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Calcium in PDB 6ag0: The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04

Enzymatic activity of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04

All present enzymatic activity of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04:
3.2.1.1;

Protein crystallography data

The structure of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04, PDB code: 6ag0 was solved by Z.F.Li, Y.L.Li, X.F.Ban, C.Y.Zhang, T.C.Jin, X.F.Xie, Z.B.Gu, C.M.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.19 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.870, 81.820, 88.780, 90.00, 105.85, 90.00
R / Rfree (%) 16.7 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 (pdb code 6ag0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04, PDB code: 6ag0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ag0

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Calcium binding site 1 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:32.1
occ:1.00
 OD1 A:ASP197 2.2 32.9 1.0
OD1 A:ASP105 2.2 31.7 1.0
OD1 A:ASP203 2.2 39.2 1.0
O A:HOH749 2.4 24.6 1.0
O A:ASP197 2.4 33.3 1.0
O A:HIS238 2.5 26.2 1.0
C A:ASP197 3.3 31.9 1.0
CG A:ASP203 3.4 37.1 1.0
CG A:ASP197 3.4 34.6 1.0
CG A:ASP105 3.4 33.6 1.0
C A:HIS238 3.6 36.9 1.0
O A:ASP105 3.8 24.4 1.0
CA A:ASP197 3.8 23.7 1.0
OD2 A:ASP203 3.8 28.7 1.0
O A:HOH751 3.9 32.5 1.0
O A:HOH708 3.9 32.2 1.0
CB A:HIS238 4.0 29.6 1.0
CA A:CA604 4.2 53.8 1.0
OD2 A:ASP105 4.2 39.4 1.0
CB A:ASP197 4.2 23.9 1.0
OD2 A:ASP197 4.4 43.9 1.0
CA A:HIS238 4.4 27.1 1.0
CB A:ASP105 4.4 27.4 1.0
N A:TYR198 4.4 30.8 1.0
CA A:ASP105 4.5 36.4 1.0
C A:ASP105 4.6 37.3 1.0
N A:ILE239 4.6 32.2 1.0
CB A:ASP203 4.6 24.0 1.0
O A:LEU204 4.7 35.7 1.0
CA A:TYR198 4.7 27.1 1.0
CA A:ILE239 4.7 27.6 1.0
CG1 A:ILE239 4.8 28.2 1.0

Calcium binding site 2 out of 8 in 6ag0

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Calcium binding site 2 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:31.9
occ:1.00
 O A:HOH785 2.3 38.0 1.0
O A:ALA184 2.3 32.9 1.0
OD2 A:ASP162 2.4 31.9 1.0
OD1 A:ASP205 2.4 38.1 1.0
OD1 A:ASP186 2.4 31.9 1.0
OD1 A:ASP162 2.5 25.5 1.0
O A:HOH725 2.7 37.4 1.0
CG A:ASP162 2.7 37.1 1.0
CG A:ASP205 3.1 37.0 1.0
CG A:ASP186 3.4 33.5 1.0
C A:ALA184 3.5 41.4 1.0
OD2 A:ASP205 3.6 36.6 1.0
N A:ASP186 3.9 28.1 1.0
OD2 A:ASP186 3.9 28.8 1.0
CB A:ASP207 4.0 64.0 1.0
CB A:ASP205 4.0 26.9 1.0
C A:TRP185 4.1 34.0 1.0
N A:ALA184 4.2 45.1 1.0
CA A:ASP186 4.2 32.3 1.0
CA A:ASP205 4.2 33.0 1.0
CB A:ASP162 4.2 24.8 1.0
CB A:ASP186 4.4 30.5 1.0
CA A:TRP185 4.4 36.3 1.0
N A:TRP185 4.5 33.4 1.0
CA A:CA604 4.5 53.8 1.0
CA A:ALA184 4.5 42.0 1.0
O A:TRP185 4.5 34.1 1.0
N A:ASP207 4.6 33.4 1.0
O2D A:ACR605 4.6 52.8 1.0
C A:ASP205 4.7 31.8 1.0
N A:MET206 4.8 30.2 1.0
CA A:ASP207 4.9 46.4 1.0

Calcium binding site 3 out of 8 in 6ag0

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Calcium binding site 3 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:37.7
occ:1.00
 O A:PHE305 2.3 23.7 1.0
OD2 A:ASP407 2.3 34.6 1.0
O A:GLY303 2.5 33.4 1.0
OD1 A:ASP430 2.5 30.6 1.0
OD2 A:ASP430 2.6 31.5 1.0
O A:HOH792 2.6 38.7 1.0
O A:SER406 2.6 32.3 1.0
CG A:ASP430 2.9 38.0 1.0
C A:GLY303 3.4 36.1 1.0
CG A:ASP407 3.4 36.0 1.0
C A:PHE305 3.5 28.8 1.0
C A:SER406 3.5 38.2 1.0
CA A:ASP407 3.7 35.4 1.0
N A:PHE305 3.9 29.7 1.0
N A:ASP407 4.0 30.0 1.0
O A:HOH823 4.0 60.1 1.0
C A:ALA304 4.1 38.0 1.0
CB A:ASP407 4.1 38.7 1.0
CG A:MET307 4.2 29.6 1.0
CA A:PHE305 4.2 33.5 1.0
N A:ALA304 4.2 32.5 1.0
CA A:GLY303 4.2 31.9 1.0
OD1 A:ASP407 4.4 39.6 1.0
CA A:ALA304 4.4 33.4 1.0
CB A:ASP430 4.5 37.5 1.0
N A:MET307 4.5 27.7 1.0
N A:ASP306 4.5 29.8 1.0
OG A:SER406 4.6 50.0 1.0
CA A:SER406 4.7 41.0 1.0
O A:ALA304 4.7 40.3 1.0
CA A:ASP306 4.7 27.3 1.0
CB A:SER406 4.7 42.7 1.0
O A:HOH720 4.7 25.4 1.0
CB A:PHE305 4.7 33.0 1.0
C A:ASP430 5.0 41.8 1.0
C A:ASP407 5.0 42.3 1.0

Calcium binding site 4 out of 8 in 6ag0

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Calcium binding site 4 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:53.8
occ:1.00
 OD2 A:ASP197 2.2 43.9 1.0
OD2 A:ASP162 2.5 31.9 1.0
OD2 A:ASP203 2.5 28.7 1.0
OD2 A:ASP186 2.5 28.8 1.0
O A:LEU204 2.6 35.7 1.0
OD1 A:ASP197 2.7 32.9 1.0
CG A:ASP197 2.8 34.6 1.0
CG A:ASP186 3.2 33.5 1.0
CG A:ASP162 3.4 37.1 1.0
O A:HOH708 3.5 32.2 1.0
CG A:ASP203 3.5 37.1 1.0
CB A:ASP162 3.7 24.8 1.0
C A:LEU204 3.7 34.5 1.0
O A:HOH749 3.8 24.6 1.0
OD1 A:ASP203 3.8 39.2 1.0
CB A:ASP186 3.8 30.5 1.0
OD1 A:ASP186 4.0 31.9 1.0
N A:ASP186 4.1 28.1 1.0
CA A:ASP205 4.1 33.0 1.0
CA A:CA601 4.2 32.1 1.0
CB A:ASP197 4.2 23.9 1.0
N A:ASP205 4.3 28.2 1.0
CA A:CA602 4.5 31.9 1.0
OD1 A:ASP162 4.5 25.5 1.0
N A:MET206 4.6 30.2 1.0
CA A:ASP186 4.6 32.3 1.0
CE3 A:TRP185 4.7 26.8 1.0
O A:ASP203 4.7 29.2 1.0
CB A:ASP203 4.8 24.0 1.0
C A:ASP203 4.8 28.8 1.0
N A:LEU204 4.8 32.3 1.0
CA A:LEU204 4.9 31.3 1.0
CA A:ASP162 5.0 32.1 1.0
C A:ASP205 5.0 31.8 1.0

Calcium binding site 5 out of 8 in 6ag0

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Calcium binding site 5 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:29.1
occ:1.00
 OD2 C:ASP162 2.3 24.2 1.0
O C:ALA184 2.4 29.9 1.0
OD2 C:ASP186 2.4 23.8 1.0
OD1 C:ASP205 2.4 22.4 1.0
OD1 C:ASP162 2.6 22.1 1.0
O C:HOH743 2.6 27.8 1.0
CG C:ASP162 2.7 23.7 1.0
CG C:ASP205 3.2 30.6 1.0
CG C:ASP186 3.4 27.6 1.0
C C:ALA184 3.6 35.0 1.0
OD2 C:ASP205 3.7 27.9 1.0
N C:ASP186 3.9 22.3 1.0
CB C:ASP207 4.0 38.9 1.0
C C:TRP185 4.1 31.4 1.0
OD1 C:ASP186 4.1 22.5 1.0
CB C:ASP205 4.1 29.5 1.0
N C:ALA184 4.1 32.2 1.0
CA C:ASP186 4.2 23.2 1.0
CB C:ASP162 4.2 21.7 1.0
CA C:ASP205 4.3 28.0 1.0
CB C:ASP186 4.4 26.4 1.0
CA C:CA604 4.4 46.1 1.0
CA C:TRP185 4.5 28.4 1.0
CA C:ALA184 4.5 29.5 1.0
O C:TRP185 4.5 25.3 1.0
N C:TRP185 4.5 29.6 1.0
N C:ASP207 4.6 35.0 1.0
O2D C:ACR605 4.7 57.4 1.0
C C:ASP205 4.8 31.4 1.0
N C:MET206 4.8 35.1 1.0
CA C:ASP207 4.9 33.8 1.0
CG C:ASP207 4.9 54.1 1.0
OD2 C:ASP197 5.0 29.9 1.0

Calcium binding site 6 out of 8 in 6ag0

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Calcium binding site 6 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:40.8
occ:1.00
 OD1 C:ASP407 2.3 38.5 1.0
O C:SER406 2.3 27.2 1.0
O C:PHE305 2.4 31.2 1.0
O C:HOH828 2.5 39.4 1.0
OD1 C:ASP430 2.5 32.2 1.0
O C:GLY303 2.5 37.6 1.0
OD2 C:ASP430 2.6 37.8 1.0
CG C:ASP430 2.9 38.9 1.0
C C:SER406 3.3 24.2 1.0
C C:GLY303 3.4 37.2 1.0
CG C:ASP407 3.5 44.6 1.0
C C:PHE305 3.6 30.8 1.0
CA C:ASP407 3.6 36.1 1.0
N C:ASP407 3.8 31.5 1.0
N C:PHE305 4.1 36.3 1.0
CB C:ASP407 4.1 37.3 1.0
CG C:MET307 4.2 31.5 1.0
CA C:GLY303 4.2 36.7 1.0
C C:ALA304 4.3 39.6 1.0
N C:ALA304 4.3 37.4 1.0
CA C:PHE305 4.4 28.7 1.0
CB C:ASP430 4.4 40.0 1.0
CA C:SER406 4.4 33.9 1.0
CB C:SER406 4.4 39.2 1.0
OG C:SER406 4.4 48.4 1.0
OD2 C:ASP407 4.5 51.8 1.0
N C:MET307 4.5 37.2 1.0
CA C:ALA304 4.5 38.7 1.0
N C:ASP306 4.6 36.4 1.0
O C:ALA304 4.8 39.6 1.0
CA C:ASP306 4.8 27.7 1.0
CB C:PHE305 4.8 37.3 1.0
O C:HOH746 4.9 30.8 1.0
C C:ASP407 4.9 37.7 1.0

Calcium binding site 7 out of 8 in 6ag0

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Calcium binding site 7 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:29.2
occ:1.00
 OD1 C:ASP203 2.3 24.1 1.0
O C:HIS238 2.3 30.0 1.0
OD1 C:ASP197 2.3 29.9 1.0
OD1 C:ASP105 2.3 20.5 1.0
O C:ASP197 2.4 32.3 1.0
CG C:ASP203 3.3 27.6 1.0
C C:ASP197 3.3 33.1 1.0
CG C:ASP197 3.5 31.6 1.0
C C:HIS238 3.5 31.0 1.0
CG C:ASP105 3.5 27.8 1.0
OD2 C:ASP203 3.7 24.8 1.0
O C:HOH704 3.8 25.1 1.0
CA C:ASP197 3.8 21.1 1.0
O C:ASP105 4.0 28.9 1.0
O C:HOH753 4.0 22.6 1.0
CB C:HIS238 4.1 26.1 1.0
CA C:CA604 4.2 46.1 1.0
CB C:ASP197 4.3 27.5 1.0
OD2 C:ASP105 4.3 26.3 1.0
CA C:HIS238 4.3 29.4 1.0
OD2 C:ASP197 4.4 29.9 1.0
N C:TYR198 4.4 28.6 1.0
N C:ILE239 4.5 27.2 1.0
CB C:ASP105 4.5 23.3 1.0
CA C:ILE239 4.6 25.8 1.0
CG1 C:ILE239 4.6 26.2 1.0
CA C:ASP105 4.6 24.6 1.0
CB C:ASP203 4.6 20.7 1.0
C C:ASP105 4.7 32.1 1.0
O C:LEU204 4.7 23.9 1.0
CA C:TYR198 4.8 31.1 1.0

Calcium binding site 8 out of 8 in 6ag0

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Calcium binding site 8 out of 8 in the The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The X-Ray Crystallographic Structure of Maltooligosaccharide-Forming Amylase From Bacillus Stearothermophilus STB04 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:46.1
occ:1.00
 OD2 C:ASP203 2.3 24.8 1.0
OD2 C:ASP197 2.4 29.9 1.0
OD2 C:ASP162 2.5 24.2 1.0
O C:LEU204 2.5 23.9 1.0
OD1 C:ASP186 2.5 22.5 1.0
OD1 C:ASP197 2.9 29.9 1.0
CG C:ASP197 3.0 31.6 1.0
CG C:ASP186 3.1 27.6 1.0
CG C:ASP162 3.4 23.7 1.0
CG C:ASP203 3.4 27.6 1.0
C C:LEU204 3.6 29.1 1.0
O C:HOH704 3.6 25.1 1.0
CB C:ASP162 3.6 21.7 1.0
OD2 C:ASP186 3.8 23.8 1.0
OD1 C:ASP203 3.9 24.1 1.0
CB C:ASP186 3.9 26.4 1.0
CA C:ASP205 4.0 28.0 1.0
CA C:CA603 4.2 29.2 1.0
N C:ASP205 4.2 27.7 1.0
N C:ASP186 4.3 22.3 1.0
CA C:CA601 4.4 29.1 1.0
N C:MET206 4.4 35.1 1.0
CB C:ASP197 4.5 27.5 1.0
OD1 C:ASP162 4.5 22.1 1.0
O C:ASP203 4.5 27.3 1.0
C C:ASP203 4.6 29.8 1.0
CB C:ASP203 4.7 20.7 1.0
N C:LEU204 4.7 26.3 1.0
CA C:ASP186 4.7 23.2 1.0
CA C:LEU204 4.8 33.2 1.0
C C:ASP205 4.8 31.4 1.0
CE3 C:TRP185 4.8 21.6 1.0
N C:ASP162 4.8 26.1 1.0
CA C:ASP162 4.9 22.5 1.0
OD1 C:ASP205 5.0 22.4 1.0
CB C:ASP205 5.0 29.5 1.0

Reference:

Z.F.Li, Y.L.Li, X.F.Ban, C.Y.Zhang, T.C.Jin, X.F.Xie, Z.B.Gu, C.M.Li. The X-Ray Crystallographic Structure of Maltotetraose-Forming Amylase From Bacillus Stearothermophilus STB04 To Be Published.
Page generated: Mon Jul 15 16:08:05 2024

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