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Calcium in PDB 5z0t: Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)

Enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne):
3.2.1.135;

Protein crystallography data

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne), PDB code: 5z0t was solved by T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.91 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.886, 50.749, 121.897, 90.00, 103.91, 90.00
R / Rfree (%) 15.8 / 18.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) (pdb code 5z0t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne), PDB code: 5z0t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5z0t

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Calcium binding site 1 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:8.5
occ:1.00
 OD1 A:ASP42 2.3 8.5 1.0
O A:ALA2 2.3 10.6 1.0
O A:ASN6 2.4 9.4 1.0
OD1 A:ASP4 2.4 8.6 1.0
OD2 A:ASP96 2.4 8.7 1.0
O A:HOH1003 2.4 8.8 1.0
O A:ASP42 2.5 8.3 1.0
CG A:ASP42 3.3 8.4 1.0
CG A:ASP96 3.3 8.8 1.0
CG A:ASP4 3.4 9.1 1.0
C A:ASP42 3.5 8.5 1.0
C A:ASN6 3.5 9.3 1.0
C A:ALA2 3.5 11.6 1.0
CA A:ASP42 3.7 8.7 1.0
OD2 A:ASP4 3.9 9.2 1.0
N A:ASP4 4.0 10.4 1.0
CB A:ASP96 4.1 8.8 1.0
OD2 A:ASP42 4.1 8.5 1.0
CB A:ASP42 4.1 8.6 1.0
N A:ALA2 4.1 12.0 1.0
OD1 A:ASP96 4.1 9.7 1.0
N A:ASN6 4.2 9.2 1.0
CA A:ASN6 4.2 9.8 1.0
N A:ASN3 4.4 11.8 1.0
CA A:ASN3 4.5 12.0 1.0
N A:VAL7 4.5 8.3 1.0
CA A:ALA2 4.5 11.6 1.0
CB A:ASN6 4.5 11.6 1.0
CB A:ASP4 4.6 9.3 1.0
CA A:VAL7 4.6 8.0 1.0
N A:ILE43 4.7 8.4 1.0
CA A:ASP4 4.7 9.9 1.0
OE1 A:GLU8 4.8 10.2 1.0
C A:ASN3 4.8 11.4 1.0
CG A:GLU8 4.8 9.3 1.0
N A:GLU8 4.9 8.2 1.0
O A:GLY41 5.0 10.3 1.0
C A:ASP4 5.0 9.3 1.0
CB A:ALA1 5.0 11.5 1.0

Calcium binding site 2 out of 6 in 5z0t

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Calcium binding site 2 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:17.7
occ:1.00
 OD1 A:ASP151 2.2 18.8 1.0
OD2 A:ASP189 2.3 17.2 1.0
OD1 A:ASN145 2.4 18.3 1.0
OD1 A:ASN150 2.4 19.4 1.0
O A:HOH826 2.5 14.3 1.0
O A:ASP147 2.5 19.4 1.0
O A:GLY187 2.5 16.0 1.0
CG A:ASN145 3.3 19.4 1.0
CG A:ASP189 3.4 16.5 1.0
CG A:ASP151 3.5 19.2 1.0
C A:ASP147 3.5 19.9 1.0
C A:GLY187 3.5 15.8 1.0
CG A:ASN150 3.6 17.9 1.0
ND2 A:ASN145 3.8 19.6 1.0
CA A:GLY187 3.9 17.3 1.0
CB A:ASP189 3.9 15.9 1.0
N A:ASP151 4.1 18.1 1.0
ND2 A:ASN150 4.2 18.4 1.0
OD2 A:ASP151 4.2 19.2 1.0
O A:ALA234 4.3 16.2 1.0
N A:ASP147 4.3 19.4 1.0
N A:SER148 4.3 20.4 1.0
CA A:ASP151 4.3 18.3 1.0
CA A:SER148 4.3 20.9 1.0
CB A:ASN145 4.4 19.4 1.0
CA A:ASP147 4.4 20.2 1.0
OD1 A:ASP189 4.4 15.9 1.0
C A:ASN150 4.4 18.8 1.0
CB A:ASP151 4.5 18.8 1.0
CA A:ASN145 4.5 19.7 1.0
N A:GLY188 4.7 16.8 1.0
C A:GLY188 4.7 15.7 1.0
C A:SER148 4.7 20.4 1.0
CB A:ASP147 4.7 21.1 1.0
O A:GLY188 4.8 16.2 1.0
N A:ASN150 4.8 19.8 1.0
CB A:ASN150 4.8 18.8 1.0
CA A:ASN150 4.9 18.9 1.0
N A:ASP189 4.9 15.4 1.0
C A:ASN145 4.9 19.9 1.0
O A:SER148 4.9 21.4 1.0
O A:HOH953 4.9 16.1 1.0
O A:ASN150 5.0 18.4 1.0
N A:GLY146 5.0 18.6 1.0

Calcium binding site 3 out of 6 in 5z0t

Go back to Calcium Binding Sites List in 5z0t
Calcium binding site 3 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:15.8
occ:1.00
 O A:PHE281 2.3 16.3 1.0
OD2 A:ASP276 2.4 13.8 1.0
O A:SER283 2.4 16.8 1.0
OE2 A:GLU288 2.4 14.2 1.0
O A:HOH1369 2.4 17.8 1.0
OD1 A:ASN279 2.4 18.0 1.0
OE1 A:GLU288 2.5 16.2 1.0
CD A:GLU288 2.8 14.8 1.0
CG A:ASN279 3.5 18.3 1.0
C A:PHE281 3.5 17.4 1.0
CG A:ASP276 3.5 13.3 1.0
C A:SER283 3.6 16.8 1.0
CA A:ASN279 3.9 17.1 1.0
CB A:ASN279 4.2 17.5 1.0
N A:PHE281 4.2 16.7 1.0
O A:HOH854 4.2 15.7 1.0
C A:SER282 4.2 18.7 1.0
CG A:GLU288 4.3 14.9 1.0
CB A:ASP276 4.3 13.0 1.0
CA A:GLN284 4.3 17.3 1.0
O A:SER282 4.3 19.3 1.0
CA A:PHE281 4.3 17.0 1.0
OD1 A:ASP276 4.4 13.7 1.0
N A:GLN284 4.4 17.0 1.0
O A:HOH1268 4.4 30.7 1.0
N A:SER283 4.4 17.2 1.0
N A:SER282 4.5 18.4 1.0
C A:ASN279 4.5 17.2 1.0
ND2 A:ASN279 4.5 20.2 1.0
CA A:SER282 4.6 19.5 1.0
N A:GLY285 4.6 14.6 1.0
CA A:SER283 4.6 17.1 1.0
CB A:PHE281 4.7 16.9 1.0
O A:HOH1187 4.8 37.1 1.0
N A:ASN280 4.9 17.1 1.0
O A:ASP276 4.9 14.1 1.0

Calcium binding site 4 out of 6 in 5z0t

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Calcium binding site 4 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:8.0
occ:1.00
 OD1 B:ASP42 2.3 8.2 1.0
O B:ASN6 2.3 8.7 1.0
O B:ALA2 2.3 9.6 1.0
OD1 B:ASP4 2.4 8.6 1.0
OD2 B:ASP96 2.4 9.0 1.0
O B:HOH935 2.5 8.7 1.0
O B:ASP42 2.5 8.3 1.0
CG B:ASP42 3.3 8.5 1.0
CG B:ASP96 3.4 8.8 1.0
C B:ASN6 3.4 9.2 1.0
CG B:ASP4 3.5 8.5 1.0
C B:ASP42 3.5 8.4 1.0
C B:ALA2 3.6 9.9 1.0
CA B:ASP42 3.7 8.4 1.0
OD2 B:ASP4 4.0 8.3 1.0
N B:ASP4 4.0 9.9 1.0
CB B:ASP96 4.1 8.7 1.0
OD2 B:ASP42 4.1 8.4 1.0
CB B:ASP42 4.1 8.3 1.0
N B:ALA2 4.1 9.8 1.0
OD1 B:ASP96 4.1 9.5 1.0
N B:ASN6 4.2 9.1 1.0
CA B:ASN6 4.2 9.8 1.0
N B:VAL7 4.4 8.6 1.0
CB B:ASN6 4.4 10.9 1.0
CA B:ASN3 4.5 11.0 1.0
N B:ASN3 4.5 10.3 1.0
CA B:ALA2 4.5 10.0 1.0
CB B:ASP4 4.6 9.0 1.0
CA B:VAL7 4.6 8.4 1.0
O B:HOH805 4.6 21.6 1.0
N B:ILE43 4.7 8.3 1.0
CG B:GLU8 4.7 8.8 1.0
OE1 B:GLU8 4.8 9.4 1.0
C B:ASN3 4.8 10.7 1.0
CA B:ASP4 4.8 9.2 1.0
N B:GLU8 4.9 8.1 1.0
CB B:ALA1 5.0 10.0 1.0
O B:GLY41 5.0 9.0 1.0
C B:ASP4 5.0 9.0 1.0

Calcium binding site 5 out of 6 in 5z0t

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Calcium binding site 5 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:10.3
occ:1.00
 OD1 B:ASP151 2.3 11.9 1.0
OD2 B:ASP189 2.3 10.4 1.0
O B:ASP147 2.4 13.1 1.0
OD1 B:ASN150 2.4 11.3 1.0
O B:HOH833 2.4 8.7 1.0
OD1 B:ASN145 2.4 10.7 1.0
O B:GLY187 2.6 9.7 1.0
CG B:ASN145 3.3 10.8 1.0
CG B:ASP189 3.4 10.8 1.0
C B:ASP147 3.4 14.0 1.0
CG B:ASN150 3.5 11.8 1.0
CG B:ASP151 3.5 12.2 1.0
C B:GLY187 3.7 9.8 1.0
ND2 B:ASN145 3.8 11.5 1.0
CB B:ASP189 3.9 10.2 1.0
ND2 B:ASN150 4.0 11.6 1.0
N B:ASP151 4.1 12.2 1.0
CA B:GLY187 4.2 10.1 1.0
N B:ASP147 4.2 13.4 1.0
N B:SER148 4.2 14.7 1.0
CA B:ASP151 4.3 12.0 1.0
O B:ALA234 4.3 11.3 1.0
CA B:SER148 4.3 15.4 1.0
OD2 B:ASP151 4.3 13.0 1.0
CA B:ASP147 4.3 13.7 1.0
CB B:ASN145 4.4 10.7 1.0
C B:ASN150 4.4 12.3 1.0
OD1 B:ASP189 4.4 10.8 1.0
CB B:ASP151 4.5 12.1 1.0
CA B:ASN145 4.6 10.9 1.0
C B:SER148 4.7 14.5 1.0
N B:ASN150 4.7 13.3 1.0
CB B:ASN150 4.7 12.3 1.0
C B:GLY188 4.7 9.9 1.0
CB B:ASP147 4.7 13.9 1.0
N B:GLY188 4.8 10.3 1.0
O B:GLY188 4.8 9.5 1.0
CA B:ASN150 4.8 12.2 1.0
O B:SER148 4.8 15.2 1.0
N B:ASP189 4.9 9.7 1.0
C B:ASN145 4.9 11.2 1.0
O B:ASN150 4.9 11.5 1.0
N B:GLY146 4.9 11.4 1.0
O B:HOH868 5.0 10.6 1.0

Calcium binding site 6 out of 6 in 5z0t

Go back to Calcium Binding Sites List in 5z0t
Calcium binding site 6 out of 6 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) Mutant A357V/Q359N/Y360E (Aqy/Vne) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:10.5
occ:1.00
 OD2 B:ASP276 2.3 9.7 1.0
O B:PHE281 2.3 11.9 1.0
O B:HOH1460 2.4 14.8 1.0
O B:SER283 2.4 11.2 1.0
OE2 B:GLU288 2.4 11.0 1.0
OD1 B:ASN279 2.4 12.1 1.0
OE1 B:GLU288 2.5 12.3 1.0
CD B:GLU288 2.8 11.1 1.0
CG B:ASN279 3.4 12.5 1.0
CG B:ASP276 3.5 9.7 1.0
C B:PHE281 3.5 12.4 1.0
C B:SER283 3.6 11.6 1.0
CA B:ASN279 3.9 12.2 1.0
CB B:ASN279 4.2 12.3 1.0
O B:HOH813 4.2 11.1 1.0
N B:PHE281 4.2 12.7 1.0
C B:SER282 4.2 12.4 1.0
CB B:ASP276 4.3 9.6 1.0
CA B:GLN284 4.3 13.2 1.0
CG B:GLU288 4.3 10.9 1.0
OD1 B:ASP276 4.3 10.4 1.0
CA B:PHE281 4.3 12.7 1.0
N B:SER283 4.4 11.6 1.0
O B:HOH1154 4.4 20.3 1.0
ND2 B:ASN279 4.4 13.3 1.0
N B:GLN284 4.4 12.6 1.0
O B:SER282 4.4 13.0 1.0
N B:SER282 4.5 12.1 1.0
C B:ASN279 4.5 12.4 1.0
CA B:SER282 4.5 12.6 1.0
CA B:SER283 4.6 11.7 1.0
O B:HOH1356 4.6 36.2 1.0
N B:GLY285 4.7 10.5 1.0
CB B:PHE281 4.7 12.9 1.0
O B:HOH1013 4.8 36.4 1.0
N B:ASN280 4.8 13.0 1.0
N B:ASN279 5.0 12.0 1.0

Reference:

T.Tonozuka, T.Nihira, M.Mizuno, A.Nishikawa, S.Kamitori. Mutagenesis-Induced Conformational Change in Domain B of A Pullulan-Hydrolyzing Alpha-Amylase Tva I Amylase V. 2 1 2018.
ISSN: ESSN 2450-9728
DOI: 10.1515/AMYLASE-2018-0001
Page generated: Mon Jul 15 15:38:07 2024

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