Atomistry » Calcium » PDB 5zyv-6ahg » 6ag0
Atomistry »
  Calcium »
    PDB 5zyv-6ahg »
      6ag0 »

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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Go back to Calcium Binding Sites List in 6ag0
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy