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Calcium in PDB 1ava: AMY2/Basi Protein-Protein Complex From Barley Seed

Enzymatic activity of AMY2/Basi Protein-Protein Complex From Barley Seed

All present enzymatic activity of AMY2/Basi Protein-Protein Complex From Barley Seed:
3.2.1.1;

Protein crystallography data

The structure of AMY2/Basi Protein-Protein Complex From Barley Seed, PDB code: 1ava was solved by F.Vallee, A.Kadziola, Y.Bourne, M.Juy, B.Svensson, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.500, 96.180, 170.150, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the AMY2/Basi Protein-Protein Complex From Barley Seed (pdb code 1ava). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the AMY2/Basi Protein-Protein Complex From Barley Seed, PDB code: 1ava:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1ava

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Calcium binding site 1 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:18.9
occ:1.00
 OD2 A:ASP148 2.2 12.9 1.0
OD1 A:ASN91 2.3 12.4 1.0
O A:GLY183 2.4 13.8 1.0
O A:HOH601 2.4 25.1 1.0
O A:ALA141 2.5 12.2 1.0
OD1 A:ASP138 2.6 16.8 1.0
OD2 A:ASP138 2.6 20.8 1.0
CG A:ASP138 3.0 20.9 1.0
CG A:ASN91 3.3 16.7 1.0
C A:GLY183 3.4 13.5 1.0
CG A:ASP148 3.4 16.2 1.0
C A:ALA141 3.6 13.0 1.0
CA A:GLY183 3.7 10.2 1.0
ND2 A:ASN91 3.7 15.5 1.0
CB A:ASP148 3.9 9.9 1.0
O A:GLY140 4.2 16.7 1.0
CA A:ASP142 4.3 11.0 1.0
C A:GLY140 4.3 14.2 1.0
N A:ASP142 4.4 14.9 1.0
O A:ASN91 4.4 19.1 1.0
OD1 A:ASP148 4.4 12.5 1.0
CB A:ASP138 4.5 19.8 1.0
N A:ALA141 4.5 14.8 1.0
N A:TYR184 4.5 14.7 1.0
CB A:ASN91 4.6 15.9 1.0
CA A:ALA141 4.7 11.3 1.0
O A:HOH643 4.7 20.7 1.0
N A:GLY140 4.8 15.8 1.0
CA A:GLY140 4.8 12.8 1.0
O A:HOH524 4.9 15.7 1.0
C A:ASP142 4.9 14.3 1.0
N A:PHE143 5.0 10.2 1.0
CA A:ASP148 5.0 14.1 1.0
SG A:CYS124 5.0 18.2 1.0

Calcium binding site 2 out of 8 in 1ava

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Calcium binding site 2 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:33.7
occ:1.00
 OE2 A:GLU108 2.1 32.8 1.0
O A:ASP113 2.4 32.9 1.0
O A:THR111 2.5 35.2 1.0
OD2 A:ASP117 2.6 32.5 1.0
OD1 A:ASP117 2.6 29.5 1.0
O A:HOH575 2.7 30.0 1.0
CD A:GLU108 2.9 31.4 1.0
CG A:ASP117 3.0 32.6 1.0
OE1 A:GLU108 3.1 37.4 1.0
C A:ASP113 3.7 31.7 1.0
C A:THR111 3.7 35.1 1.0
OG1 A:THR111 4.1 30.0 1.0
N A:GLY109 4.1 24.3 1.0
N A:THR111 4.1 33.2 1.0
O A:ARG115 4.2 29.7 1.0
O A:HOH521 4.2 49.8 1.0
C A:PRO112 4.3 34.5 1.0
N A:ASP113 4.3 31.1 1.0
CG A:GLU108 4.3 29.1 1.0
N A:GLY110 4.4 28.2 1.0
CB A:ASP117 4.5 31.6 1.0
CA A:ALA114 4.5 31.4 1.0
O A:PRO112 4.5 36.7 1.0
CA A:THR111 4.5 30.2 1.0
N A:ALA114 4.5 29.6 1.0
CA A:ASP113 4.6 32.5 1.0
N A:PRO112 4.6 37.0 1.0
CA A:PRO112 4.7 35.1 1.0
N A:ARG115 4.7 28.6 1.0
C A:ALA114 4.7 29.4 1.0
CA A:GLY109 4.8 25.2 1.0
CA A:GLU108 4.8 26.2 1.0
C A:GLU108 4.9 24.3 1.0
CB A:THR111 4.9 27.0 1.0
O A:HOH522 5.0 36.2 1.0

Calcium binding site 3 out of 8 in 1ava

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Calcium binding site 3 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:28.1
occ:1.00
 O A:HOH584 2.2 9.9 1.0
O A:ALA146 2.2 18.8 1.0
OD1 A:ASP148 2.3 12.5 1.0
O A:PHE143 2.3 19.5 1.0
OD2 A:ASP127 2.3 18.6 1.0
OD1 A:ASP142 2.4 17.7 1.0
CG A:ASP127 3.1 20.3 1.0
OD1 A:ASP127 3.2 20.0 1.0
CG A:ASP142 3.3 15.0 1.0
C A:ALA146 3.4 15.8 1.0
CG A:ASP148 3.4 16.2 1.0
C A:PHE143 3.5 17.0 1.0
N A:ASP148 3.5 11.8 1.0
OD2 A:ASP142 3.6 13.4 1.0
N A:PHE143 3.8 10.2 1.0
CB A:ASP148 3.9 9.9 1.0
C A:PRO147 3.9 15.5 1.0
CA A:PRO147 4.1 15.7 1.0
N A:PRO147 4.1 15.7 1.0
CA A:ASP148 4.2 14.1 1.0
CA A:PHE143 4.2 14.7 1.0
O A:HOH675 4.3 44.6 1.0
O A:HOH524 4.3 15.7 1.0
N A:ALA146 4.3 17.1 1.0
N A:GLY144 4.4 17.8 1.0
OD2 A:ASP148 4.4 12.9 1.0
O A:GLY144 4.5 22.6 1.0
CB A:ASP127 4.5 15.7 1.0
CA A:ALA146 4.5 15.4 1.0
CA A:GLY144 4.6 18.0 1.0
C A:GLY144 4.6 19.7 1.0
CB A:ASP142 4.6 13.6 1.0
CB A:PHE143 4.6 15.4 1.0
C A:ASP142 4.7 14.3 1.0
O A:HOH743 4.7 32.2 1.0
O A:PRO147 4.8 17.7 1.0
CA A:ASP142 4.9 11.0 1.0

Calcium binding site 4 out of 8 in 1ava

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Calcium binding site 4 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:32.3
occ:1.00
 O C:HOH185 2.1 28.7 1.0
O A:HOH644 2.2 22.1 1.0
O A:HOH612 2.3 31.3 1.0
O A:HOH597 2.4 14.7 1.0
O A:HOH741 2.4 31.7 1.0
O A:HOH795 2.7 27.9 1.0
O A:HOH611 2.9 29.6 1.0
OE2 C:GLU168 3.9 30.9 1.0
O A:HOH614 4.1 33.4 1.0
O A:HOH607 4.1 22.9 1.0
OD1 A:ASP179 4.4 16.8 1.0
O A:HOH742 4.4 25.6 1.0
CG C:GLU168 4.6 20.3 1.0
OD2 A:ASP289 4.6 9.8 1.0
CD1 A:PHE180 4.6 19.0 1.0
OE2 A:GLU204 4.7 11.9 1.0
OH C:TYR170 4.7 27.3 1.0
OE1 A:GLU204 4.7 12.0 1.0
CD C:GLU168 4.7 26.9 1.0
O A:HOH615 4.7 27.0 1.0
OD1 A:ASP289 4.8 9.5 1.0
O C:HOH182 4.8 16.3 1.0
OD2 A:ASP179 4.8 15.0 1.0
CE1 A:PHE143 5.0 19.6 1.0
CG A:ASP289 5.0 10.7 1.0

Calcium binding site 5 out of 8 in 1ava

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Calcium binding site 5 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:18.2
occ:1.00
 O B:GLY183 2.3 23.7 1.0
OD1 B:ASN91 2.3 12.7 1.0
OD2 B:ASP148 2.4 19.8 1.0
OD1 B:ASP138 2.4 21.3 1.0
O B:ALA141 2.5 14.2 1.0
O B:HOH582 2.6 16.8 1.0
OD2 B:ASP138 2.6 26.1 1.0
CG B:ASP138 2.9 24.1 1.0
C B:GLY183 3.3 23.8 1.0
CG B:ASN91 3.4 14.3 1.0
CG B:ASP148 3.5 21.5 1.0
C B:ALA141 3.7 17.0 1.0
CA B:GLY183 3.7 20.3 1.0
ND2 B:ASN91 3.8 13.0 1.0
CB B:ASP148 3.9 21.6 1.0
O B:GLY140 4.2 19.5 1.0
C B:GLY140 4.3 19.6 1.0
O B:ASN91 4.3 19.3 1.0
CA B:ASP142 4.3 15.8 1.0
CB B:ASP138 4.4 24.5 1.0
N B:ASP142 4.5 16.4 1.0
N B:TYR184 4.5 19.8 1.0
N B:ALA141 4.5 16.8 1.0
OD1 B:ASP148 4.6 20.7 1.0
N B:GLY140 4.6 21.4 1.0
CB B:ASN91 4.7 17.6 1.0
CA B:ALA141 4.7 15.5 1.0
CA B:GLY140 4.8 17.6 1.0
O B:HOH628 4.8 23.5 1.0
O B:HOH515 4.8 17.2 1.0
SG B:CYS124 4.9 20.5 1.0
CA B:TYR184 5.0 22.5 1.0

Calcium binding site 6 out of 8 in 1ava

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Calcium binding site 6 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:43.5
occ:1.00
 O B:ASP113 2.1 39.4 1.0
O B:HOH664 2.2 29.9 1.0
O B:THR111 2.3 36.9 1.0
OD2 B:ASP117 2.3 35.3 1.0
OE2 B:GLU108 2.8 34.4 1.0
OD1 B:ASP117 2.8 37.1 1.0
CG B:ASP117 2.9 36.0 1.0
OE1 B:GLU108 3.1 37.8 1.0
CD B:GLU108 3.3 35.1 1.0
C B:ASP113 3.3 40.3 1.0
C B:THR111 3.5 40.0 1.0
N B:ASP113 4.0 41.5 1.0
C B:PRO112 4.0 44.1 1.0
OG1 B:THR111 4.0 33.0 1.0
N B:THR111 4.1 39.5 1.0
N B:ALA114 4.2 38.9 1.0
CA B:ASP113 4.3 39.7 1.0
CA B:ALA114 4.3 38.3 1.0
O B:PRO112 4.3 43.5 1.0
CA B:THR111 4.4 38.2 1.0
N B:PRO112 4.4 42.1 1.0
CB B:ASP117 4.4 34.6 1.0
CA B:PRO112 4.4 43.3 1.0
O B:ARG115 4.5 32.5 1.0
N B:GLY109 4.6 32.4 1.0
C B:ALA114 4.6 36.2 1.0
N B:GLY110 4.7 36.8 1.0
N B:ARG115 4.8 36.7 1.0
CG B:GLU108 4.8 33.8 1.0
CB B:THR111 4.9 36.0 1.0

Calcium binding site 7 out of 8 in 1ava

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Calcium binding site 7 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:22.1
occ:1.00
 O B:ALA146 2.2 21.6 1.0
O B:HOH581 2.3 22.9 1.0
OD1 B:ASP148 2.3 20.7 1.0
O B:PHE143 2.4 19.1 1.0
OD1 B:ASP142 2.5 18.9 1.0
OD2 B:ASP127 2.5 18.7 1.0
CG B:ASP127 3.1 21.2 1.0
OD1 B:ASP127 3.2 26.0 1.0
CG B:ASP142 3.3 19.3 1.0
C B:ALA146 3.4 19.4 1.0
C B:PHE143 3.4 18.2 1.0
CG B:ASP148 3.4 21.5 1.0
N B:ASP148 3.5 19.8 1.0
OD2 B:ASP142 3.5 20.5 1.0
N B:PHE143 3.8 20.0 1.0
C B:PRO147 3.9 22.4 1.0
CB B:ASP148 4.0 21.6 1.0
CA B:PRO147 4.0 23.8 1.0
N B:PRO147 4.1 23.1 1.0
CA B:PHE143 4.2 17.3 1.0
CA B:ASP148 4.2 20.5 1.0
N B:GLY144 4.3 21.1 1.0
N B:ALA146 4.3 20.6 1.0
CA B:GLY144 4.4 18.2 1.0
CA B:ALA146 4.4 22.2 1.0
OD2 B:ASP148 4.4 19.8 1.0
O B:HOH515 4.5 17.2 1.0
CB B:ASP127 4.5 22.4 1.0
C B:GLY144 4.6 17.8 1.0
CB B:ASP142 4.6 18.9 1.0
O B:HOH669 4.6 30.2 1.0
CB B:PHE143 4.6 19.1 1.0
O B:GLY144 4.7 20.8 1.0
C B:ASP142 4.7 17.6 1.0
O B:PRO147 4.7 22.4 1.0
CA B:ASP142 4.9 15.8 1.0

Calcium binding site 8 out of 8 in 1ava

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Calcium binding site 8 out of 8 in the AMY2/Basi Protein-Protein Complex From Barley Seed


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of AMY2/Basi Protein-Protein Complex From Barley Seed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:36.0
occ:1.00
 O B:HOH573 2.1 30.2 1.0
O B:HOH576 2.3 24.6 1.0
O D:HOH336 2.4 27.2 1.0
O B:HOH572 2.4 27.8 1.0
O B:HOH617 2.5 42.6 1.0
O B:HOH616 2.6 26.0 1.0
O B:HOH652 2.9 36.3 1.0
O B:HOH577 3.8 19.4 1.0
O B:HOH578 4.0 25.0 1.0
OD1 B:ASP179 4.3 14.3 1.0
OD2 B:ASP289 4.4 16.8 1.0
OE2 D:GLU168 4.5 24.3 1.0
O B:HOH651 4.6 32.8 1.0
OD1 B:ASP289 4.7 15.2 1.0
OH D:TYR170 4.7 29.1 1.0
CG D:GLU168 4.8 17.1 1.0
CG B:ASP289 4.9 15.3 1.0
OD2 B:ASP179 4.9 13.4 1.0
OE2 B:GLU204 4.9 11.7 1.0
OE1 B:GLU204 5.0 15.5 1.0
CD1 B:PHE180 5.0 16.4 1.0

Reference:

F.Vallee, A.Kadziola, Y.Bourne, M.Juy, K.W.Rodenburg, B.Svensson, R.Haser. Barley Alpha-Amylase Bound to Its Endogenous Protein Inhibitor Basi: Crystal Structure of the Complex at 1.9 A Resolution. Structure V. 6 649 1998.
ISSN: ISSN 0969-2126
PubMed: 9634702
DOI: 10.1016/S0969-2126(98)00066-5
Page generated: Sat Dec 12 02:48:48 2020

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