Magnesium in PDB 8dw6: T4 Bacteriophage Primosome with Single-Strand Dna, State 3

The structure of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3 (pdb code 8dw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3, PDB code: 8dw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 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 CE B:LYS203 4.7 58.3 1.0 O B:LYS203 4.7 65.2 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 T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.1 occ:1.00 O1B C:AGS501 1.9 52.9 1.0 OE2 C:GLU227 2.0 68.2 1.0 OG C:SER204 2.5 48.8 1.0 O3G C:AGS501 2.8 59.5 1.0 CD C:GLU227 3.0 68.1 1.0 PB C:AGS501 3.2 33.1 1.0 OE1 C:GLU227 3.6 69.3 1.0 CB C:SER204 3.6 44.3 1.0 O3B C:AGS501 3.7 47.2 1.0 PG C:AGS501 3.9 56.0 1.0 O1A C:AGS501 4.1 49.9 1.0 O3A C:AGS501 4.1 41.0 1.0 OD2 C:ASP311 4.1 71.7 1.0 OD1 C:ASP311 4.2 68.2 1.0 CG C:GLU227 4.2 64.3 1.0 O2B C:AGS501 4.3 60.1 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 N C:SER204 4.6 36.7 1.0 NH2 B:ARG407 4.6 38.7 1.0 CA C:SER204 4.7 33.8 1.0 PA C:AGS501 4.7 35.8 1.0 CG C:MET228 4.7 62.5 1.0 O2G C:AGS501 4.7 54.8 1.0 CZ B:ARG407 4.8 42.2 1.0

Magnesium binding site 3 out of 5 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 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 T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 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 T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 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