Magnesium in PDB 8gao: Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q

The structure of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q (pdb code 8gao). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q, PDB code: 8gao:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:46.0 occ:1.00 O3B B:AGS501 1.9 58.7 1.0 NE2 B:GLN227 2.1 30.0 1.0 O3G B:AGS501 2.3 72.1 1.0 PG B:AGS501 2.4 73.5 1.0 CD B:GLN227 2.6 30.0 1.0 OE1 B:GLN227 2.7 30.0 1.0 PB B:AGS501 2.9 54.6 1.0 O2G B:AGS501 3.0 64.7 1.0 O3A B:AGS501 3.1 61.4 1.0 O2B B:AGS501 3.1 68.4 1.0 NZ B:LYS203 3.7 64.3 1.0 OG B:SER204 3.8 56.3 1.0 CG B:GLN227 3.8 30.0 1.0 NH2 A:ARG407 4.2 44.9 1.0 O1B B:AGS501 4.2 57.3 1.0 CZ A:ARG407 4.2 44.8 1.0 CB B:SER204 4.3 49.2 1.0 S1G B:AGS501 4.3 67.2 1.0 NE A:ARG407 4.3 41.0 1.0 O2A B:AGS501 4.4 65.3 1.0 PA B:AGS501 4.4 58.5 1.0 NH1 A:ARG407 4.8 48.7 1.0 CE B:LYS203 4.8 58.3 1.0 CB B:GLN227 4.8 30.0 1.0 CD A:ARG407 5.0 41.7 1.0

Magnesium binding site 2 out of 5 in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:71.1 occ:1.00 O3G C:AGS501 1.9 59.5 1.0 O1B C:AGS501 2.3 52.9 1.0 OE1 C:GLN227 2.3 30.0 1.0 PG C:AGS501 3.0 56.0 1.0 OG C:SER204 3.1 48.8 1.0 O2G C:AGS501 3.1 54.8 1.0 CD C:GLN227 3.4 30.0 1.0 PB C:AGS501 3.5 33.1 1.0 O3B C:AGS501 3.7 47.2 1.0 CB C:SER204 4.0 44.3 1.0 NE2 C:GLN227 4.2 30.0 1.0 NH2 B:ARG407 4.2 38.7 1.0 CZ B:ARG407 4.4 42.2 1.0 O3A C:AGS501 4.4 41.0 1.0 OD1 C:ASP311 4.5 68.2 1.0 OD2 C:ASP311 4.5 71.7 1.0 CG C:GLN227 4.5 30.0 1.0 S1G C:AGS501 4.6 65.7 1.0 CB C:GLN227 4.6 30.0 1.0 O2B C:AGS501 4.7 60.1 1.0 NH1 B:ARG407 4.7 44.7 1.0 O1A C:AGS501 4.7 49.9 1.0 N C:SER204 4.8 36.7 1.0 CG C:ASP311 4.8 66.5 1.0 CE C:LYS203 4.9 42.8 1.0 NE B:ARG407 4.9 37.7 1.0 CG C:MET228 5.0 62.5 1.0 PA C:AGS501 5.0 35.8 1.0

Magnesium binding site 3 out of 5 in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:72.8 occ:1.00 O2B D:AGS501 2.5 52.3 1.0 S1G D:AGS501 2.6 73.5 1.0 NE2 D:GLN227 2.7 30.0 1.0 O2G D:AGS501 2.8 57.0 1.0 PG D:AGS501 2.9 76.3 1.0 O3B D:AGS501 3.0 62.1 1.0 PB D:AGS501 3.4 40.7 1.0 CD D:GLN227 3.8 30.0 1.0 OD2 D:ASP311 4.2 65.6 1.0 O1B D:AGS501 4.3 46.7 1.0 OD1 D:ASP311 4.3 64.2 1.0 OE1 D:GLN227 4.4 30.0 1.0 O3G D:AGS501 4.5 53.1 1.0 NH2 C:ARG407 4.5 39.8 1.0 O3A D:AGS501 4.5 45.1 1.0 CB D:SER204 4.5 42.2 1.0 O1A D:AGS501 4.5 52.5 1.0 O2A D:AGS501 4.6 49.6 1.0 CG D:GLN227 4.7 30.0 1.0 CG D:ASP311 4.7 62.3 1.0 PA D:AGS501 4.8 30.9 1.0 CZ C:ARG407 4.9 40.3 1.0 N D:SER204 4.9 42.5 1.0 NE C:ARG407 5.0 35.2 1.0

Magnesium binding site 4 out of 5 in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:54.5 occ:1.00 O3G E:AGS501 2.0 50.9 1.0 O1B E:AGS501 2.1 51.8 1.0 NE2 E:GLN227 2.7 30.0 1.0 PB E:AGS501 3.2 56.6 1.0 PG E:AGS501 3.3 63.6 1.0 OG E:SER204 3.3 54.1 1.0 O3B E:AGS501 3.5 53.0 1.0 CD E:GLN227 3.8 30.0 1.0 O3A E:AGS501 4.0 50.8 1.0 NH2 D:ARG407 4.1 48.1 1.0 CB E:SER204 4.2 43.8 1.0 S1G E:AGS501 4.3 64.8 1.0 OE1 E:GLN227 4.3 30.0 1.0 O2G E:AGS501 4.4 54.2 1.0 O2B E:AGS501 4.5 58.2 1.0 CB E:GLN227 4.7 30.0 1.0 OD1 E:ASP311 4.7 82.2 1.0 CZ D:ARG407 4.8 41.9 1.0 CG E:GLN227 4.8 30.0 1.0 O1A E:AGS501 4.9 52.9 1.0 OD2 E:ASP311 5.0 80.0 1.0 N E:SER204 5.0 33.1 1.0

Magnesium binding site 5 out of 5 in the Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacteriophage T4 Stalled Primosome with Mutant GP41-E227Q within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:60.9 occ:1.00 O2A F:AGS501 1.9 66.7 1.0 O3G F:AGS501 1.9 69.2 1.0 O2B F:AGS501 2.1 56.7 1.0 O3B F:AGS501 2.7 69.4 1.0 PG F:AGS501 2.7 76.0 1.0 PB F:AGS501 2.8 59.2 1.0 NE2 F:GLN227 2.9 30.0 1.0 PA F:AGS501 3.0 48.6 1.0 O3A F:AGS501 3.4 62.2 1.0 O2G F:AGS501 3.4 69.7 1.0 OG F:SER204 3.5 54.9 1.0 O1A F:AGS501 3.5 61.0 1.0 CB F:SER204 3.8 55.6 1.0 CD F:GLN227 3.8 30.0 1.0 O1B F:AGS501 4.2 62.9 1.0 OE1 F:GLN227 4.3 30.0 1.0 O5' F:AGS501 4.4 64.9 1.0 S1G F:AGS501 4.5 80.3 1.0 NH2 E:ARG407 4.5 56.8 1.0 NH2 F:ARG236 4.5 57.2 1.0 N F:SER204 4.6 58.0 1.0 CG F:GLN227 4.8 30.0 1.0 NE E:ARG407 4.8 51.0 1.0 CZ E:ARG407 4.8 57.1 1.0 CA F:SER204 4.9 52.0 1.0 SD F:MET228 4.9 78.3 1.0 CE F:MET228 4.9 63.9 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