Calcium in PDB 3irh: Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp

The structure of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp, PDB code: 3irh was solved by I.I.Vorontsov, G.Minasov, L.Shuvalova, J.S.Brunzelle, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	149.253, 188.660, 67.822, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24.4

The binding sites of Calcium atom in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp (pdb code 3irh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp, PDB code: 3irh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca457 b:31.7 occ:1.00 OD2 A:ASP183 2.1 42.0 1.0 NE2 A:HIS110 2.1 40.2 1.0 O A:HOH525 2.2 40.5 1.0 NE2 A:HIS66 2.2 33.0 1.0 OD2 A:ASP111 2.3 50.0 1.0 O A:HOH533 2.7 50.7 1.0 CG A:ASP183 2.9 38.6 1.0 CD2 A:HIS110 3.0 41.6 1.0 CD2 A:HIS66 3.0 32.3 1.0 OD1 A:ASP183 3.1 41.0 1.0 CG A:ASP111 3.1 44.7 1.0 CE1 A:HIS110 3.1 42.2 1.0 CE1 A:HIS66 3.3 33.5 1.0 OD1 A:ASP111 3.4 46.9 1.0 CG A:HIS110 4.2 41.4 1.0 ND1 A:HIS110 4.2 41.9 1.0 CG A:HIS66 4.2 34.1 1.0 CB A:ASP183 4.2 37.3 1.0 CB A:ASP111 4.3 40.6 1.0 ND1 A:HIS66 4.4 35.0 1.0 O A:HOH474 4.4 42.9 1.0 CG2 A:VAL70 4.5 33.3 1.0 CD2 A:TYR187 4.6 37.0 1.0 CA A:ASP183 4.8 37.1 1.0 O A:ASP183 4.8 37.1 1.0 O A:HOH536 5.0 41.9 1.0

Calcium binding site 2 out of 4 in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca457 b:29.3 occ:1.00 OD1 B:ASP183 2.0 45.8 1.0 NE2 B:HIS66 2.2 33.4 1.0 OD2 B:ASP111 2.3 52.5 1.0 O B:HOH570 2.3 50.8 1.0 NE2 B:HIS110 2.3 43.8 1.0 CG B:ASP183 3.0 41.3 1.0 CD2 B:HIS66 3.0 29.6 1.0 CD2 B:HIS110 3.1 45.5 1.0 CG B:ASP111 3.2 46.4 1.0 CE1 B:HIS66 3.3 27.9 1.0 OD2 B:ASP183 3.3 47.0 1.0 CE1 B:HIS110 3.5 44.4 1.0 OD1 B:ASP111 3.6 49.7 1.0 O B:HOH559 4.1 46.1 1.0 CG B:HIS66 4.2 29.5 1.0 CB B:ASP183 4.3 37.8 1.0 CG B:HIS110 4.3 42.7 1.0 ND1 B:HIS66 4.3 28.9 1.0 CG2 B:VAL70 4.5 30.5 1.0 ND1 B:HIS110 4.5 44.6 1.0 CB B:ASP111 4.5 41.3 1.0 CD2 B:TYR187 4.5 39.0 1.0 O B:ASP183 4.6 37.7 1.0 CA B:ASP183 4.7 38.3 1.0 O1A B:DTP459 4.7 68.3 0.7 C B:ASP183 4.9 37.7 1.0

Calcium binding site 3 out of 4 in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca457 b:35.5 occ:1.00 OD1 C:ASP183 2.1 43.1 1.0 NE2 C:HIS110 2.3 47.3 1.0 NE2 C:HIS66 2.3 35.2 1.0 OD2 C:ASP111 2.4 51.8 1.0 CG C:ASP183 2.9 41.7 1.0 OD2 C:ASP183 3.1 44.4 1.0 CG C:ASP111 3.1 45.8 1.0 CD2 C:HIS66 3.1 32.4 1.0 CD2 C:HIS110 3.2 46.8 1.0 OD1 C:ASP111 3.2 47.0 1.0 CE1 C:HIS110 3.3 49.6 1.0 CE1 C:HIS66 3.4 35.4 1.0 CB C:ASP183 4.3 39.6 1.0 CG C:HIS110 4.3 45.2 1.0 ND1 C:HIS110 4.3 47.9 1.0 O C:HOH472 4.3 42.3 1.0 CG C:HIS66 4.3 35.4 1.0 CB C:ASP111 4.4 42.8 1.0 ND1 C:HIS66 4.5 36.9 1.0 CD2 C:TYR187 4.5 39.0 1.0 CG2 C:VAL70 4.7 35.0 1.0 CA C:ASP183 4.8 39.7 1.0 CE2 C:TYR187 4.9 39.8 1.0 OE1 C:GLN48 4.9 45.5 1.0 O C:ASP183 4.9 38.8 1.0

Calcium binding site 4 out of 4 in the Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Datp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca457 b:34.4 occ:1.00 OD2 D:ASP183 2.0 43.1 1.0 NE2 D:HIS110 2.2 49.6 1.0 O D:HOH519 2.3 49.7 1.0 NE2 D:HIS66 2.3 30.4 1.0 OD2 D:ASP111 2.4 50.8 1.0 CG D:ASP183 3.0 39.9 1.0 CD2 D:HIS110 3.0 47.4 1.0 CD2 D:HIS66 3.1 31.3 1.0 CG D:ASP111 3.2 47.0 1.0 OD1 D:ASP183 3.3 43.4 1.0 CE1 D:HIS110 3.3 49.1 1.0 OD1 D:ASP111 3.4 49.5 1.0 CE1 D:HIS66 3.4 29.6 1.0 CG D:HIS110 4.2 47.0 1.0 O2A D:DTP459 4.2 82.0 0.7 CB D:ASP183 4.3 37.8 1.0 ND1 D:HIS110 4.3 48.7 1.0 CG D:HIS66 4.3 32.7 1.0 CB D:ASP111 4.4 43.4 1.0 ND1 D:HIS66 4.5 33.3 1.0 CG2 D:VAL70 4.6 29.2 1.0 CD2 D:TYR187 4.6 35.8 1.0 CA D:ASP183 4.7 38.3 1.0 O D:ASP183 4.9 37.5 1.0

I.I.Vorontsov, G.Minasov, O.Kiryukhina, J.S.Brunzelle, L.Shuvalova, W.F.Anderson. Characterization of the Deoxynucleotide Triphosphate Triphosphohydrolase (Dntpase) Activity of the EF1143 Protein From Enterococcus Faecalis and Crystal Structure of the Activator-Substrate Complex. J.Biol.Chem. V. 286 33158 2011.
ISSN: ISSN 0021-9258
PubMed: 21757692
DOI: 10.1074/JBC.M111.250456