Calcium in PDB 3vm5: Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris

The structure of Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris, PDB code: 3vm5 was solved by K.Mizutani, M.Toyoda, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.73 / 2.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.045, 83.045, 174.228, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 24.8

The structure of Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris (pdb code 3vm5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris, PDB code: 3vm5:

Calcium binding site 1 out of 1 in the Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:34.6 occ:1.00 O A:HOH552 2.4 30.7 1.0 O A:ARG158 2.5 30.6 1.0 O A:HOH553 2.5 27.7 1.0 O A:HIS201 2.6 32.5 1.0 OD2 A:ASP167 2.6 34.8 1.0 OD1 A:ASP167 2.7 37.9 1.0 O A:HOH554 2.9 33.2 1.0 ND2 A:ASN100 2.9 39.0 1.0 CG A:ASP167 3.0 40.0 1.0 OD1 A:ASN100 3.1 31.7 1.0 CG A:ASN100 3.3 30.4 1.0 C A:HIS201 3.6 30.1 1.0 C A:ARG158 3.6 35.7 1.0 O A:ASN100 4.1 31.4 1.0 CA A:ARG158 4.2 35.1 1.0 CG A:MET202 4.2 27.1 1.0 CB A:HIS201 4.3 30.6 1.0 N A:MET202 4.3 30.6 1.0 ND2 A:ASN137 4.4 39.0 1.0 CA A:MET202 4.4 30.2 1.0 CB A:ASP167 4.5 42.9 1.0 CA A:HIS201 4.5 30.1 1.0 CB A:ASN100 4.6 23.8 1.0 O A:LEU168 4.6 32.9 1.0 N A:ASP159 4.7 34.6 1.0 O A:CYS160 4.8 34.1 1.0 O A:VAL157 4.8 33.5 1.0 CA A:ASN100 4.9 24.3 1.0 C A:ASN100 4.9 27.6 1.0 CB A:MET202 4.9 28.7 1.0 CB A:ARG158 4.9 35.0 1.0

K.Mizutani, M.Toyoda, Y.Otake, S.Yoshioka, N.Takahashi, B.Mikami. Structural and Functional Characterization of Recombinant Medaka Fish Alpha-Amylase Expressed in Yeast Pichia Pastoris. Biochim.Biophys.Acta V.1824 954 2012.
ISSN: ISSN 0006-3002
PubMed: 22613096
DOI: 10.1016/J.BBAPAP.2012.05.005