Calcium in PDB 2d8w: Structure of Hyper-Vil-Trypsin

All present enzymatic activity of Structure of Hyper-Vil-Trypsin:
3.4.21.4;

The structure of Structure of Hyper-Vil-Trypsin, PDB code: 2d8w was solved by H.Miyatake, T.Hasegawa, A.Yamano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.31 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.323, 58.197, 66.620, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.6

The structure of Structure of Hyper-Vil-Trypsin also contains other interesting chemical elements:

Iodine

(I)

7 atoms

The binding sites of Calcium atom in the Structure of Hyper-Vil-Trypsin (pdb code 2d8w). 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 Structure of Hyper-Vil-Trypsin, PDB code: 2d8w:

Calcium binding site 1 out of 1 in the Structure of Hyper-Vil-Trypsin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Hyper-Vil-Trypsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:21.5 occ:1.00 OE1 A:GLU58 2.4 20.5 1.0 O A:VAL63 2.5 20.3 1.0 O A:ASN60 2.5 16.0 1.0 O A:HOH495 2.5 19.8 1.0 O A:HOH496 2.6 19.3 1.0 OE2 A:GLU68 2.6 24.4 1.0 CD A:GLU58 3.4 20.6 1.0 C A:VAL63 3.5 20.6 1.0 CD A:GLU68 3.5 22.1 1.0 CG A:GLU68 3.6 22.4 1.0 C A:ASN60 3.7 18.1 1.0 OE2 A:GLU58 3.8 20.0 1.0 CA A:VAL64 4.1 21.7 1.0 N A:GLU65 4.1 22.1 1.0 N A:VAL64 4.2 20.5 1.0 OE1 A:GLU65 4.2 22.8 1.0 N A:VAL63 4.3 19.7 1.0 CA A:ILE61 4.3 18.8 1.0 O A:HOH412 4.3 18.5 1.0 N A:ASN60 4.4 18.6 1.0 N A:ILE61 4.4 18.0 1.0 CA A:VAL63 4.5 19.6 1.0 CG A:GLU65 4.5 25.0 1.0 N A:ASP59 4.5 20.0 1.0 C A:VAL64 4.6 23.0 1.0 C A:ILE61 4.6 18.7 1.0 CA A:ASN60 4.6 18.1 1.0 OE1 A:GLU68 4.6 21.6 1.0 CG A:GLU58 4.7 18.4 1.0 CD A:GLU65 4.8 24.9 1.0 CA A:GLU58 4.8 19.6 1.0 CB A:GLU65 4.8 24.6 1.0 N A:ASN62 4.9 17.2 1.0 CB A:GLU58 5.0 19.5 1.0 CB A:ASN60 5.0 19.9 1.0

H.Miyatake, T.Hasegawa, A.Yamano. New Methods to Prepare Iodinated Derivatives By Vaporizing Iodine Labelling (Vil) and Hydrogen Peroxide Vil (Hyper-Vil) Acta Crystallogr.,Sect.D V. 62 280 2006.
ISSN: ISSN 0907-4449
PubMed: 16510975
DOI: 10.1107/S0907444905041909