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Sodium 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
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4uzu

Go back to Sodium Binding Sites List in 4uzu
Sodium 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 Sodium with other atoms in the Na 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:Na1491

b:13.1
occ:1.00
 OD2 A:ASP201 2.3 14.2 1.0
OD2 A:ASP162 2.3 13.1 1.0
O A:LEU202 2.4 12.4 1.0
OD2 A:ASP195 2.4 11.6 1.0
OD2 A:ASP184 2.5 14.3 1.0
OD1 A:ASP195 2.9 11.7 1.0
CG A:ASP195 3.0 13.1 1.0
CG A:ASP184 3.3 14.2 1.0
CG A:ASP162 3.3 13.6 1.0
CG A:ASP201 3.4 13.1 1.0
C A:LEU202 3.4 13.0 1.0
O A:HOH2201 3.7 13.2 1.0
CB A:ASP162 3.7 13.3 1.0
O A:HOH2110 3.7 12.9 1.0
OD1 A:ASP184 3.8 14.9 1.0
OD1 A:ASP201 3.8 13.3 1.0
CA A:ASP203 3.9 12.3 1.0
N A:ASP203 4.1 12.2 1.0
CB A:ASP184 4.1 13.0 1.0
CA A:CA1484 4.2 12.6 1.0
N A:MET204 4.3 14.7 1.0
N A:ASP184 4.3 11.6 1.0
OD1 A:ASP162 4.4 14.9 1.0
CA A:CA1483 4.4 12.8 1.0
CB A:ASP195 4.5 11.8 1.0
N A:LEU202 4.5 13.3 1.0
O A:ASP201 4.6 12.2 1.0
C A:ASP201 4.6 12.8 1.0
CA A:LEU202 4.6 12.8 1.0
CB A:ASP201 4.6 13.1 1.0
C A:ASP203 4.6 12.8 1.0
CE3 A:TRP183 4.8 9.2 1.0
N A:ASP162 4.9 12.7 1.0
CA A:ASP184 4.9 12.3 1.0
CA A:ASP162 4.9 12.5 1.0
CB A:ASP203 4.9 11.5 1.0

Sodium binding site 2 out of 3 in 4uzu

Go back to Sodium Binding Sites List in 4uzu
Sodium 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 Sodium with other atoms in the Na 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:Na1492

b:23.8
occ:1.00
 O A:HOH2145 2.2 18.4 1.0
O A:HOH2144 2.3 20.5 1.0
O A:HOH2143 2.4 12.5 1.0
OD2 A:ASP125 3.8 11.5 1.0
OD1 A:ASP125 4.2 10.1 1.0
CB A:ASN127 4.2 8.2 1.0
O A:HOH2061 4.3 23.9 1.0
CG A:ASP125 4.5 10.5 1.0
ND2 A:ASN127 4.5 7.7 1.0
CG A:ASN127 4.9 8.3 1.0

Sodium binding site 3 out of 3 in 4uzu

Go back to Sodium Binding Sites List in 4uzu
Sodium 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 Sodium with other atoms in the Na 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:Na1490

b:20.9
occ:1.00
 O A:HOH2242 2.3 29.0 1.0
O A:HOH2261 2.3 18.2 1.0
OD1 A:ASP232 2.3 11.4 1.0
O A:HOH2241 2.5 21.8 1.0
OE1 A:GLU262 2.5 14.8 1.0
CD A:GLU262 3.3 13.5 1.0
CG A:ASP232 3.3 11.8 1.0
OE2 A:GLU262 3.5 14.4 1.0
OD2 A:ASP232 3.8 12.0 1.0
O A:HOH2243 3.9 17.4 1.0
O A:HOH2247 3.9 18.9 1.0
N A:ALA233 3.9 11.6 1.0
O A:HOH2100 4.0 30.6 1.0
OD2 A:ASP329 4.1 16.2 1.0
NH2 A:ARG230 4.2 10.9 1.0
CB A:ALA233 4.3 11.1 1.0
CA A:ALA233 4.3 12.0 1.0
O A:HOH2318 4.4 18.9 1.0
NH1 A:ARG230 4.5 10.6 1.0
CB A:ASP232 4.6 11.1 1.0
CG A:GLU262 4.7 13.1 1.0
CA A:ASP232 4.7 10.9 1.0
C A:ASP232 4.7 11.9 1.0
CZ A:ARG230 4.8 11.0 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: Mon Oct 7 18:47:59 2024

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