Magnesium in PDB 8g0z: Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome

The binding sites of Magnesium atom in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome (pdb code 8g0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome, PDB code: 8g0z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.0 occ:1.00 O3B B:AGS501 2.3 58.7 1.0 O3G B:AGS501 2.6 72.1 1.0 OE1 B:GLN227 2.7 30.0 1.0 PG B:AGS501 2.7 73.5 1.0 CD B:GLN227 3.0 30.0 1.0 O2G B:AGS501 3.1 64.7 1.0 NE2 B:GLN227 3.2 30.0 1.0 PB B:AGS501 3.4 54.6 1.0 O3A B:AGS501 3.5 61.4 1.0 O2B B:AGS501 3.8 68.4 1.0 OG B:SER204 3.8 56.3 1.0 NZ B:LYS203 4.1 64.3 1.0 CG B:GLN227 4.1 30.0 1.0 CZ A:ARG407 4.5 44.8 1.0 NE A:ARG407 4.6 41.0 1.0 S1G B:AGS501 4.6 67.2 1.0 NH1 A:ARG407 4.6 48.7 1.0 O1B B:AGS501 4.6 57.3 1.0 CB B:SER204 4.6 49.2 1.0 CG B:MET228 4.7 66.4 1.0 O2A B:AGS501 4.7 65.3 1.0 CB B:GLN227 4.8 30.0 1.0 PA B:AGS501 4.8 58.5 1.0 SD B:MET228 4.8 89.2 1.0 CD A:ARG407 4.9 41.7 1.0 NH2 A:ARG407 5.0 44.9 1.0

Magnesium binding site 2 out of 5 in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.1 occ:1.00 O3G C:AGS501 2.2 59.5 1.0 O1B C:AGS501 3.7 52.9 1.0 OG C:SER204 3.7 48.8 1.0 PG C:AGS501 3.7 56.0 1.0 OD2 C:ASP311 3.9 71.7 1.0 OD1 C:ASP311 4.1 68.2 1.0 CG C:MET228 4.1 62.5 1.0 OE1 C:GLN227 4.2 30.0 1.0 CG C:ASP311 4.2 66.5 1.0 O3B C:AGS501 4.4 47.2 1.0 SD C:MET228 4.4 80.2 1.0 O2G C:AGS501 4.4 54.8 1.0 NH2 B:ARG407 4.7 38.7 1.0 PB C:AGS501 4.7 33.1 1.0 CB C:TYR312 4.8 60.4 1.0 S1G C:AGS501 4.9 65.7 1.0 CD C:GLN227 4.9 30.0 1.0

Magnesium binding site 3 out of 5 in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome 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 OE1 D:GLN227 3.0 30.0 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 CD D:GLN227 4.0 30.0 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 NE2 D:GLN227 4.6 30.0 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 CG D:GLN227 5.0 30.0 1.0 N D:SER204 5.0 42.5 1.0

Magnesium binding site 4 out of 5 in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:54.5 occ:1.00 O1B E:AGS501 2.4 51.8 1.0 O3G E:AGS501 2.6 50.9 1.0 OE1 E:GLN227 3.3 30.0 1.0 PB E:AGS501 3.3 56.6 1.0 O3B E:AGS501 3.4 53.0 1.0 PG E:AGS501 3.7 63.6 1.0 OG E:SER204 3.8 54.1 1.0 O2B E:AGS501 4.1 58.2 1.0 NH2 D:ARG407 4.2 48.1 1.0 CD E:GLN227 4.5 30.0 1.0 OD1 E:ASP311 4.5 82.2 1.0 O2G E:AGS501 4.6 54.2 1.0 O3A E:AGS501 4.7 50.8 1.0 OD2 E:ASP311 4.8 80.0 1.0 CB E:GLN227 4.9 30.0 1.0 CG E:ASP311 4.9 81.7 1.0 CB E:SER204 5.0 43.8 1.0 CE E:LYS203 5.0 46.2 1.0

Magnesium binding site 5 out of 5 in the Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mutant Bacteriophage T4 GP41 Helicase Hexamer Bound with Single Strand Dna and Atpgammas in the Stalled Primosome within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:60.9 occ:1.00 O3G F:AGS501 1.8 69.2 1.0 O2B F:AGS501 2.2 56.7 1.0 NE2 F:GLN227 2.3 30.0 1.0 CD F:GLN227 2.8 30.0 1.0 OG F:SER204 3.1 54.9 1.0 PG F:AGS501 3.3 76.0 1.0 PB F:AGS501 3.4 59.2 1.0 OE1 F:GLN227 3.5 30.0 1.0 CG F:GLN227 3.6 30.0 1.0 O3B F:AGS501 3.6 69.4 1.0 O2A F:AGS501 4.1 66.7 1.0 OD2 F:ASP311 4.1 73.3 1.0 O1B F:AGS501 4.1 62.9 1.0 O2G F:AGS501 4.2 69.7 1.0 OD1 F:ASP311 4.2 66.7 1.0 CB F:SER204 4.3 55.6 1.0 S1G F:AGS501 4.5 80.3 1.0 CG F:ASP311 4.5 69.5 1.0 O3A F:AGS501 4.6 62.2 1.0 SD F:MET228 4.7 78.3 1.0 CB F:GLN227 4.8 30.0 1.0 N F:SER204 4.8 58.0 1.0 CE F:LYS203 4.8 56.1 1.0 PA F:AGS501 4.9 48.6 1.0 CG F:MET228 4.9 72.0 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