Magnesium in PDB 8dtp: Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna

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

Magnesium binding site 1 out of 5 in the Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.0 occ:1.00 O3B B:AGS501 2.0 58.7 1.0 OE2 B:GLU227 2.0 64.5 1.0 O3A B:AGS501 2.5 61.4 1.0 PB B:AGS501 2.7 54.6 1.0 OG B:SER204 2.8 56.3 1.0 CD B:GLU227 3.0 64.7 1.0 PG B:AGS501 3.1 73.5 1.0 OE1 B:GLU227 3.4 66.0 1.0 O3G B:AGS501 3.4 72.1 1.0 CB B:SER204 3.5 49.2 1.0 O2B B:AGS501 3.6 68.4 1.0 O2G B:AGS501 3.7 64.7 1.0 NZ B:LYS203 3.7 64.3 1.0 PA B:AGS501 3.9 58.5 1.0 O1B B:AGS501 3.9 57.3 1.0 O2A B:AGS501 4.1 65.3 1.0 CG B:GLU227 4.3 59.1 1.0 O B:GLY202 4.4 74.2 1.0 N B:SER204 4.5 48.0 1.0 O1A B:AGS501 4.6 66.6 1.0 CA B:SER204 4.6 43.1 1.0 C B:LYS203 4.7 56.7 1.0 O B:LYS203 4.7 65.2 1.0 CE B:LYS203 4.7 58.3 1.0 OD1 B:ASP311 4.7 66.8 1.0 S1G B:AGS501 4.8 67.2 1.0 O5' B:AGS501 5.0 52.4 1.0 OD2 B:ASP311 5.0 70.1 1.0

Magnesium binding site 2 out of 5 in the Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.1 occ:1.00 OE2 C:GLU227 2.0 68.2 1.0 O1B C:AGS501 2.1 52.9 1.0 O3G C:AGS501 2.4 59.5 1.0 OG C:SER204 2.6 48.8 1.0 CD C:GLU227 3.0 68.1 1.0 PB C:AGS501 3.5 33.1 1.0 OE1 C:GLU227 3.6 69.3 1.0 CB C:SER204 3.6 44.3 1.0 PG C:AGS501 3.7 56.0 1.0 O3B C:AGS501 4.0 47.2 1.0 O1A C:AGS501 4.0 49.9 1.0 OD2 C:ASP311 4.1 71.7 1.0 O3A C:AGS501 4.2 41.0 1.0 CG C:GLU227 4.2 64.3 1.0 OD1 C:ASP311 4.2 68.2 1.0 O2G C:AGS501 4.2 54.8 1.0 PA C:AGS501 4.5 35.8 1.0 CG C:ASP311 4.5 66.5 1.0 SD C:MET228 4.5 80.2 1.0 CE C:MET228 4.6 65.5 1.0 O2B C:AGS501 4.6 60.1 1.0 NH2 B:ARG407 4.6 38.7 1.0 N C:SER204 4.7 36.7 1.0 CG C:MET228 4.7 62.5 1.0 CA C:SER204 4.7 33.8 1.0 O2A C:AGS501 4.8 53.8 1.0 CZ B:ARG407 4.8 42.2 1.0

Magnesium binding site 3 out of 5 in the Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:72.8 occ:1.00 O2B D:AGS501 2.2 52.3 1.0 S1G D:AGS501 2.5 73.5 1.0 O2G D:AGS501 2.8 57.0 1.0 PG D:AGS501 2.9 76.3 1.0 O3B D:AGS501 3.1 62.1 1.0 PB D:AGS501 3.2 40.7 1.0 CB D:SER204 3.7 42.2 1.0 O1B D:AGS501 4.0 46.7 1.0 O2A D:AGS501 4.1 49.6 1.0 OD2 D:ASP311 4.2 65.6 1.0 OG D:SER204 4.3 47.3 1.0 OD1 D:ASP311 4.4 64.2 1.0 O3A D:AGS501 4.4 45.1 1.0 O3G D:AGS501 4.4 53.1 1.0 OE1 D:GLU227 4.5 67.0 1.0 NZ D:LYS203 4.6 49.7 1.0 PA D:AGS501 4.7 30.9 1.0 CG D:ASP311 4.7 62.3 1.0 NH2 C:ARG407 4.7 39.8 1.0 O1A D:AGS501 4.7 52.5 1.0 CA D:SER204 4.9 36.6 1.0 O D:GLY202 5.0 59.6 1.0 N D:SER204 5.0 42.5 1.0

Magnesium binding site 4 out of 5 in the Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:54.5 occ:1.00 O2G E:AGS501 2.0 54.2 1.0 O2B E:AGS501 2.0 58.2 1.0 PB E:AGS501 3.2 56.6 1.0 PG E:AGS501 3.4 63.6 1.0 O1B E:AGS501 3.6 51.8 1.0 N E:ASN200 3.7 49.9 1.0 O3B E:AGS501 3.7 53.0 1.0 NZ E:LYS203 3.8 53.8 1.0 NH2 D:ARG407 3.8 48.1 1.0 NE2 E:GLN355 4.1 58.0 1.0 NZ D:LYS405 4.2 37.9 1.0 CG1 E:VAL199 4.2 51.3 1.0 O3G E:AGS501 4.4 50.9 1.0 CA E:VAL199 4.4 45.5 1.0 O D:ALA379 4.4 53.3 1.0 CA E:ASN200 4.5 46.5 1.0 O3A E:AGS501 4.5 50.8 1.0 C E:VAL199 4.5 50.0 1.0 S1G E:AGS501 4.6 64.8 1.0 CE D:LYS405 4.6 41.2 1.0 CA D:ALA379 4.7 43.9 1.0 CB E:VAL199 4.7 47.4 1.0 CE E:LYS203 4.7 46.2 1.0 CG2 E:VAL199 5.0 49.1 1.0 O1A E:AGS501 5.0 52.9 1.0

Magnesium binding site 5 out of 5 in the Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Close State of T4 Bacteriophage GP41 Hexamer Bound with Single Strand Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:60.9 occ:1.00 O2B F:AGS501 2.0 56.7 1.0 OG F:SER204 2.2 54.9 1.0 O3G F:AGS501 2.6 69.2 1.0 CB F:SER204 3.4 55.6 1.0 PB F:AGS501 3.5 59.2 1.0 OE1 F:GLU227 3.6 79.2 1.0 O2A F:AGS501 3.7 66.7 1.0 OD2 F:ASP311 3.8 73.3 1.0 OD1 F:ASP311 3.8 66.7 1.0 PG F:AGS501 3.8 76.0 1.0 O3B F:AGS501 3.9 69.4 1.0 CG F:ASP311 4.2 69.5 1.0 N F:SER204 4.2 58.0 1.0 O1B F:AGS501 4.3 62.9 1.0 O3A F:AGS501 4.4 62.2 1.0 CA F:SER204 4.4 52.0 1.0 CD F:GLU227 4.4 79.3 1.0 PA F:AGS501 4.4 48.6 1.0 SD F:MET228 4.6 78.3 1.0 O1A F:AGS501 4.6 61.0 1.0 CE F:MET228 4.6 63.9 1.0 CG F:MET228 4.8 72.0 1.0 O2G F:AGS501 4.8 69.7 1.0 OE2 F:GLU227 4.9 78.9 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