Calcium in PDB 1e7d: Endonuclease VII (Endovii) Ffrom Phage T4

All present enzymatic activity of Endonuclease VII (Endovii) Ffrom Phage T4:
3.1.22.4;

The structure of Endonuclease VII (Endovii) Ffrom Phage T4, PDB code: 1e7d was solved by H.C.A.Raaijmakers, O.Vix, I.Toro, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.900, 37.400, 74.000, 90.00, 108.20, 90.00
R / Rfree (%)	24.5 / 31.5

The structure of Endonuclease VII (Endovii) Ffrom Phage T4 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Endonuclease VII (Endovii) Ffrom Phage T4 (pdb code 1e7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Endonuclease VII (Endovii) Ffrom Phage T4, PDB code: 1e7d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Endonuclease VII (Endovii) Ffrom Phage T4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Endonuclease VII (Endovii) Ffrom Phage T4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1159 b:30.1 occ:1.00 OD1 A:ASP40 2.4 26.5 1.0 O A:HOH2007 2.4 30.9 1.0 OD1 A:ASN62 2.5 23.9 1.0 OE1 A:GLU65 3.1 24.0 1.0 CG A:ASP40 3.6 26.2 1.0 CG A:ASN62 3.7 23.4 1.0 CD A:GLU65 4.2 24.4 1.0 ND2 A:ASN62 4.3 20.6 1.0 O A:HIS41 4.4 23.6 1.0 OD2 A:ASP40 4.4 25.9 1.0 CB A:ASP40 4.4 27.3 1.0 CA A:ASP40 4.4 26.0 1.0 NH1 A:ARG54 4.4 15.0 1.0 N A:HIS41 4.5 27.4 1.0 OE2 A:GLU65 4.7 23.7 1.0 O A:ASN62 4.8 20.3 1.0 CE1 A:HIS43 4.8 26.3 1.0 CB A:ASN62 4.9 23.3 1.0

Calcium binding site 2 out of 2 in the Endonuclease VII (Endovii) Ffrom Phage T4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Endonuclease VII (Endovii) Ffrom Phage T4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1159 b:29.0 occ:1.00 OD1 B:ASN62 2.4 22.1 1.0 OD1 B:ASP40 2.5 23.5 1.0 OE1 B:GLU65 2.7 8.9 1.0 CG B:ASN62 3.4 16.8 1.0 CG B:ASP40 3.7 19.3 1.0 CD B:GLU65 3.8 15.0 1.0 ND2 B:ASN62 4.0 15.5 1.0 CE1 B:HIS38 4.0 19.4 1.0 OE2 B:GLU65 4.1 11.7 1.0 NH2 B:ARG54 4.2 15.5 1.0 OD2 B:ASP40 4.4 18.6 1.0 NE2 B:HIS43 4.4 23.9 1.0 O B:HIS41 4.4 30.0 1.0 O B:ASN62 4.5 13.2 1.0 CE1 B:HIS43 4.6 24.1 1.0 ND1 B:HIS38 4.6 18.8 1.0 CB B:ASN62 4.6 15.4 1.0 CB B:ASP40 4.7 18.4 1.0 NE2 B:HIS38 4.8 18.9 1.0 N B:HIS41 4.8 24.8 1.0 CA B:ASP40 4.8 20.2 1.0 CA B:ASN62 4.9 14.6 1.0

H.C.A.Raaijmakers, I.Toro, R.Birkenbihl, B.Kemper, D.Suck. Conformational Flexibility in T4 Endonuclease VII Revealed By Crystallography: Implications For Substrate Binding and Cleavage J.Mol.Biol. V. 308 311 2001.
ISSN: ISSN 0022-2836
PubMed: 11327769
DOI: 10.1006/JMBI.2001.4592