Calcium in PDB 3bcf: Alpha-Amylase B From Halothermothrix Orenii

All present enzymatic activity of Alpha-Amylase B From Halothermothrix Orenii:
3.2.1.1;

The structure of Alpha-Amylase B From Halothermothrix Orenii, PDB code: 3bcf was solved by T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	226.620, 77.820, 50.330, 90.00, 99.38, 90.00
R / Rfree (%)	19.1 / 22.9

The structure of Alpha-Amylase B From Halothermothrix Orenii also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Alpha-Amylase B From Halothermothrix Orenii (pdb code 3bcf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Alpha-Amylase B From Halothermothrix Orenii, PDB code: 3bcf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Alpha-Amylase B From Halothermothrix Orenii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Alpha-Amylase B From Halothermothrix Orenii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:35.0 occ:1.00 O A:SER303 2.3 36.7 1.0 OE1 A:GLU323 2.3 41.8 1.0 OD1 A:ASP305 2.3 39.7 1.0 OD1 A:ASP321 2.3 32.9 1.0 O A:HOH742 2.4 37.3 1.0 OD1 A:ASP283 2.4 31.0 1.0 OD2 A:ASP283 2.5 33.6 1.0 CG A:ASP283 2.7 35.4 1.0 CG A:ASP321 3.1 40.9 1.0 CD A:GLU323 3.3 46.5 1.0 CG A:ASP305 3.3 38.0 1.0 C A:SER303 3.6 38.9 1.0 OD2 A:ASP321 3.6 43.2 1.0 CG A:GLU323 3.8 45.7 1.0 OD2 A:ASP305 3.9 36.5 1.0 CB A:GLU323 4.0 44.9 1.0 CB A:ASP321 4.0 39.1 1.0 N A:ASP305 4.2 35.7 1.0 CA A:ASP321 4.2 37.1 1.0 N A:SER303 4.2 42.7 1.0 CB A:ASP283 4.3 34.2 1.0 OG A:SER303 4.3 44.0 1.0 OE2 A:GLU323 4.3 51.7 1.0 NA A:NA704 4.4 29.8 1.0 N A:GLU323 4.4 42.5 1.0 C A:TRP304 4.4 36.2 1.0 CA A:ASP305 4.5 37.3 1.0 CB A:ASP305 4.5 38.5 1.0 CA A:SER303 4.5 41.1 1.0 N A:TRP304 4.5 36.4 1.0 C A:ASP321 4.6 37.2 1.0 CA A:TRP304 4.6 35.8 1.0 N A:TYR322 4.7 36.2 1.0 CA A:GLU323 4.8 44.5 1.0 O A:TRP304 4.9 34.4 1.0 OD2 A:ASP313 4.9 35.4 1.0

Calcium binding site 2 out of 4 in the Alpha-Amylase B From Halothermothrix Orenii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Alpha-Amylase B From Halothermothrix Orenii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:30.0 occ:1.00 OD1 A:ASN232 2.2 31.0 1.0 OD1 A:ASP313 2.3 31.0 1.0 O A:ASP313 2.3 31.8 1.0 O A:HOH727 2.4 31.9 1.0 OD1 A:ASP319 2.4 28.3 1.0 O A:HIS354 2.4 32.2 1.0 CG A:ASP319 3.1 33.7 1.0 C A:ASP313 3.2 33.7 1.0 OD2 A:ASP319 3.3 32.2 1.0 CG A:ASP313 3.4 35.4 1.0 CG A:ASN232 3.5 36.9 1.0 C A:HIS354 3.5 35.2 1.0 CA A:ASP313 3.6 34.3 1.0 O A:HOH721 3.9 35.6 1.0 O A:ASN232 4.0 41.8 1.0 O A:HOH707 4.0 33.3 1.0 CB A:ASP313 4.1 32.8 1.0 N A:TYR314 4.3 34.6 1.0 ND2 A:ASN232 4.3 41.9 1.0 CB A:HIS354 4.3 34.6 1.0 OD2 A:ASP313 4.3 35.4 1.0 NA A:NA704 4.4 29.8 1.0 CA A:ILE355 4.4 36.6 1.0 N A:ILE355 4.4 37.0 1.0 CB A:ASN232 4.4 39.2 1.0 CA A:HIS354 4.5 35.8 1.0 CB A:ASP319 4.6 33.4 1.0 CA A:TYR314 4.7 36.0 1.0 CA A:ASN232 4.7 38.0 1.0 C A:ASN232 4.7 38.3 1.0 CG1 A:ILE355 4.8 36.6 1.0 O A:VAL320 4.9 34.5 1.0 O A:GLU312 4.9 31.4 1.0 N A:ASP313 5.0 34.6 1.0

Calcium binding site 3 out of 4 in the Alpha-Amylase B From Halothermothrix Orenii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Alpha-Amylase B From Halothermothrix Orenii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:43.7 occ:1.00 O A:HOH790 2.2 42.0 1.0 O A:ALA517 2.3 39.9 1.0 OD1 A:ASP518 2.3 47.4 1.0 OD1 A:ASP541 2.3 47.8 1.0 O A:ALA419 2.3 39.9 1.0 OD2 A:ASP541 2.4 44.0 1.0 CG A:ASP541 2.7 46.1 1.0 C A:ALA517 3.2 42.9 1.0 CG A:ASP518 3.4 46.3 1.0 C A:ALA419 3.5 38.6 1.0 CA A:ASP518 3.7 45.2 1.0 N A:ALA419 3.8 38.8 1.0 N A:ASP518 3.8 43.8 1.0 CB A:ASP518 4.0 44.9 1.0 CG A:MET421 4.1 37.7 1.0 CB A:ASP541 4.2 46.6 1.0 CA A:ALA517 4.3 42.6 1.0 CA A:ALA419 4.3 38.7 1.0 OD2 A:ASP518 4.4 49.5 1.0 CB A:ALA517 4.5 41.8 1.0 N A:TYR420 4.5 38.8 1.0 O A:HOH905 4.5 51.8 1.0 N A:MET421 4.5 38.4 1.0 C A:GLY418 4.6 39.3 1.0 CA A:GLY418 4.6 39.8 1.0 CA A:TYR420 4.7 38.6 1.0 C A:ASP518 4.8 45.8 1.0 C A:ASP541 5.0 46.6 1.0

Calcium binding site 4 out of 4 in the Alpha-Amylase B From Halothermothrix Orenii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Alpha-Amylase B From Halothermothrix Orenii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:58.9 occ:1.00 OD1 A:ASP533 2.3 52.9 1.0 O A:HOH959 2.3 56.4 1.0 O A:PHE527 2.3 53.6 1.0 O A:VAL530 2.4 52.3 1.0 C A:PHE527 3.4 53.0 1.0 CG A:ASP533 3.5 52.2 1.0 N A:PHE527 3.5 51.0 1.0 C A:VAL530 3.6 53.8 1.0 C A:GLY526 3.8 50.7 1.0 CA A:GLY526 4.0 50.2 1.0 CA A:PHE527 4.1 51.8 1.0 OD2 A:ASP533 4.1 52.7 1.0 N A:ASP533 4.1 51.6 1.0 O A:ASP533 4.2 49.1 1.0 N A:GLY532 4.4 53.4 1.0 N A:PRO528 4.4 54.5 1.0 CA A:VAL530 4.4 54.7 1.0 C A:ASP533 4.5 49.7 1.0 N A:ALA531 4.5 53.5 1.0 O A:SER525 4.5 47.8 1.0 N A:VAL530 4.5 55.2 1.0 CB A:ASP533 4.6 50.8 1.0 CA A:ALA531 4.6 53.6 1.0 CA A:ASP533 4.6 51.2 1.0 O A:PRO528 4.6 55.0 1.0 CB A:VAL530 4.6 54.8 1.0 CA A:PRO528 4.6 55.0 1.0 O A:GLY526 4.6 52.0 1.0 C A:ALA531 4.7 53.6 1.0 C A:PRO528 4.7 55.4 1.0 OE1 A:GLN556 4.8 48.1 1.0 CB A:PHE527 4.9 51.1 1.0

T.-C.Tan, B.N.Mijts, K.Swaminathan, B.K.C.Patel, C.Divne. Crystal Structure of the Polyextremophilic Alpha-Amylase Amyb From Halothermothrix Orenii: Details of A Productive Enzyme-Substrate Complex and An N Domain with A Role in Binding Raw Starch J.Mol.Biol. V. 378 850 2008.
ISSN: ISSN 0022-2836
PubMed: 18387632
DOI: 10.1016/J.JMB.2008.02.041