Nickel in PDB 4lrl: Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp

The structure of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp, PDB code: 4lrl was solved by I.I.Vorontsov, G.Minasov, L.Shuvalova, A.Joachimiak, W.F.Anderson, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.86 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.541, 144.625, 155.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.5

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

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:35.5 occ:1.00 O A:HOH801 2.1 32.4 1.0 NE2 A:HIS110 2.2 26.3 1.0 OD2 A:ASP183 2.2 25.6 1.0 OD2 A:ASP111 2.2 27.8 1.0 NE2 A:HIS66 2.3 18.8 1.0 O A:HOH651 2.5 39.2 1.0 CG A:ASP183 3.0 26.3 1.0 CG A:ASP111 3.1 26.5 1.0 CD2 A:HIS110 3.1 26.9 1.0 CD2 A:HIS66 3.1 18.6 1.0 CE1 A:HIS110 3.2 25.6 1.0 CE1 A:HIS66 3.3 19.7 1.0 OD1 A:ASP183 3.3 30.1 1.0 OD1 A:ASP111 3.4 26.9 1.0 CG A:HIS110 4.2 26.3 1.0 ND1 A:HIS110 4.3 25.6 1.0 CB A:ASP111 4.3 25.4 1.0 CB A:ASP183 4.3 25.5 1.0 CG A:HIS66 4.3 20.1 1.0 ND1 A:HIS66 4.4 19.5 1.0 O A:HOH624 4.4 31.5 1.0 CD2 A:TYR187 4.5 27.2 1.0 CG2 A:VAL70 4.6 23.5 1.0 CA A:ASP183 4.8 25.5 1.0 NE2 A:GLN48 4.8 26.7 1.0 O A:HOH625 4.9 33.6 1.0 O A:ASP183 4.9 25.4 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:52.5 occ:1.00 OD2 B:ASP183 2.1 37.6 1.0 NE2 B:HIS110 2.1 38.1 1.0 NE2 B:HIS66 2.3 28.2 1.0 O B:HOH786 2.4 54.7 1.0 OD2 B:ASP111 2.4 37.9 1.0 O B:HOH742 2.6 47.8 1.0 CG B:ASP183 2.9 37.2 1.0 CD2 B:HIS110 2.9 39.7 1.0 CD2 B:HIS66 3.1 27.7 1.0 CG B:ASP111 3.2 36.5 1.0 CE1 B:HIS110 3.2 38.2 1.0 OD1 B:ASP183 3.2 41.3 1.0 CE1 B:HIS66 3.3 27.0 1.0 OD1 B:ASP111 3.4 38.0 1.0 CG B:HIS110 4.1 39.5 1.0 CB B:ASP183 4.2 37.1 1.0 ND1 B:HIS110 4.2 39.0 1.0 CG B:HIS66 4.3 28.6 1.0 CG2 B:VAL70 4.3 30.0 1.0 ND1 B:HIS66 4.4 28.8 1.0 CB B:ASP111 4.5 35.9 1.0 O B:HOH630 4.5 44.0 1.0 CD2 B:TYR187 4.7 36.8 1.0 CA B:ASP183 4.7 36.1 1.0 NE2 B:GLN48 4.9 31.4 1.0 O B:ASP183 4.9 34.7 1.0 O B:HOH705 5.0 50.2 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:46.0 occ:1.00 OD2 C:ASP183 2.1 31.3 1.0 O C:HOH756 2.1 39.8 1.0 NE2 C:HIS66 2.2 29.1 1.0 NE2 C:HIS110 2.2 37.2 1.0 OD2 C:ASP111 2.2 35.3 1.0 O C:HOH747 2.4 40.2 1.0 CG C:ASP183 2.9 30.0 1.0 CD2 C:HIS110 3.0 37.8 1.0 CD2 C:HIS66 3.0 27.9 1.0 CG C:ASP111 3.1 34.4 1.0 OD1 C:ASP183 3.2 33.1 1.0 CE1 C:HIS66 3.2 27.4 1.0 CE1 C:HIS110 3.3 37.1 1.0 OD1 C:ASP111 3.3 34.0 1.0 CG C:HIS110 4.2 37.3 1.0 CB C:ASP183 4.2 30.5 1.0 CG C:HIS66 4.2 28.1 1.0 ND1 C:HIS66 4.3 27.0 1.0 ND1 C:HIS110 4.3 37.5 1.0 O C:HOH626 4.3 39.0 1.0 CB C:ASP111 4.4 34.1 1.0 CD2 C:TYR187 4.5 28.1 1.0 CG2 C:VAL70 4.6 25.6 1.0 O C:HOH696 4.6 51.0 1.0 O C:HOH748 4.7 46.0 1.0 CA C:ASP183 4.7 29.8 1.0 O C:ASP183 4.9 29.1 1.0 NE2 C:GLN48 4.9 27.3 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of An Enterococcus Faecalis Hd-Domain Protein Complexed with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni501 b:49.0 occ:1.00 OD2 D:ASP183 2.1 34.9 1.0 NE2 D:HIS66 2.2 31.2 1.0 O D:HOH725 2.2 47.0 1.0 NE2 D:HIS110 2.3 37.7 1.0 OD2 D:ASP111 2.3 40.0 1.0 O D:HOH698 2.3 50.8 1.0 CG D:ASP183 2.9 34.6 1.0 CD2 D:HIS66 3.1 30.3 1.0 CD2 D:HIS110 3.1 38.5 1.0 OD1 D:ASP183 3.1 35.3 1.0 CG D:ASP111 3.2 39.3 1.0 CE1 D:HIS66 3.3 30.4 1.0 CE1 D:HIS110 3.3 37.1 1.0 OD1 D:ASP111 3.5 42.3 1.0 O D:HOH624 4.3 43.7 1.0 CB D:ASP183 4.3 33.9 1.0 CG D:HIS66 4.3 30.6 1.0 CG D:HIS110 4.3 37.7 1.0 ND1 D:HIS66 4.3 31.3 1.0 ND1 D:HIS110 4.3 37.9 1.0 CB D:ASP111 4.4 37.4 1.0 CG2 D:VAL70 4.5 27.2 1.0 CD2 D:TYR187 4.5 32.9 1.0 NE2 D:GLN48 4.7 30.9 1.0 CA D:ASP183 4.8 32.9 1.0 O D:ASP183 4.9 31.6 1.0

I.I.Vorontsov, Y.Wu, M.Delucia, G.Minasov, J.Mehrens, L.Shuvalova, W.F.Anderson, J.Ahn. Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase From Enterococcus Faecalis. J.Biol.Chem. V. 289 2815 2014.
ISSN: ISSN 0021-9258
PubMed: 24338016
DOI: 10.1074/JBC.M113.524207