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Calcium in PDB 4uzu: Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Enzymatic activity of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

All present enzymatic activity of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution:
3.2.1.1;

Protein crystallography data

The structure of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution, PDB code: 4uzu was solved by W.A.Offen, C.Anderson, T.V.Borchert, K.S.Wilson, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.92 / 1.90
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.180, 108.180, 181.490, 90.00, 90.00, 90.00
R / Rfree (%) 16.993 / 21.029

Other elements in 4uzu:

The structure of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution (pdb code 4uzu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution, PDB code: 4uzu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4uzu

Go back to Calcium Binding Sites List in 4uzu
Calcium binding site 1 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1483

b:12.8
occ:1.00
 O A:HOH2199 2.2 11.0 1.0
O A:ALA182 2.3 9.9 1.0
OD1 A:ASP184 2.3 14.9 1.0
OD1 A:ASP162 2.4 14.9 1.0
OD2 A:ASP162 2.5 13.1 1.0
OD1 A:ASP203 2.5 11.3 1.0
O A:HOH2185 2.5 11.1 1.0
CG A:ASP162 2.8 13.6 1.0
CG A:ASP203 3.3 12.2 1.0
CG A:ASP184 3.4 14.2 1.0
C A:ALA182 3.6 11.1 1.0
N A:ASP184 3.8 11.6 1.0
OD2 A:ASP203 3.9 12.0 1.0
OD2 A:ASP184 4.0 14.3 1.0
C A:TRP183 4.1 11.5 1.0
CB A:ASP203 4.1 11.5 1.0
CA A:ASP184 4.2 12.3 1.0
N A:ALA182 4.2 10.9 1.0
CB A:ASP162 4.2 13.3 1.0
CA A:ASP203 4.2 12.3 1.0
OD2 A:ASP205 4.3 24.6 1.0
CB A:ASP184 4.4 13.0 1.0
NA A:NA1491 4.4 13.1 1.0
CA A:ALA182 4.5 10.7 1.0
CB A:ASP205 4.5 21.6 1.0
N A:TRP183 4.5 10.9 1.0
CA A:TRP183 4.5 11.2 1.0
O A:TRP183 4.7 11.0 1.0
N A:ASP205 4.7 18.4 1.0
C A:ASP203 4.7 12.8 1.0
N A:MET204 4.8 14.7 1.0
OD2 A:ASP195 4.8 11.6 1.0
CG A:ASP205 4.9 24.3 1.0
CB A:ALA182 4.9 9.9 1.0

Calcium binding site 2 out of 3 in 4uzu

Go back to Calcium Binding Sites List in 4uzu
Calcium binding site 2 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1484

b:12.6
occ:1.00
 O A:ASP195 2.3 12.2 1.0
O A:HIS236 2.3 15.2 1.0
OD1 A:ASP195 2.3 11.7 1.0
OD1 A:ASP201 2.3 13.3 1.0
OD1 A:ASP105 2.4 11.0 1.0
O A:HOH2110 2.5 12.9 1.0
C A:ASP195 3.2 12.0 1.0
CG A:ASP201 3.4 13.1 1.0
CG A:ASP195 3.5 13.1 1.0
C A:HIS236 3.5 12.9 1.0
CG A:ASP105 3.6 10.8 1.0
OD2 A:ASP201 3.7 14.2 1.0
CA A:ASP195 3.8 11.8 1.0
O A:ASP105 3.9 14.6 1.0
O A:HOH2201 3.9 13.2 1.0
O A:HOH2111 4.0 10.3 1.0
CB A:HIS236 4.1 12.0 1.0
NA A:NA1491 4.2 13.1 1.0
OD2 A:ASP105 4.2 11.2 1.0
CB A:ASP195 4.2 11.8 1.0
N A:TYR196 4.3 11.5 1.0
CA A:HIS236 4.3 12.4 1.0
OD2 A:ASP195 4.4 11.6 1.0
N A:ILE237 4.5 13.2 1.0
CB A:ASP105 4.6 12.1 1.0
CA A:TYR196 4.6 11.7 1.0
CA A:ILE237 4.6 13.3 1.0
C A:ASP105 4.7 13.2 1.0
CA A:ASP105 4.7 12.8 1.0
CG1 A:ILE237 4.7 13.4 1.0
O A:LEU202 4.7 12.4 1.0
CB A:ASP201 4.7 13.1 1.0

Calcium binding site 3 out of 3 in 4uzu

Go back to Calcium Binding Sites List in 4uzu
Calcium binding site 3 out of 3 in the Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1485

b:16.9
occ:1.00
 O A:GLY301 2.3 18.1 1.0
O A:HOH2298 2.3 18.5 1.0
O A:PHE303 2.3 14.4 1.0
OD1 A:ASP405 2.4 18.7 1.0
O A:SER404 2.4 15.8 1.0
OD1 A:ASP428 2.4 17.1 1.0
OD2 A:ASP428 2.6 17.0 1.0
CG A:ASP428 2.9 17.0 1.0
C A:GLY301 3.4 18.7 1.0
C A:SER404 3.4 15.9 1.0
CG A:ASP405 3.5 18.4 1.0
C A:PHE303 3.5 14.8 1.0
CA A:ASP405 3.8 15.1 1.0
N A:PHE303 3.9 15.3 1.0
N A:ASP405 4.0 14.1 1.0
C A:ALA302 4.0 16.7 1.0
N A:ALA302 4.2 17.2 1.0
CB A:ASP405 4.2 16.6 1.0
CA A:PHE303 4.2 14.8 1.0
CG A:MET305 4.3 13.6 1.0
CA A:GLY301 4.3 17.4 1.0
CA A:ALA302 4.4 17.8 1.0
CB A:ASP428 4.4 16.4 1.0
OD2 A:ASP405 4.4 21.1 1.0
O A:HOH2297 4.4 26.5 0.5
OG A:SER404 4.5 18.6 1.0
N A:MET305 4.5 12.3 1.0
O A:HOH2299 4.5 20.5 1.0
N A:ASP304 4.5 12.9 1.0
O A:ALA302 4.5 16.9 1.0
CA A:SER404 4.6 15.7 1.0
CB A:SER404 4.6 16.7 1.0
O A:HOH2366 4.6 36.9 1.0
CA A:ASP304 4.6 13.1 1.0
O A:HOH2292 4.8 13.1 1.0
CB A:PHE303 4.8 16.2 1.0

Reference:

W.A.Offen, A.Viksoe-Nielsen, T.V.Borchert, K.S.Wilson, G.J.Davies. Three-Dimensional Structure of A Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution Acta Crystallogr.,Sect.F V. 71 66 2015.
ISSN: ISSN 1744-3091
PubMed: 25615972
DOI: 10.1107/S2053230X14026508
Page generated: Sun Jul 14 13:54:58 2024

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