Magnesium in PDB 5oea: Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3)

The structure of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3), PDB code: 5oea 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)	45.90 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	101.476, 102.981, 103.044, 90.98, 119.37, 117.18
R / Rfree (%)	19 / 25.3

The binding sites of Magnesium atom in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3) (pdb code 5oea). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3), PDB code: 5oea:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (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 Atp-Gamma-S (Crystal Form 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:88.5 occ:1.00 O2G A:AGS501 2.1 0.1 1.0 OG1 A:THR48 2.1 82.4 1.0 O A:HOH604 2.1 97.2 1.0 O A:HOH602 2.1 86.7 1.0 O A:HOH606 2.1 72.7 1.0 O1B A:AGS501 2.1 0.6 1.0 CB A:THR48 3.2 78.3 1.0 PG A:AGS501 3.4 0.9 1.0 PB A:AGS501 3.4 0.9 1.0 O3B A:AGS501 3.6 0.6 1.0 OD1 A:ASP142 3.9 71.2 1.0 O3G A:AGS501 3.9 0.1 1.0 CG2 A:THR48 4.0 77.0 1.0 ND2 A:ASN169 4.0 62.5 1.0 CA A:THR48 4.3 77.6 1.0 N A:THR48 4.4 77.1 1.0 O3A A:AGS501 4.4 0.7 1.0 O2B A:AGS501 4.4 0.5 1.0 OD2 A:ASP142 4.6 71.5 1.0 NZ A:LYS47 4.6 76.9 1.0 O2A A:AGS501 4.6 0.7 1.0 CG A:ASP142 4.6 70.1 1.0 PA A:AGS501 4.9 0.9 1.0 S1G A:AGS501 5.0 0.6 1.0 O1A A:AGS501 5.0 0.5 1.0

Magnesium binding site 2 out of 4 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:64.0 occ:1.00 O2G B:AGS501 2.1 65.6 1.0 O B:HOH601 2.1 65.5 1.0 O B:HOH604 2.1 70.6 1.0 OG1 B:THR48 2.1 67.0 1.0 O B:HOH603 2.1 67.5 1.0 O2B B:AGS501 2.2 61.4 1.0 CB B:THR48 3.2 66.5 1.0 PG B:AGS501 3.4 69.8 1.0 PB B:AGS501 3.5 61.8 1.0 OD1 B:ASP142 3.8 66.3 1.0 O3B B:AGS501 3.8 66.8 1.0 O3G B:AGS501 3.8 67.2 1.0 CG2 B:THR48 4.0 65.8 1.0 OD1 B:ASN169 4.1 70.6 1.0 O3A B:AGS501 4.2 64.1 1.0 OD2 B:ASP142 4.3 67.8 1.0 N B:THR48 4.3 69.7 1.0 CA B:THR48 4.3 67.9 1.0 CG B:ASP142 4.4 68.2 1.0 O1A B:AGS501 4.5 66.5 1.0 O2A B:AGS501 4.6 65.2 1.0 O1B B:AGS501 4.7 63.5 1.0 PA B:AGS501 4.7 65.9 1.0 S1G B:AGS501 5.0 62.3 1.0

Magnesium binding site 3 out of 4 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:0.2 occ:1.00 O2G D:AGS501 2.1 0.5 1.0 O D:HOH605 2.1 95.3 1.0 O D:HOH601 2.1 99.9 1.0 OG1 D:THR48 2.1 98.0 1.0 O D:HOH603 2.1 93.0 1.0 O2B D:AGS501 2.2 0.4 1.0 CB D:THR48 3.2 93.0 1.0 PB D:AGS501 3.4 0.8 1.0 PG D:AGS501 3.4 0.1 1.0 OD1 D:ASP142 3.5 0.3 1.0 CG2 D:THR48 3.5 95.5 1.0 O3B D:AGS501 3.7 0.6 1.0 O3A D:AGS501 3.8 0.5 1.0 OD1 D:ASN169 4.1 84.8 1.0 O3G D:AGS501 4.1 0.3 1.0 O D:HOH607 4.3 68.9 1.0 OD2 D:ASP142 4.3 99.5 1.0 CG D:ASP142 4.3 96.5 1.0 CA D:THR48 4.5 89.3 1.0 O1B D:AGS501 4.7 0.5 1.0 NZ D:LYS47 4.7 91.0 1.0 CG D:GLU143 4.8 93.4 1.0 N D:THR48 4.9 88.4 1.0 S1G D:AGS501 4.9 0.8 1.0 CB D:ASN81 5.0 89.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E in Complex with Atp-Gamma-S (Crystal Form 3) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:79.8 occ:1.00 O E:HOH603 2.1 77.9 1.0 OG1 E:THR48 2.1 81.7 1.0 O2G E:AGS501 2.1 78.4 1.0 O E:HOH606 2.1 80.4 1.0 O E:HOH602 2.1 77.7 1.0 O1B E:AGS501 2.2 84.3 1.0 PG E:AGS501 3.2 77.0 1.0 CB E:THR48 3.3 82.6 1.0 PB E:AGS501 3.3 83.8 1.0 O3B E:AGS501 3.3 82.4 1.0 O1A E:AGS501 3.6 88.0 1.0 O3G E:AGS501 3.7 77.7 1.0 OD1 E:ASP142 3.8 87.3 1.0 CG2 E:THR48 4.1 81.8 1.0 ND2 E:ASN169 4.3 89.3 1.0 O3A E:AGS501 4.3 86.6 1.0 CA E:THR48 4.4 83.3 1.0 N E:THR48 4.4 83.1 1.0 OD2 E:ASP142 4.4 91.4 1.0 O2B E:AGS501 4.4 86.6 1.0 CG E:ASP142 4.5 85.8 1.0 PA E:AGS501 4.6 91.2 1.0 OD1 E:ASN169 4.9 0.0 1.0 S1G E:AGS501 4.9 76.9 1.0 NZ E:LYS47 5.0 81.0 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