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Calcium in PDB 5z0u: Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11)

Enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11)

All present enzymatic activity of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11):
3.2.1.135;

Protein crystallography data

The structure of Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11), PDB code: 5z0u was solved by T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 1.37
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.972, 54.022, 77.907, 90.00, 100.07, 90.00
R / Rfree (%) 13.8 / 15

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11) (pdb code 5z0u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11), PDB code: 5z0u:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5z0u

Go back to Calcium Binding Sites List in 5z0u
Calcium binding site 1 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11)


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) 11 Residues (From A363 to N373) Deletion Mutant (DEL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:10.2
occ:1.00
 OD1 A:ASP42 2.3 10.1 1.0
O A:ALA2 2.3 11.6 1.0
O A:ASN6 2.3 11.0 1.0
OD2 A:ASP96 2.4 10.3 1.0
OD1 A:ASP4 2.4 13.1 1.0
O A:HOH906 2.4 12.3 1.0
O A:ASP42 2.5 9.3 1.0
CG A:ASP42 3.4 9.9 1.0
CG A:ASP96 3.4 10.4 1.0
CG A:ASP4 3.4 13.4 1.0
C A:ASN6 3.5 11.2 1.0
C A:ASP42 3.5 9.4 1.0
C A:ALA2 3.6 12.4 1.0
CA A:ASP42 3.8 9.5 1.0
OD2 A:ASP4 3.9 14.1 1.0
N A:ASP4 4.0 13.2 1.0
N A:ALA2 4.1 12.2 1.0
CB A:ASP96 4.1 9.8 1.0
N A:ASN6 4.2 11.5 1.0
CB A:ASP42 4.2 9.6 1.0
OD2 A:ASP42 4.2 9.8 1.0
OD1 A:ASP96 4.2 11.3 1.0
CA A:ASN6 4.2 11.9 1.0
N A:ASN3 4.5 12.5 1.0
N A:VAL7 4.5 10.6 1.0
CA A:ASN3 4.5 13.4 1.0
CA A:ALA2 4.5 12.6 1.0
CB A:ASN6 4.5 12.8 1.0
CB A:ASP4 4.6 13.4 1.0
CA A:VAL7 4.7 10.3 1.0
OE1 A:GLU8 4.7 13.5 1.0
CA A:ASP4 4.7 13.0 1.0
C A:ASN3 4.7 13.6 1.0
N A:ILE43 4.7 9.3 1.0
CG A:GLU8 4.8 11.5 1.0
O A:HOH1242 4.9 25.6 1.0
CB A:ALA1 4.9 12.4 1.0
C A:ASP4 4.9 12.7 1.0
N A:GLU8 5.0 10.2 1.0
O A:GLY41 5.0 10.0 1.0

Calcium binding site 2 out of 3 in 5z0u

Go back to Calcium Binding Sites List in 5z0u
Calcium binding site 2 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11)


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) 11 Residues (From A363 to N373) Deletion Mutant (DEL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:6.9
occ:1.00
 OD1 A:ASP151 2.3 8.3 1.0
OD2 A:ASP189 2.4 6.4 1.0
O A:ASP147 2.4 9.3 1.0
OD1 A:ASN150 2.4 8.4 1.0
O A:HOH902 2.4 7.5 1.0
OD1 A:ASN145 2.5 7.6 1.0
O A:GLY187 2.5 6.9 1.0
CG A:ASN145 3.3 7.4 1.0
CG A:ASP189 3.4 6.2 1.0
C A:ASP147 3.5 10.3 1.0
CG A:ASN150 3.5 8.3 1.0
C A:GLY187 3.5 6.3 1.0
CG A:ASP151 3.5 8.4 1.0
ND2 A:ASN145 3.8 7.6 1.0
CB A:ASP189 3.9 6.3 1.0
CA A:GLY187 4.0 6.5 1.0
ND2 A:ASN150 4.0 8.2 1.0
N A:ASP151 4.1 8.2 1.0
N A:ASP147 4.1 9.1 1.0
CA A:ASP147 4.3 10.1 1.0
OD2 A:ASP151 4.3 9.0 1.0
CA A:ASP151 4.3 8.4 1.0
O A:ALA234 4.3 7.6 1.0
OD1 A:ASP189 4.4 6.3 1.0
N A:SER148 4.4 11.3 1.0
CA A:SER148 4.4 11.5 1.0
C A:ASN150 4.4 8.1 1.0
CB A:ASN145 4.5 7.2 1.0
CB A:ASP151 4.5 8.3 1.0
CA A:ASN145 4.6 7.0 1.0
N A:GLY188 4.7 6.2 1.0
C A:GLY188 4.7 6.0 1.0
CB A:ASP147 4.7 11.4 1.0
CB A:ASN150 4.8 8.3 1.0
C A:SER148 4.8 10.1 1.0
N A:ASN150 4.8 8.5 1.0
O A:GLY188 4.8 6.1 1.0
N A:GLY146 4.9 7.2 1.0
CA A:ASN150 4.9 8.3 1.0
O A:ASN150 4.9 8.4 1.0
N A:ASP189 4.9 6.0 1.0
C A:ASN145 4.9 7.0 1.0
O A:HOH934 5.0 7.5 1.0

Calcium binding site 3 out of 3 in 5z0u

Go back to Calcium Binding Sites List in 5z0u
Calcium binding site 3 out of 3 in the Thermoactinomyces Vulgaris R-47 Alpha-Amylase I (Tva I) 11 Residues (From A363 to N373) Deletion Mutant (DEL11)


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) 11 Residues (From A363 to N373) Deletion Mutant (DEL11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:14.4
occ:1.00
 OD2 A:ASP276 2.3 13.2 1.0
O A:HOH1403 2.3 21.2 1.0
O A:PHE281 2.4 14.2 1.0
OD1 A:ASN279 2.4 17.8 1.0
O A:SER283 2.4 14.0 1.0
OE2 A:GLU288 2.5 15.1 1.0
OE1 A:GLU288 2.6 17.8 1.0
CD A:GLU288 2.9 14.7 1.0
CG A:ASN279 3.5 18.3 1.0
CG A:ASP276 3.5 12.7 1.0
C A:PHE281 3.5 15.2 1.0
C A:SER283 3.7 13.8 1.0
CA A:ASN279 3.9 17.7 1.0
N A:PHE281 4.2 15.2 1.0
CB A:ASN279 4.2 18.3 1.0
O A:HOH851 4.2 12.7 1.0
C A:SER282 4.2 15.1 1.0
CA A:GLN284 4.3 14.4 1.0
CB A:ASP276 4.3 11.8 1.0
O A:SER282 4.3 15.3 1.0
CA A:PHE281 4.3 15.4 1.0
OD1 A:ASP276 4.4 13.8 1.0
CG A:GLU288 4.4 14.8 1.0
N A:SER283 4.4 14.3 1.0
N A:GLN284 4.4 14.2 1.0
C A:ASN279 4.5 17.7 1.0
ND2 A:ASN279 4.5 20.8 1.0
N A:SER282 4.5 15.6 1.0
N A:GLY285 4.6 12.4 1.0
CB A:PHE281 4.6 15.5 1.0
CA A:SER282 4.6 15.6 1.0
CA A:SER283 4.7 13.9 1.0
N A:ASN280 4.9 17.1 1.0
O A:HOH1072 4.9 35.1 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: Wed Jul 9 12:07:44 2025

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