH2478 2.5 15.5 1.0
OE1 A:GLU288 2.5 13.8 1.0
CD A:GLU288 2.8 13.0 1.0
CG A:ASN279 3.5 15.2 1.0
CG A:ASP276 3.5 9.5 1.0
C A:PHE281 3.5 14.1 1.0
C A:SER283 3.6 14.2 1.0
CA A:ASN279 3.8 13.4 1.0
CB A:ASN279 4.0 14.8 1.0
O A:HOH2159 4.1 13.1 1.0
N A:PHE281 4.2 13.2 1.0
C A:SER282 4.2 15.5 1.0
CB A:ASP276 4.3 10.0 1.0
CA A:GLN284 4.3 14.4 1.0
CG A:GLU288 4.3 13.2 1.0
CA A:PHE281 4.3 13.8 1.0
N A:SER283 4.3 15.0 1.0
C A:ASN279 4.3 14.2 1.0
O A:SER282 4.4 15.9 1.0
OD1 A:ASP276 4.4 9.5 1.0
N A:GLN284 4.4 14.3 1.0
O A:HOH2724 4.5 27.1 1.0
N A:SER282 4.5 15.2 1.0
ND2 A:ASN279 4.6 18.1 1.0
N A:GLY285 4.6 12.1 1.0
CA A:SER282 4.6 16.6 1.0
CA A:SER283 4.6 14.6 1.0
CB A:PHE281 4.7 13.6 1.0
N A:ASN280 4.7 14.0 1.0
O A:ASN279 4.9 14.7 1.0
N A:ASN279 4.9 13.3 1.0
C A:GLN284 5.0 12.8 1.0
O A:ASP276 5.0 11.5 1.0

Calcium binding site 4 out of 6 in 1ji1

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Calcium binding site 4 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2004

b:7.8
occ:1.00
 O B:ALA2 2.3 7.7 1.0
OD1 B:ASP42 2.3 6.5 1.0
O B:ASN6 2.3 6.3 1.0
OD2 B:ASP96 2.4 7.9 1.0
OD1 B:ASP4 2.4 6.3 1.0
O B:HOH2098 2.4 5.8 1.0
O B:ASP42 2.6 5.7 1.0
CG B:ASP42 3.3 7.5 1.0
CG B:ASP96 3.3 7.3 1.0
C B:ASN6 3.5 6.7 1.0
CG B:ASP4 3.5 7.5 1.0
C B:ASP42 3.5 5.2 1.0
C B:ALA2 3.5 8.5 1.0
CA B:ASP42 3.8 5.5 1.0
N B:ASP4 3.9 8.8 1.0
OD2 B:ASP4 4.0 7.2 1.0
OD1 B:ASP96 4.1 7.6 1.0
OD2 B:ASP42 4.1 6.2 1.0
N B:ALA2 4.1 8.7 1.0
CB B:ASP42 4.1 6.4 1.0
CB B:ASP96 4.1 6.8 1.0
N B:ASN6 4.1 7.1 1.0
CA B:ASN6 4.2 7.5 1.0
CA B:ASN3 4.4 9.0 1.0
N B:ASN3 4.4 8.2 1.0
N B:VAL7 4.4 5.9 1.0
CA B:ALA2 4.5 8.1 1.0
CB B:ASN6 4.5 8.7 1.0
O B:HOH2512 4.6 26.9 1.0
CB B:ASP4 4.6 8.1 1.0
CA B:VAL7 4.6 5.1 1.0
C B:ASN3 4.7 9.6 1.0
CA B:ASP4 4.7 8.0 1.0
CG B:GLU8 4.7 6.0 1.0
OE1 B:GLU8 4.8 7.7 1.0
N B:ILE43 4.8 5.2 1.0
N B:GLU8 4.9 4.4 1.0
C B:ASP4 4.9 7.3 1.0
CB B:ALA1 5.0 8.6 1.0

Calcium binding site 5 out of 6 in 1ji1

Go back to Calcium Binding Sites List in 1ji1
Calcium binding site 5 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2005

b:10.1
occ:1.00
 OD2 B:ASP151 2.3 11.2 1.0
OD1 B:ASN150 2.3 10.6 1.0
O B:ASP147 2.4 12.4 1.0
OD2 B:ASP189 2.4 9.4 1.0
O B:HOH2526 2.4 8.4 1.0
OD1 B:ASN145 2.5 10.2 1.0
O B:GLY187 2.6 9.4 1.0
CG B:ASN145 3.3 9.7 1.0
C B:ASP147 3.4 13.9 1.0
CG B:ASP189 3.4 11.0 1.0
CG B:ASN150 3.5 11.3 1.0
CG B:ASP151 3.6 13.5 1.0
C B:GLY187 3.7 9.5 1.0
ND2 B:ASN145 3.7 11.0 1.0
CB B:ASP189 3.9 8.6 1.0
N B:ASP151 4.0 11.2 1.0
ND2 B:ASN150 4.0 10.8 1.0
CA B:GLY187 4.2 9.7 1.0
N B:SER148 4.2 13.8 1.0
N B:ASP147 4.2 13.4 1.0
CA B:SER148 4.2 13.9 1.0
CA B:ASP151 4.2 12.0 1.0
O B:ALA234 4.3 9.6 1.0
CA B:ASP147 4.3 13.7 1.0
OD1 B:ASP151 4.3 13.5 1.0
CB B:ASN145 4.4 10.0 1.0
C B:ASN150 4.4 11.3 1.0
OD1 B:ASP189 4.4 10.2 1.0
CB B:ASP151 4.5 12.8 1.0
CA B:ASN145 4.5 11.1 1.0
C B:SER148 4.6 13.4 1.0
CB B:ASP147 4.7 13.6 1.0
N B:ASN150 4.7 13.1 1.0
CB B:ASN150 4.7 12.6 1.0
C B:GLY188 4.7 9.2 1.0
N B:ASP189 4.8 9.3 1.0
O B:GLY188 4.8 10.1 1.0
CA B:ASN150 4.8 11.0 1.0
N B:GLY188 4.8 11.2 1.0
C B:ASN145 4.9 11.9 1.0
O B:SER148 4.9 14.4 1.0
O B:ASN150 4.9 10.9 1.0
N B:GLY146 4.9 11.6 1.0

Calcium binding site 6 out of 6 in 1ji1

Go back to Calcium Binding Sites List in 1ji1
Calcium binding site 6 out of 6 in the Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of Thermoactinomyces Vulgaris R-47 Alpha- Amylase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2006

b:9.0
occ:1.00
 O B:PHE281 2.3 10.2 1.0
OD2 B:ASP276 2.4 9.0 1.0
OE2 B:GLU288 2.4 11.4 1.0
OD1 B:ASN279 2.4 11.7 1.0
O B:HOH2156 2.4 14.6 1.0
O B:SER283 2.5 9.3 1.0
OE1 B:GLU288 2.5 12.3 1.0
CD B:GLU288 2.8 9.0 1.0
CG B:ASN279 3.5 10.1 1.0
C B:PHE281 3.5 10.2 1.0
CG B:ASP276 3.5 8.2 1.0
C B:SER283 3.6 8.8 1.0
CA B:ASN279 3.9 9.9 1.0
CB B:ASN279 4.1 10.1 1.0
O B:HOH2229 4.2 9.5 1.0
N B:PHE281 4.2 9.9 1.0
C B:SER282 4.2 10.8 1.0
N B:SER283 4.3 9.3 1.0
CG B:GLU288 4.3 9.4 1.0
O B:HOH2738 4.3 15.9 1.0
CA B:GLN284 4.3 10.6 1.0
CB B:ASP276 4.3 8.6 1.0
CA B:PHE281 4.3 9.8 1.0
OD1 B:ASP276 4.4 8.3 1.0
C B:ASN279 4.4 10.8 1.0
N B:GLN284 4.4 9.6 1.0
N B:SER282 4.4 9.6 1.0
ND2 B:ASN279 4.5 12.8 1.0
CA B:SER282 4.5 11.1 1.0
O B:SER282 4.6 12.1 1.0
N B:GLY285 4.7 7.8 1.0
CA B:SER283 4.7 9.3 1.0
CB B:PHE281 4.7 9.9 1.0
N B:ASN280 4.8 10.6 1.0
O B:ASN279 4.9 11.2 1.0
N B:ASN279 5.0 9.3 1.0

Reference:

S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano. Crystal Structures and Structural Comparison of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 (Tvai) at 1.6 A Resolution and Alpha-Amylase 2 (Tvaii) at 2.3 A Resolution. J.Mol.Biol. V. 318 443 2002.
ISSN: ISSN 0022-2836
PubMed: 12051850
DOI: 10.1016/S0022-2836(02)00111-0
Page generated: Thu Jul 11 10:45:13 2024

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