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Calcium in PDB 1rp8: Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose

Enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose

All present enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose, PDB code: 1rp8 was solved by X.Robert, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.14 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.000, 72.500, 62.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose (pdb code 1rp8). 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 Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose, PDB code: 1rp8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1rp8

Go back to Calcium Binding Sites List in 1rp8
Calcium binding site 1 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose


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 Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:8.9
occ:1.00
 O A:ALA142 2.3 10.4 1.0
OD2 A:ASP149 2.3 8.2 1.0
O A:GLY184 2.4 9.6 1.0
OD1 A:ASN92 2.4 7.3 1.0
OD2 A:ASP139 2.4 9.4 1.0
O A:HOH630 2.4 9.2 1.0
OD1 A:ASP139 2.6 10.5 1.0
CG A:ASP139 2.9 9.0 1.0
C A:GLY184 3.4 9.7 1.0
CG A:ASP149 3.4 8.0 1.0
CG A:ASN92 3.5 7.3 1.0
C A:ALA142 3.5 10.6 1.0
CB A:ASP149 3.8 6.8 1.0
CA A:GLY184 3.8 9.9 1.0
ND2 A:ASN92 3.9 4.4 1.0
O A:GLY141 4.1 9.1 1.0
C A:GLY141 4.1 11.0 1.0
CA A:ASP143 4.3 10.9 1.0
N A:ASP143 4.3 9.9 1.0
O A:ASN92 4.3 8.8 1.0
N A:ALA142 4.3 10.6 1.0
CB A:ASP139 4.4 8.0 1.0
N A:TYR185 4.5 7.5 1.0
OD1 A:ASP149 4.5 8.8 1.0
CA A:ALA142 4.5 9.7 1.0
N A:GLY141 4.6 11.0 1.0
CA A:GLY141 4.7 9.0 1.0
O A:HOH809 4.7 7.6 1.0
CB A:ASN92 4.8 5.2 1.0
O A:HOH754 4.8 9.7 1.0
CA A:ASP149 4.9 7.8 1.0
CA A:TYR185 4.9 8.3 1.0
SG A:CYS125 5.0 10.7 1.0
C A:ASN92 5.0 7.5 1.0

Calcium binding site 2 out of 3 in 1rp8

Go back to Calcium Binding Sites List in 1rp8
Calcium binding site 2 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose


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 Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:12.2
occ:1.00
 OD2 A:ASP118 2.4 7.3 1.0
O A:ASP114 2.4 18.0 1.0
OE2 A:GLU109 2.4 15.3 1.0
O A:HOH604 2.5 7.0 1.0
O A:HOH656 2.5 14.9 1.0
OD1 A:ASP118 2.6 8.5 1.0
O A:THR112 2.6 17.5 1.0
OE1 A:GLU109 2.8 15.9 1.0
CG A:ASP118 2.8 8.5 1.0
CD A:GLU109 3.0 12.9 1.0
C A:ASP114 3.6 19.3 1.0
C A:THR112 3.7 19.8 1.0
N A:THR112 4.2 16.9 1.0
N A:GLY110 4.3 6.4 1.0
OG1 A:THR112 4.3 16.7 1.0
CB A:ASP118 4.3 9.4 1.0
C A:SER113 4.4 22.0 1.0
CA A:GLY115 4.4 14.6 1.0
O A:HOH1090 4.4 16.6 1.0
N A:ASP114 4.4 21.1 1.0
CG A:GLU109 4.5 11.9 1.0
O A:ARG116 4.5 8.3 1.0
N A:GLY115 4.5 16.4 1.0
CA A:THR112 4.5 17.0 1.0
O A:SER113 4.6 22.6 1.0
N A:GLY111 4.6 11.8 1.0
CA A:ASP114 4.6 20.4 1.0
N A:SER113 4.7 20.8 1.0
C A:GLY115 4.7 14.2 1.0
O A:HOH843 4.7 15.6 1.0
O A:HOH1525 4.7 32.4 1.0
CA A:SER113 4.8 22.9 1.0
N A:ARG116 4.9 13.6 1.0
CA A:GLY110 5.0 9.3 1.0

Calcium binding site 3 out of 3 in 1rp8

Go back to Calcium Binding Sites List in 1rp8
Calcium binding site 3 out of 3 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose


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 Barley Alpha-Amylase Isozyme 1 (AMY1) Inactive Mutant D180A in Complex with Maltoheptaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:9.0
occ:1.00
 O A:ALA147 2.3 11.3 1.0
OD2 A:ASP128 2.3 11.0 1.0
O A:HOH788 2.3 9.2 1.0
O A:PHE144 2.4 9.5 1.0
OD1 A:ASP143 2.4 14.2 1.0
OD1 A:ASP149 2.4 8.8 1.0
CG A:ASP143 3.1 12.8 1.0
CG A:ASP128 3.2 12.4 1.0
OD2 A:ASP143 3.3 13.1 1.0
C A:PHE144 3.4 8.9 1.0
CG A:ASP149 3.4 8.0 1.0
C A:ALA147 3.5 10.2 1.0
N A:ASP149 3.5 9.0 1.0
OD1 A:ASP128 3.6 11.4 1.0
N A:PHE144 3.8 10.7 1.0
CB A:ASP149 4.0 6.8 1.0
C A:PRO148 4.1 9.3 1.0
CA A:PRO148 4.2 8.9 1.0
CA A:PHE144 4.2 9.4 1.0
CA A:ASP149 4.2 7.8 1.0
N A:PRO148 4.3 10.4 1.0
N A:ALA145 4.3 11.1 1.0
N A:ALA147 4.4 10.9 1.0
CA A:ALA145 4.4 12.7 1.0
CB A:ASP128 4.4 10.1 1.0
OD2 A:ASP149 4.5 8.2 1.0
CB A:ASP143 4.5 13.2 1.0
CA A:ALA147 4.5 11.0 1.0
C A:ALA145 4.6 15.0 1.0
O A:ALA145 4.6 17.4 1.0
CB A:PHE144 4.6 8.8 1.0
C A:ASP143 4.7 10.8 1.0
O A:HOH809 4.8 7.6 1.0
CA A:ASP143 4.8 10.9 1.0
O A:PRO148 4.9 6.5 1.0
O A:HOH1450 5.0 29.1 1.0

Reference:

X.Robert, R.Haser, H.Mori, B.Svensson, N.Aghajari. Oligosaccharide Binding to Barley {Alpha}-Amylase 1 J.Biol.Chem. V. 280 32968 2005.
ISSN: ISSN 0021-9258
PubMed: 16030022
DOI: 10.1074/JBC.M505515200
Page generated: Thu Jul 11 22:14:50 2024

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