Magnesium in PDB 5oeb: Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3)

The structure of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3), PDB code: 5oeb was solved by R.G.Xu, H.T.Jenkins, S.J.Greive, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	100.878, 102.859, 103.029, 91.13, 117.16, 119.17
R / Rfree (%)	23.7 / 27.8

The binding sites of Magnesium atom in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3) (pdb code 5oeb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3), PDB code: 5oeb:

Magnesium binding site 1 out of 1 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Adp (Crystal Form 3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:78.2 occ:1.00 OG1 B:THR48 2.2 71.5 1.0 O B:HOH609 2.2 78.7 1.0 O B:HOH602 2.2 76.0 1.0 O B:HOH606 2.2 73.7 1.0 O1B B:ADP501 2.2 84.0 1.0 O B:HOH611 2.2 77.8 1.0 PB B:ADP501 3.3 86.2 1.0 O2B B:ADP501 3.5 89.8 1.0 CB B:THR48 3.5 67.9 1.0 O3A B:ADP501 3.9 88.7 1.0 CG2 B:THR48 4.0 64.8 1.0 ND2 B:ASN169 4.0 59.6 1.0 OD1 B:ASP142 4.1 68.8 1.0 NZ B:LYS47 4.3 64.6 1.0 ND2 B:ASN171 4.3 58.5 1.0 CA B:THR48 4.6 68.8 1.0 O3B B:ADP501 4.6 85.7 1.0 N B:THR48 4.7 68.8 1.0 CG B:ASN169 4.9 60.1 1.0 O B:HOH615 4.9 38.2 1.0 OD1 B:ASN169 5.0 64.6 1.0

R.G.Xu, H.T.Jenkins, A.A.Antson, S.J.Greive. Structure of the Large Terminase From A Hyperthermophilic Virus Reveals A Unique Mechanism For Oligomerization and Atp Hydrolysis. Nucleic Acids Res. V. 45 13029 2017.
ISSN: ESSN 1362-4962
PubMed: 29069443
DOI: 10.1093/NAR/GKX947