Calcium in PDB 3qgv: Crystal Structure of A Thermostable Amylase Variant

All present enzymatic activity of Crystal Structure of A Thermostable Amylase Variant:
3.2.1.1;

The structure of Crystal Structure of A Thermostable Amylase Variant, PDB code: 3qgv was solved by K.L.Hein, G.Ganshaw, R.Bott, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.900, 59.900, 272.410, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.7

The structure of Crystal Structure of A Thermostable Amylase Variant also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Thermostable Amylase Variant (pdb code 3qgv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Thermostable Amylase Variant, PDB code: 3qgv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Thermostable Amylase Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Thermostable Amylase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:29.3 occ:1.00 O A:GLY157 2.5 31.3 1.0 O A:GLY202 2.5 26.7 1.0 OD1 A:ASN110 2.5 28.7 1.0 O A:HOH437 2.5 28.7 1.0 OD2 A:ASP164 2.6 35.9 1.0 OD1 A:ASP164 2.6 28.2 1.0 OD1 A:ASP155 2.6 31.2 1.0 OD2 A:ASP155 2.6 26.2 1.0 CG A:ASP164 2.9 37.2 1.0 CG A:ASP155 3.0 34.5 1.0 C A:GLY202 3.5 25.6 1.0 CG A:ASN110 3.6 31.3 1.0 C A:GLY157 3.7 37.8 1.0 CA A:GLY202 4.1 25.7 1.0 O A:ASN110 4.1 29.9 1.0 ND2 A:ASN110 4.1 24.0 1.0 N A:GLY157 4.3 31.1 1.0 O A:HOH478 4.3 36.9 1.0 CB A:ASP164 4.4 31.3 1.0 CB A:ASP155 4.5 29.1 1.0 N A:TYR203 4.5 25.8 1.0 CA A:GLY157 4.6 32.8 1.0 CB A:TYR203 4.6 25.3 1.0 N A:THR158 4.6 38.1 1.0 CA A:THR158 4.6 36.3 1.0 O A:ILE165 4.7 31.3 1.0 ND1 A:HIS147 4.7 38.0 1.0 CE1 A:HIS147 4.7 41.8 1.0 CA A:TYR203 4.7 26.1 1.0 CB A:ASN110 4.8 22.9 1.0 O A:HOH633 4.8 25.1 1.0 C A:ASN110 4.9 32.4 1.0 CA A:ASN110 4.9 27.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Thermostable Amylase Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Thermostable Amylase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:58.2 occ:1.00 O A:GLY24 2.5 43.3 1.0 O A:HOH617 2.5 51.7 1.0 O A:HOH576 2.6 51.0 1.0 O A:HOH550 2.6 55.0 1.0 OE2 A:GLU80 2.7 60.6 1.0 OE1 A:GLU80 2.7 55.0 1.0 OE1 A:GLU88 2.7 56.1 1.0 OE2 A:GLU88 2.9 54.6 1.0 CD A:GLU80 3.0 59.0 1.0 CD A:GLU88 3.1 49.9 1.0 C A:GLY24 3.6 48.6 1.0 CA A:GLY24 4.3 49.2 1.0 O A:HOH457 4.3 39.7 1.0 CA A:GLY84 4.4 39.0 1.0 O A:GLY23 4.5 52.2 1.0 OD2 A:ASP28 4.5 58.8 1.0 CG A:GLU80 4.6 57.4 1.0 CG A:GLU88 4.6 47.2 1.0 N A:SER85 4.6 47.2 1.0 N A:ILE25 4.7 40.0 1.0 CA A:ILE25 4.9 51.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Thermostable Amylase Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Thermostable Amylase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.1 occ:1.00 OD2 A:ASP347 2.5 37.9 1.0 O A:HOH608 2.6 47.0 1.0 OE1 A:GLU350 2.6 35.9 1.0 OD1 A:ASP349 2.7 48.7 1.0 O A:HOH580 2.8 56.2 1.0 OD1 A:ASP347 2.8 35.8 1.0 CG A:ASP347 3.0 34.5 1.0 CG A:ASP349 3.6 50.4 1.0 CD A:GLU350 3.7 37.2 1.0 OD2 A:ASP349 3.9 64.8 1.0 CG A:GLU350 4.0 36.1 1.0 NH2 A:ARG377 4.3 35.5 1.0 OD1 A:ASN348 4.3 55.5 0.5 CB A:ASP347 4.4 32.5 1.0 CB A:GLU350 4.4 35.7 1.0 N A:ASP349 4.6 38.1 1.0 N A:GLU350 4.6 35.0 1.0 OH A:TYR345 4.7 40.9 1.0 OE2 A:GLU350 4.8 37.1 1.0 ND2 A:ASN348 4.8 49.6 0.5 O A:HOH562 4.8 48.9 1.0 CG A:ASN348 4.8 49.2 0.5 CB A:ASP349 4.9 42.0 1.0 C A:ASP349 4.9 40.4 1.0 CA A:ASP349 4.9 40.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Thermostable Amylase Variant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Thermostable Amylase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:59.2 occ:1.00 OD1 A:ASP252 2.4 37.8 1.0 OD2 A:ASP256 2.4 37.8 1.0 O A:HOH610 2.5 49.8 1.0 O A:HOH578 2.5 49.0 1.0 O A:ILE292 2.5 43.0 1.0 O A:HOH579 2.6 43.2 1.0 CG A:ASP252 3.3 40.5 1.0 CG A:ASP256 3.3 37.3 1.0 CB A:ASP256 3.6 33.9 1.0 OD2 A:ASP252 3.6 41.5 1.0 C A:ILE292 3.7 40.2 1.0 O A:HOH606 3.8 49.0 1.0 CD1 A:TRP294 4.3 73.8 1.0 CA A:ILE293 4.4 38.5 1.0 N A:TRP294 4.5 33.2 1.0 OD1 A:ASP256 4.5 41.2 1.0 N A:ILE293 4.5 37.0 1.0 CB A:ILE292 4.6 37.7 1.0 CA A:ILE292 4.7 34.0 1.0 CB A:ASP252 4.7 39.2 1.0 O A:HOH567 4.8 45.2 1.0 CG1 A:ILE292 4.9 39.0 1.0 O A:ASP252 4.9 33.4 1.0 NE1 A:TRP294 5.0 81.6 1.0 C A:ILE293 5.0 36.6 1.0

K.L.Hein, G.Ganshaw, R.Bott, P.Nissen. Structure of A Highly Mutated, Thermostable \Xce\XB1-Amylase Variant To Be Published.