Magnesium in PDB 8duo: Dna-Free T4 Bacteriophage GP41 Hexamer

The binding sites of Magnesium atom in the Dna-Free T4 Bacteriophage GP41 Hexamer (pdb code 8duo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Dna-Free T4 Bacteriophage GP41 Hexamer, PDB code: 8duo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Dna-Free T4 Bacteriophage GP41 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna-Free T4 Bacteriophage GP41 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.0 occ:1.00 O2A B:AGS501 2.2 70.8 1.0 OE2 B:GLU227 2.4 69.9 1.0 OG B:SER204 2.7 59.4 1.0 CB B:SER204 3.0 56.6 1.0 O3B B:AGS501 3.2 60.8 1.0 CD B:GLU227 3.2 70.4 1.0 O2G B:AGS501 3.3 78.9 1.0 PA B:AGS501 3.4 67.4 1.0 OE1 B:GLU227 3.6 67.2 1.0 PG B:AGS501 3.7 75.1 1.0 SD B:MET228 3.9 79.8 1.0 O1A B:AGS501 4.0 74.9 1.0 O3A B:AGS501 4.0 61.4 1.0 S1G B:AGS501 4.1 70.6 1.0 CE B:MET228 4.1 65.3 1.0 PB B:AGS501 4.3 60.2 1.0 CG B:GLU227 4.3 67.2 1.0 NE A:ARG407 4.5 64.7 1.0 CA B:SER204 4.5 55.6 1.0 NH2 A:ARG407 4.6 64.3 1.0 O1B B:AGS501 4.7 73.7 1.0 O5' B:AGS501 4.7 66.5 1.0 CZ A:ARG407 4.8 63.1 1.0 NH2 B:ARG236 4.9 61.0 1.0 N B:SER204 4.9 57.8 1.0 CG B:MET228 4.9 64.1 1.0

Magnesium binding site 2 out of 5 in the Dna-Free T4 Bacteriophage GP41 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna-Free T4 Bacteriophage GP41 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:60.3 occ:1.00 OE1 C:GLU227 2.5 65.2 1.0 O2G C:AGS501 2.8 58.0 1.0 OE2 C:GLU227 2.9 63.6 1.0 O1A C:AGS501 2.9 66.6 1.0 CD C:GLU227 3.0 63.9 1.0 O3A C:AGS501 3.1 54.0 1.0 PA C:AGS501 3.2 49.9 1.0 NH1 C:ARG236 3.3 59.5 1.0 O2A C:AGS501 3.3 50.8 1.0 O3G C:AGS501 3.4 57.4 1.0 O1B C:AGS501 3.5 47.9 1.0 PG C:AGS501 3.6 55.9 1.0 CB C:SER204 3.8 46.7 1.0 PB C:AGS501 3.8 38.5 1.0 OG C:SER204 3.9 45.2 1.0 O3B C:AGS501 4.1 51.3 1.0 ND2 C:ASN200 4.2 50.0 1.0 CZ C:ARG236 4.3 56.3 1.0 CG C:MET228 4.3 56.8 1.0 NH2 C:ARG236 4.3 48.5 1.0 SD C:MET228 4.3 74.7 1.0 CG C:GLU227 4.5 59.9 1.0 O5' C:AGS501 4.8 47.1 1.0 CA C:SER204 5.0 35.1 1.0

Magnesium binding site 3 out of 5 in the Dna-Free T4 Bacteriophage GP41 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna-Free T4 Bacteriophage GP41 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:49.7 occ:1.00 O2B D:AGS501 2.4 29.5 1.0 CB D:SER204 2.9 35.1 1.0 OD2 D:ASP311 3.1 50.4 1.0 CE D:MET228 3.1 51.8 1.0 S1G D:AGS501 3.1 56.9 1.0 N D:SER204 3.4 22.8 1.0 CA D:SER204 3.5 24.3 1.0 PB D:AGS501 3.6 18.3 1.0 OG D:SER204 3.8 41.1 1.0 O3B D:AGS501 3.9 23.7 1.0 CG D:ASP311 3.9 52.6 1.0 OD1 D:ASP311 3.9 56.9 1.0 CG D:MET228 4.0 53.1 1.0 CB D:LYS203 4.2 29.5 1.0 PG D:AGS501 4.2 41.6 1.0 O3A D:AGS501 4.2 19.8 1.0 CD1 D:LEU207 4.4 37.9 1.0 SD D:MET228 4.4 70.5 1.0 C D:LYS203 4.4 21.5 1.0 OE1 D:GLU227 4.8 58.5 1.0 O1B D:AGS501 4.9 19.7 1.0 CA D:LYS203 5.0 17.4 1.0 C D:SER204 5.0 26.4 1.0

Magnesium binding site 4 out of 5 in the Dna-Free T4 Bacteriophage GP41 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna-Free T4 Bacteriophage GP41 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:20.8 occ:1.00 O1B E:AGS501 1.8 41.4 1.0 OE1 E:GLU227 1.9 47.5 1.0 OE2 E:GLU227 2.1 50.4 1.0 CD E:GLU227 2.2 46.8 1.0 OG E:SER204 2.4 50.8 1.0 PB E:AGS501 2.8 49.9 1.0 O2B E:AGS501 3.1 51.0 1.0 O2A E:AGS501 3.6 51.6 1.0 CG E:GLU227 3.7 38.9 1.0 CB E:SER204 3.8 47.8 1.0 O2G E:AGS501 3.9 38.7 1.0 O3A E:AGS501 3.9 40.6 1.0 O3B E:AGS501 4.0 36.4 1.0 PA E:AGS501 4.4 43.8 1.0 CB E:GLU227 4.4 39.0 1.0 PG E:AGS501 4.7 24.0 1.0 N E:SER204 4.7 37.6 1.0 CA E:SER204 4.7 34.2 1.0 CE E:LYS203 4.8 43.6 1.0 O5' E:AGS501 4.9 44.0 1.0

Magnesium binding site 5 out of 5 in the Dna-Free T4 Bacteriophage GP41 Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dna-Free T4 Bacteriophage GP41 Hexamer within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:25.9 occ:1.00 OH F:TYR312 1.9 61.5 1.0 OG F:SER204 2.0 55.0 1.0 O3A F:AGS501 2.0 21.6 1.0 O2B F:AGS501 2.1 59.3 1.0 O2G F:AGS501 2.2 47.1 1.0 PB F:AGS501 2.3 42.6 1.0 O2A F:AGS501 2.5 58.5 1.0 O3B F:AGS501 2.7 49.6 1.0 PA F:AGS501 2.8 23.9 1.0 PG F:AGS501 2.9 49.8 1.0 CB F:SER204 3.0 46.6 1.0 CZ F:TYR312 3.2 62.1 1.0 N F:SER204 3.3 48.8 1.0 CE F:MET228 3.4 44.8 1.0 O3G F:AGS501 3.6 40.6 1.0 CA F:SER204 3.8 40.1 1.0 O1B F:AGS501 3.8 63.9 1.0 O1A F:AGS501 3.9 44.9 1.0 CE2 F:TYR312 3.9 61.1 1.0 O5' F:AGS501 3.9 43.3 1.0 CE1 F:TYR312 4.2 55.1 1.0 C F:LYS203 4.5 40.7 1.0 CB F:LYS203 4.5 38.0 1.0 S1G F:AGS501 4.6 59.3 1.0 N F:LYS203 4.6 27.1 1.0 CG F:LYS203 4.7 42.8 1.0 CD F:LYS203 4.7 43.6 1.0 CA F:LYS203 4.8 37.1 1.0 C5' F:AGS501 4.8 56.6 1.0 SD F:MET228 4.9 43.0 1.0 OD2 F:ASP311 4.9 64.3 1.0 C F:SER204 5.0 40.9 1.0

X.Feng, M.M.Spiering, R.De Luna Almeida Santos, S.J.Benkovic, H.Li. Structural Basis of the T4 Bacteriophage Primosome Assembly and Primer Synthesis. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205424
DOI: 10.1101/2023.05.03.539249