Magnesium in PDB 8dkr: Pseudomonas-Phage E217 Terl Nuclease Domain

The structure of Pseudomonas-Phage E217 Terl Nuclease Domain, PDB code: 8dkr was solved by G.Cingolani, R.Lokareddy, D.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.93 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.601, 62.628, 149.253, 90, 90, 90
R / Rfree (%)	21.7 / 24.3

The binding sites of Magnesium atom in the Pseudomonas-Phage E217 Terl Nuclease Domain (pdb code 8dkr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pseudomonas-Phage E217 Terl Nuclease Domain, PDB code: 8dkr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pseudomonas-Phage E217 Terl Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pseudomonas-Phage E217 Terl Nuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:37.1 occ:1.00 OD2 B:ASP298 1.9 45.8 1.0 O B:HOH619 2.0 46.5 1.0 O B:VAL246 2.2 42.3 1.0 OD2 B:ASP248 2.3 52.2 1.0 O B:HOH659 2.5 43.8 1.0 O B:HOH601 2.9 38.7 1.0 CG B:ASP298 3.1 46.4 1.0 CG B:ASP248 3.2 55.4 1.0 C B:VAL246 3.4 42.8 1.0 OD1 B:ASP248 3.5 48.5 1.0 N B:VAL246 3.9 37.7 1.0 OD1 B:ASP298 3.9 40.8 1.0 CA B:VAL246 4.0 41.4 1.0 CB B:ASP298 4.0 41.2 1.0 CB B:VAL246 4.0 38.8 1.0 O B:ILE300 4.1 40.5 1.0 OD1 B:ASP245 4.1 41.2 1.0 CB B:ASP248 4.5 52.1 1.0 N B:ALA247 4.5 40.9 1.0 C B:ALA247 4.6 50.8 1.0 N B:ASP248 4.7 54.9 1.0 CG1 B:VAL246 4.8 38.7 1.0 CG B:ASP245 4.8 39.8 1.0 CA B:ALA247 4.8 46.0 1.0 O B:ALA247 4.9 49.2 1.0 OD2 B:ASP245 5.0 44.3 1.0

Magnesium binding site 2 out of 3 in the Pseudomonas-Phage E217 Terl Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pseudomonas-Phage E217 Terl Nuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.4 occ:1.00 OD2 A:ASP298 2.0 35.6 1.0 O A:VAL246 2.2 28.7 1.0 OD2 A:ASP248 2.2 46.3 1.0 O A:HOH606 2.3 36.5 1.0 CG A:ASP248 3.1 50.2 1.0 CG A:ASP298 3.2 39.6 1.0 OD1 A:ASP248 3.3 34.9 1.0 C A:VAL246 3.4 35.1 1.0 OD1 A:ASP298 3.8 38.4 1.0 N A:VAL246 4.1 35.4 1.0 CA A:VAL246 4.1 35.7 1.0 O A:ILE300 4.2 38.2 1.0 O A:HOH629 4.2 47.8 1.0 CB A:VAL246 4.2 34.0 1.0 CB A:ASP298 4.3 35.0 1.0 OD1 A:ASP245 4.3 41.4 1.0 CB A:ASP248 4.5 46.4 1.0 N A:ALA247 4.5 33.9 1.0 C A:ALA247 4.5 42.3 1.0 N A:ASP248 4.6 43.9 1.0 CA A:ALA247 4.7 34.4 1.0 O A:ALA247 4.8 37.7 1.0 CG1 A:VAL246 4.9 33.7 1.0 NZ A:LYS425 4.9 48.7 1.0 CG A:ASP245 5.0 41.7 1.0

Magnesium binding site 3 out of 3 in the Pseudomonas-Phage E217 Terl Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pseudomonas-Phage E217 Terl Nuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:21.7 occ:1.00 O A:HOH613 1.9 34.8 1.0 NE2 A:HIS305 2.1 33.6 1.0 O A:HOH622 2.2 35.8 1.0 CE1 A:HIS305 3.0 39.9 1.0 CD2 A:HIS305 3.1 41.3 1.0 OE2 A:GLU274 4.2 45.3 1.0 ND1 A:HIS305 4.2 37.1 1.0 OE1 A:GLU274 4.2 43.6 1.0 CG A:HIS305 4.2 37.7 1.0 CD A:GLU274 4.6 43.5 1.0 O A:GLY301 4.8 37.5 1.0

R.K.Lokareddy, C.D.Hou, S.G.Doll, F.Li, R.E.Gillilan, F.Forti, D.S.Horner, F.Briani, G.Cingolani. Terminase Subunits From the Pseudomonas-Phage E217. J.Mol.Biol. V. 434 67799 2022.
ISSN: ESSN 1089-8638
PubMed: 36007626
DOI: 10.1016/J.JMB.2022.167799