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Calcium in PDB 1p6w: Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)

Enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)

All present enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4):
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4), PDB code: 1p6w 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) 46.52 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.430, 72.100, 60.880, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) (pdb code 1p6w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4), PDB code: 1p6w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1p6w

Go back to Calcium Binding Sites List in 1p6w
Calcium binding site 1 out of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)


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) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:7.4
occ:1.00
 OD2 A:ASP149 2.3 8.8 1.0
O A:GLY184 2.4 6.0 1.0
OD2 A:ASP139 2.4 13.2 1.0
OD1 A:ASN92 2.4 7.2 1.0
O A:ALA142 2.4 9.4 1.0
O A:HOH630 2.5 1.2 1.0
OD1 A:ASP139 2.6 10.9 1.0
CG A:ASP139 2.8 11.7 1.0
C A:GLY184 3.4 6.7 1.0
CG A:ASN92 3.4 7.9 1.0
CG A:ASP149 3.4 8.1 1.0
C A:ALA142 3.6 10.4 1.0
ND2 A:ASN92 3.8 5.3 1.0
CA A:GLY184 3.8 5.6 1.0
O A:GLY141 3.9 10.1 1.0
CB A:ASP149 3.9 7.7 1.0
C A:GLY141 4.0 11.1 1.0
CA A:ASP143 4.3 10.1 1.0
CB A:ASP139 4.3 9.0 1.0
N A:ASP143 4.3 10.1 1.0
N A:ALA142 4.4 11.4 1.0
O A:ASN92 4.4 8.4 1.0
N A:TYR185 4.5 7.1 1.0
OD1 A:ASP149 4.5 10.4 1.0
N A:GLY141 4.5 11.7 1.0
CA A:GLY141 4.6 11.5 1.0
CA A:ALA142 4.6 9.6 1.0
O A:HOH809 4.7 14.2 1.0
CB A:ASN92 4.8 7.9 1.0
O A:HOH754 4.8 10.2 1.0
SG A:CYS125 4.8 9.4 1.0
CA A:TYR185 4.9 7.1 1.0
CA A:ASP149 5.0 9.0 1.0

Calcium binding site 2 out of 4 in 1p6w

Go back to Calcium Binding Sites List in 1p6w
Calcium binding site 2 out of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)


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) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:15.2
occ:1.00
 O A:ASP114 2.3 15.6 1.0
O A:HOH656 2.5 14.7 1.0
O A:HOH604 2.5 9.7 1.0
OE2 A:GLU109 2.5 12.9 1.0
OD2 A:ASP118 2.5 13.3 1.0
O A:THR112 2.6 17.6 1.0
OD1 A:ASP118 2.6 12.2 1.0
CG A:ASP118 2.9 13.3 1.0
OE1 A:GLU109 2.9 15.9 1.0
CD A:GLU109 3.0 13.2 1.0
C A:ASP114 3.6 18.1 1.0
C A:THR112 3.7 17.8 1.0
N A:THR112 4.1 14.3 1.0
C A:SER113 4.2 19.0 1.0
OG1 A:THR112 4.2 15.3 1.0
N A:ASP114 4.3 19.0 1.0
O A:HOH1636 4.3 24.6 1.0
O A:SER113 4.4 20.7 1.0
N A:GLY110 4.4 10.1 1.0
CB A:ASP118 4.4 12.7 1.0
O A:ARG116 4.4 11.7 1.0
CA A:GLY115 4.4 16.7 1.0
N A:GLY115 4.5 16.8 1.0
CA A:THR112 4.5 15.8 1.0
CG A:GLU109 4.5 13.7 1.0
CA A:ASP114 4.5 18.9 1.0
N A:GLY111 4.5 11.4 1.0
O A:HOH1090 4.6 27.8 1.0
O A:HOH843 4.6 11.6 1.0
N A:SER113 4.6 18.0 1.0
N A:ARG116 4.7 15.0 1.0
C A:GLY115 4.7 16.1 1.0
CA A:SER113 4.7 19.7 1.0
O A:HOH1530 4.9 23.1 1.0

Calcium binding site 3 out of 4 in 1p6w

Go back to Calcium Binding Sites List in 1p6w
Calcium binding site 3 out of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)


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) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:12.3
occ:1.00
 O A:PHE144 2.3 9.1 1.0
O A:ALA147 2.3 11.2 1.0
O A:HOH788 2.3 8.8 1.0
OD2 A:ASP128 2.3 9.8 1.0
OD1 A:ASP143 2.4 13.8 1.0
OD1 A:ASP149 2.4 10.4 1.0
CG A:ASP143 3.1 11.7 1.0
OD2 A:ASP143 3.2 13.6 1.0
CG A:ASP128 3.3 12.9 1.0
C A:PHE144 3.3 11.5 1.0
CG A:ASP149 3.4 8.1 1.0
C A:ALA147 3.5 10.9 1.0
N A:ASP149 3.6 9.5 1.0
OD1 A:ASP128 3.7 11.0 1.0
N A:PHE144 3.7 10.7 1.0
CB A:ASP149 3.9 7.7 1.0
C A:PRO148 4.0 9.4 1.0
CA A:PHE144 4.1 11.3 1.0
CA A:PRO148 4.2 10.0 1.0
N A:ALA145 4.2 11.9 1.0
CA A:ASP149 4.2 9.0 1.0
N A:ALA147 4.3 12.2 1.0
N A:PRO148 4.3 10.5 1.0
CA A:ALA145 4.3 12.3 1.0
O A:HOH1152 4.4 21.0 1.0
OD2 A:ASP149 4.4 8.8 1.0
CB A:ASP143 4.5 11.0 1.0
C A:ALA145 4.5 11.9 1.0
O A:ALA145 4.5 12.7 1.0
CA A:ALA147 4.5 11.8 1.0
CB A:PHE144 4.5 13.8 1.0
CB A:ASP128 4.6 11.8 1.0
O A:HOH809 4.6 14.2 1.0
C A:ASP143 4.7 10.9 1.0
O A:PRO148 4.8 8.2 1.0
CA A:ASP143 4.8 10.1 1.0

Calcium binding site 4 out of 4 in 1p6w

Go back to Calcium Binding Sites List in 1p6w
Calcium binding site 4 out of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:15.8
occ:1.00
 O A:HOH1548 2.4 26.2 1.0
O A:HOH1546 2.5 7.4 1.0
O A:HOH1550 2.5 22.4 1.0
O A:HOH1545 2.5 11.8 1.0
O A:HOH1547 2.9 13.7 1.0
O A:HOH1523 3.0 17.5 1.0
O A:HOH1544 3.7 14.9 1.0
O A:HOH641 4.1 9.1 1.0
O A:HOH709 4.6 10.8 1.0
O A:HOH676 4.6 20.4 1.0
OD1 A:ASP180 4.6 3.5 1.0
O A:HOH1621 4.6 28.0 1.0
OD2 A:ASP291 4.7 10.8 1.0
OD1 A:ASP291 4.7 12.8 1.0
OE2 A:GLU205 4.8 15.5 1.0
OE1 A:GLU205 4.8 10.2 1.0
CG A:ASP291 5.0 12.2 1.0

Reference:

X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, N.Aghajari. The Structure of Barley Alpha-Amylase Isozyme 1 Reveals A Novel Role of Domain C in Substrate Recognition and Binding: A Pair of Sugar Tongs Structure V. 11 973 2003.
ISSN: ISSN 0969-2126
PubMed: 12906828
DOI: 10.1016/S0969-2126(03)00151-5
Page generated: Thu Jul 11 13:39:50 2024

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