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Calcium in PDB 2qpu: Sugar Tongs Mutant S378P in Complex with Acarbose

Enzymatic activity of Sugar Tongs Mutant S378P in Complex with Acarbose

All present enzymatic activity of Sugar Tongs Mutant S378P in Complex with Acarbose:
3.2.1.1;

Protein crystallography data

The structure of Sugar Tongs Mutant S378P in Complex with Acarbose, PDB code: 2qpu was solved by N.Aghajari, M.H.Jensen, S.Tranier, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.26 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 218.930, 89.650, 62.080, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.9

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Sugar Tongs Mutant S378P in Complex with Acarbose (pdb code 2qpu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Sugar Tongs Mutant S378P in Complex with Acarbose, PDB code: 2qpu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 2qpu

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Calcium binding site 1 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:10.6
occ:1.00
OD1 A:ASN92 2.3 10.1 1.0
O A:GLY184 2.3 10.6 1.0
OD1 A:ASP149 2.4 10.0 1.0
O A:ALA142 2.4 9.9 1.0
O A:HOH4027 2.4 9.7 1.0
OD2 A:ASP139 2.5 9.4 1.0
OD1 A:ASP139 2.5 8.8 1.0
CG A:ASP139 2.8 10.7 1.0
C A:GLY184 3.3 11.2 1.0
CG A:ASN92 3.4 10.3 1.0
CG A:ASP149 3.5 10.9 1.0
C A:ALA142 3.6 10.7 1.0
CA A:GLY184 3.8 9.5 1.0
ND2 A:ASN92 3.9 9.7 1.0
CB A:ASP149 3.9 10.7 1.0
O A:GLY141 4.1 10.8 1.0
C A:GLY141 4.1 11.9 1.0
O A:ASN92 4.3 9.7 1.0
CA A:ASP143 4.3 12.0 1.0
N A:ALA142 4.3 11.6 1.0
CB A:ASP139 4.3 10.5 1.0
N A:ASP143 4.4 10.9 1.0
N A:TYR185 4.5 9.5 1.0
OD2 A:ASP149 4.5 11.3 1.0
CA A:ALA142 4.6 11.4 1.0
N A:GLY141 4.6 10.7 1.0
CA A:GLY141 4.7 11.1 1.0
CB A:ASN92 4.7 9.5 1.0
O A:HOH4073 4.9 15.1 1.0
O A:HOH4125 4.9 13.4 1.0
C A:ASN92 5.0 8.8 1.0
CA A:TYR185 5.0 11.0 1.0
CA A:ASP149 5.0 8.9 1.0

Calcium binding site 2 out of 12 in 2qpu

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Calcium binding site 2 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:18.4
occ:1.00
O A:HOH4042 2.3 25.3 1.0
OD2 A:ASP118 2.4 14.2 1.0
OE2 A:GLU109 2.5 20.5 1.0
O A:ASP114 2.5 26.6 1.0
O A:HOH4004 2.5 22.5 1.0
O A:THR112 2.6 23.5 1.0
OD1 A:ASP118 2.7 16.5 1.0
CG A:ASP118 2.9 18.1 1.0
CD A:GLU109 3.2 22.4 1.0
OE1 A:GLU109 3.3 27.5 1.0
C A:ASP114 3.7 26.3 1.0
C A:THR112 3.7 25.5 1.0
O A:SER113 4.0 31.4 1.0
N A:THR112 4.1 20.6 1.0
C A:SER113 4.2 29.6 1.0
OG1 A:THR112 4.3 25.2 1.0
N A:GLY110 4.3 13.2 1.0
CA A:GLY115 4.4 23.9 1.0
CB A:ASP118 4.4 15.9 1.0
O A:ARG116 4.5 18.2 1.0
N A:GLY111 4.5 15.8 1.0
CA A:THR112 4.5 23.8 1.0
N A:GLY115 4.5 24.6 1.0
N A:ASP114 4.6 29.4 1.0
N A:SER113 4.6 26.8 1.0
CG A:GLU109 4.7 20.6 1.0
O A:HOH4493 4.7 23.4 1.0
C A:GLY115 4.7 23.0 1.0
CA A:ASP114 4.7 28.0 1.0
CA A:SER113 4.8 29.3 1.0
N A:ARG116 4.9 22.4 1.0
CA A:GLY110 4.9 13.3 1.0

Calcium binding site 3 out of 12 in 2qpu

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Calcium binding site 3 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:12.3
occ:1.00
O A:ALA147 2.3 13.8 1.0
OD2 A:ASP149 2.3 11.3 1.0
O A:PHE144 2.3 12.8 1.0
O A:HOH4106 2.4 16.6 1.0
OD2 A:ASP143 2.4 12.3 1.0
OD2 A:ASP128 2.4 15.0 1.0
CG A:ASP143 3.3 12.4 1.0
C A:PHE144 3.3 14.5 1.0
CG A:ASP149 3.4 10.9 1.0
CG A:ASP128 3.4 15.6 1.0
C A:ALA147 3.5 13.6 1.0
N A:ASP149 3.5 9.2 1.0
OD1 A:ASP143 3.5 13.4 1.0
N A:PHE144 3.7 12.4 1.0
OD1 A:ASP128 3.8 17.9 1.0
CB A:ASP149 3.9 10.7 1.0
C A:PRO148 3.9 11.9 1.0
CA A:PHE144 4.1 14.5 1.0
CA A:PRO148 4.1 12.3 1.0
CA A:ASP149 4.2 8.9 1.0
O A:HOH4320 4.2 24.9 1.0
N A:PRO148 4.2 14.5 1.0
N A:ALA145 4.2 15.5 1.0
N A:ALA147 4.4 16.4 1.0
OD1 A:ASP149 4.4 10.0 1.0
CA A:ALA145 4.4 17.6 1.0
CB A:PHE144 4.5 15.9 1.0
O A:HOH4125 4.5 13.4 1.0
O A:ALA145 4.5 19.1 1.0
CA A:ALA147 4.5 14.7 1.0
C A:ALA145 4.5 18.2 1.0
CB A:ASP143 4.6 13.9 1.0
CB A:ASP128 4.7 15.0 1.0
O A:PRO148 4.7 9.6 1.0
C A:ASP143 4.7 13.4 1.0
CA A:ASP143 4.9 12.0 1.0

Calcium binding site 4 out of 12 in 2qpu

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Calcium binding site 4 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:29.9
occ:1.00
O A:HOH4395 2.4 15.3 1.0
O A:HOH4365 2.4 34.7 1.0
O A:HOH4149 2.5 22.1 1.0
O A:HOH4064 2.5 23.5 1.0
O A:HOH4367 2.5 27.1 1.0
O A:HOH4396 2.6 36.2 1.0
O A:HOH4069 3.1 40.3 1.0
O A:HOH4394 3.9 22.8 1.0
O A:HOH4033 4.2 16.8 1.0
O A:HOH4050 4.6 27.0 1.0
OD2 A:ASP291 4.6 12.8 1.0
OD1 A:ASP180 4.7 12.1 1.0
OE2 A:GLU205 4.7 13.7 1.0
O A:HOH4062 4.7 27.2 1.0
OE1 A:GLU205 4.8 16.2 1.0
OD1 A:ASP291 4.8 14.3 1.0
CG A:ASP291 5.0 13.8 1.0

Calcium binding site 5 out of 12 in 2qpu

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Calcium binding site 5 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:9.9
occ:1.00
OD2 B:ASP149 2.3 7.0 1.0
O B:GLY184 2.4 9.5 1.0
OD1 B:ASN92 2.4 8.7 1.0
O B:HOH4315 2.4 9.2 1.0
OD2 B:ASP139 2.4 10.5 1.0
O B:ALA142 2.5 10.2 1.0
OD1 B:ASP139 2.6 9.9 1.0
CG B:ASP139 2.9 11.4 1.0
C B:GLY184 3.4 10.2 1.0
CG B:ASP149 3.4 9.8 1.0
CG B:ASN92 3.4 8.9 1.0
C B:ALA142 3.6 11.6 1.0
CB B:ASP149 3.9 7.3 1.0
ND2 B:ASN92 3.9 7.5 1.0
CA B:GLY184 3.9 8.7 1.0
C B:GLY141 4.1 11.8 1.0
O B:GLY141 4.1 12.0 1.0
N B:ALA142 4.3 11.3 1.0
O B:ASN92 4.3 8.1 1.0
CA B:ASP143 4.4 12.8 1.0
CB B:ASP139 4.4 10.4 1.0
N B:ASP143 4.4 13.1 1.0
OD1 B:ASP149 4.5 11.5 1.0
N B:TYR185 4.5 8.8 1.0
CA B:ALA142 4.6 12.7 1.0
N B:GLY141 4.6 11.5 1.0
CA B:GLY141 4.6 11.8 1.0
O B:HOH4405 4.7 14.8 1.0
CB B:ASN92 4.7 10.3 1.0
O B:HOH4357 4.7 8.9 1.0
SG B:CYS125 4.9 12.0 1.0
CA B:ASP149 5.0 8.9 1.0
CA B:TYR185 5.0 9.5 1.0

Calcium binding site 6 out of 12 in 2qpu

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Calcium binding site 6 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:16.6
occ:1.00
O B:HOH4330 2.4 15.6 1.0
OD2 B:ASP118 2.4 13.0 1.0
O B:ASP114 2.4 16.4 1.0
OE2 B:GLU109 2.5 12.6 1.0
O B:HOH4293 2.5 14.7 1.0
O B:THR112 2.5 15.7 1.0
OD1 B:ASP118 2.6 14.7 1.0
OE1 B:GLU109 2.9 13.5 1.0
CG B:ASP118 2.9 14.9 1.0
CD B:GLU109 3.0 13.0 1.0
C B:ASP114 3.6 18.2 1.0
C B:THR112 3.7 17.6 1.0
N B:THR112 4.1 14.9 1.0
OG1 B:THR112 4.2 18.2 1.0
C B:SER113 4.3 20.1 1.0
N B:GLY110 4.3 9.5 1.0
O B:SER113 4.3 20.6 1.0
O B:HOH4602 4.3 24.6 1.0
CA B:GLY115 4.4 16.2 1.0
CB B:ASP118 4.4 13.4 1.0
N B:ASP114 4.4 19.8 1.0
N B:GLY115 4.4 17.8 1.0
O B:ARG116 4.5 13.5 1.0
CG B:GLU109 4.5 12.0 1.0
CA B:THR112 4.5 16.2 1.0
N B:GLY111 4.5 11.1 1.0
CA B:ASP114 4.6 19.3 1.0
O B:HOH4610 4.6 31.8 1.0
C B:GLY115 4.7 15.7 1.0
N B:SER113 4.7 18.7 1.0
O B:HOH4352 4.7 22.4 1.0
CA B:SER113 4.8 20.9 1.0
N B:ARG116 4.8 15.5 1.0
CA B:GLY110 5.0 11.6 1.0
CA B:GLU109 5.0 11.3 1.0

Calcium binding site 7 out of 12 in 2qpu

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Calcium binding site 7 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:13.5
occ:1.00
O B:ALA147 2.2 10.2 1.0
O B:PHE144 2.3 13.0 1.0
O B:HOH4390 2.3 12.3 1.0
OD2 B:ASP128 2.4 11.5 1.0
OD1 B:ASP149 2.4 11.5 1.0
OD1 B:ASP143 2.5 14.5 1.0
CG B:ASP143 3.2 15.7 1.0
CG B:ASP128 3.3 14.3 1.0
C B:PHE144 3.3 14.2 1.0
OD2 B:ASP143 3.4 18.1 1.0
CG B:ASP149 3.4 9.8 1.0
C B:ALA147 3.4 11.0 1.0
N B:ASP149 3.5 8.4 1.0
OD1 B:ASP128 3.6 13.7 1.0
N B:PHE144 3.8 13.0 1.0
CB B:ASP149 3.9 7.3 1.0
C B:PRO148 4.0 9.0 1.0
CA B:PHE144 4.1 14.8 1.0
CA B:PRO148 4.1 9.6 1.0
CA B:ASP149 4.2 8.9 1.0
N B:ALA145 4.2 14.4 1.0
N B:PRO148 4.2 10.1 1.0
CA B:ALA145 4.3 14.4 1.0
N B:ALA147 4.3 13.8 1.0
OD2 B:ASP149 4.5 7.0 1.0
CB B:PHE144 4.5 14.9 1.0
CA B:ALA147 4.5 10.7 1.0
CB B:ASP128 4.5 11.8 1.0
C B:ALA145 4.5 15.4 1.0
CB B:ASP143 4.6 13.8 1.0
O B:HOH4762 4.6 30.0 1.0
O B:HOH4405 4.7 14.8 1.0
O B:ALA145 4.7 14.6 1.0
C B:ASP143 4.7 14.2 1.0
O B:PRO148 4.7 9.3 1.0
CE2 B:TYR131 4.9 14.4 1.0
CA B:ASP143 4.9 12.8 1.0
CD2 B:TYR131 4.9 12.4 1.0

Calcium binding site 8 out of 12 in 2qpu

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Calcium binding site 8 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:19.4
occ:1.00
O B:HOH4557 2.3 15.3 1.0
O1 B:EDO2001 2.4 25.0 1.0
O2 B:EDO2001 2.5 26.3 1.0
O B:HOH4801 2.5 21.1 1.0
O B:HOH4542 2.5 25.2 1.0
O B:HOH4353 2.5 25.7 1.0
O B:HOH4558 2.6 25.8 1.0
C1 B:EDO2001 3.3 27.3 1.0
C2 B:EDO2001 3.4 27.9 1.0
O B:HOH4556 4.0 16.2 1.0
O B:HOH4322 4.2 9.6 1.0
O B:HOH4337 4.6 17.9 1.0
OD1 B:ASP180 4.6 8.4 1.0
OE2 B:GLU205 4.6 13.1 1.0
OE1 B:GLU205 4.7 11.3 1.0
OD2 B:ASP291 4.7 10.8 1.0
OD1 B:ASP291 4.8 13.2 1.0
O B:HOH4347 4.8 17.3 1.0

Calcium binding site 9 out of 12 in 2qpu

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Calcium binding site 9 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca500

b:7.7
occ:1.00
O C:GLY184 2.3 9.5 1.0
OD2 C:ASP149 2.4 7.6 1.0
O C:ALA142 2.4 11.9 1.0
OD1 C:ASN92 2.4 7.4 1.0
OD2 C:ASP139 2.4 10.4 1.0
O C:HOH4160 2.5 7.6 1.0
OD1 C:ASP139 2.6 10.1 1.0
CG C:ASP139 2.9 10.9 1.0
C C:GLY184 3.3 10.1 1.0
CG C:ASN92 3.4 7.7 1.0
CG C:ASP149 3.5 8.8 1.0
C C:ALA142 3.6 9.3 1.0
CA C:GLY184 3.8 9.0 1.0
ND2 C:ASN92 3.9 8.4 1.0
CB C:ASP149 3.9 7.3 1.0
C C:GLY141 4.1 8.6 1.0
O C:GLY141 4.2 10.0 1.0
N C:ALA142 4.3 8.8 1.0
CA C:ASP143 4.3 10.4 1.0
O C:ASN92 4.3 6.1 1.0
N C:ASP143 4.4 10.6 1.0
CB C:ASP139 4.4 8.2 1.0
N C:TYR185 4.5 8.4 1.0
OD1 C:ASP149 4.5 9.0 1.0
N C:GLY141 4.6 9.7 1.0
CA C:GLY141 4.6 9.9 1.0
CA C:ALA142 4.6 9.2 1.0
CB C:ASN92 4.7 6.9 1.0
O C:HOH4200 4.8 9.3 1.0
O C:HOH4245 4.8 12.2 1.0
SG C:CYS125 4.9 9.6 1.0
CA C:TYR185 4.9 8.7 1.0
CA C:ASP149 5.0 7.6 1.0
C C:ASN92 5.0 6.6 1.0

Calcium binding site 10 out of 12 in 2qpu

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Calcium binding site 10 out of 12 in the Sugar Tongs Mutant S378P in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Sugar Tongs Mutant S378P in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:16.0
occ:1.00
O C:ASP114 2.4 18.1 1.0
OD2 C:ASP118 2.4 11.9 1.0
O C:HOH4176 2.4 11.9 1.0
OE2 C:GLU109 2.4 13.5 1.0
O C:HOH4137 2.4 12.9 1.0
O C:THR112 2.5 13.5 1.0
OD1 C:ASP118 2.6 12.2 1.0
CG C:ASP118 2.9 13.2 1.0
OE1 C:GLU109 2.9 14.5 1.0
CD C:GLU109 3.0 14.8 1.0
C C:ASP114 3.6 17.5 1.0
C C:THR112 3.7 16.6 1.0
N C:THR112 4.1 14.2 1.0
OG1 C:THR112 4.2 17.6 1.0
N C:GLY110 4.3 10.6 1.0
C C:SER113 4.3 19.8 1.0
N C:ASP114 4.3 19.5 1.0
O C:HOH4082 4.3 27.9 1.0
CB C:ASP118 4.4 10.9 1.0
O C:SER113 4.4 22.9 1.0
CA C:GLY115 4.4 16.0 1.0
O C:ARG116 4.4 12.5 1.0
O C:HOH4074 4.5 25.5 1.0
N C:GLY115 4.5 17.7 1.0
CG C:GLU109 4.5 13.6 1.0
CA C:THR112 4.5 15.4 1.0
N C:GLY111 4.5 10.9 1.0
CA C:ASP114 4.6 20.0 1.0
O C:HOH4450 4.6 31.0 1.0
N C:SER113 4.6 17.0 1.0
O C:HOH4440 4.7 24.9 1.0
C C:GLY115 4.7 16.1 1.0
CA C:SER113 4.7 19.9 1.0
N C:ARG116 4.9 15.4 1.0
CA C:GLY110 4.9 11.8 1.0
CA C:GLU109 5.0 12.4 1.0

Reference:

S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhoft, M.Willemoes, S.Tranier, R.Haser, B.Svensson. The 'Pair of Sugar Tongs' Site on the Non-Catalytic Domain C of Barley Alpha-Amylase Participates in Substrate Binding and Activity Febs J. V. 274 5055 2007.
ISSN: ISSN 1742-464X
PubMed: 17803687
DOI: 10.1111/J.1742-4658.2007.06024.X
Page generated: Sat Dec 12 03:51:11 2020

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