Magnesium in PDB 8btg: Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System

The binding sites of Magnesium atom in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System (pdb code 8btg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System, PDB code: 8btg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:61.2 occ:1.00 OD1 A:ASP215 2.0 20.0 1.0 O2G A:ATP501 2.3 67.9 1.0 O1G A:ATP501 2.4 67.9 1.0 OD2 A:ASP215 2.4 20.0 1.0 CG A:ASP215 2.5 20.0 1.0 PG A:ATP501 2.6 67.9 1.0 OD1 A:ASP214 3.0 15.3 1.0 O3G A:ATP501 3.4 67.9 1.0 O2B A:ATP501 3.9 67.9 1.0 CB A:ASP215 3.9 20.0 1.0 O3B A:ATP501 4.1 67.9 1.0 CG A:ASP214 4.2 15.3 1.0 OD1 A:ASP248 4.4 30.9 1.0 CA A:ASP215 4.5 20.0 1.0 N A:ASP215 4.6 20.0 1.0 PB A:ATP501 4.6 67.9 1.0 NE2 A:GLN217 4.7 20.7 1.0 OG A:SER246 4.7 18.1 1.0 OD2 A:ASP248 4.8 30.9 1.0 OD2 A:ASP214 4.8 15.3 1.0 OG1 A:THR158 4.8 28.0 1.0 NZ A:LYS157 4.9 28.3 1.0

Magnesium binding site 2 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:33.1 occ:1.00 OD1 B:ASP214 2.5 17.4 1.0 O1G B:ATP501 2.6 12.1 1.0 OG B:SER246 3.2 17.3 1.0 CE B:LYS157 3.3 9.6 1.0 CG B:ASP214 3.5 17.4 1.0 NZ B:LYS157 3.7 9.6 1.0 CB B:SER246 3.9 17.3 1.0 N B:ASP215 3.9 13.6 1.0 PG B:ATP501 4.0 12.1 1.0 OD2 B:ASP214 4.0 17.4 1.0 OG1 B:THR158 4.2 9.9 1.0 CB B:LYS157 4.2 9.6 1.0 CB B:ASP215 4.2 13.6 1.0 CA B:ASP215 4.2 13.6 1.0 CG B:ASP215 4.5 13.6 1.0 CD B:LYS157 4.5 9.6 1.0 OD1 B:ASP215 4.6 13.6 1.0 CB B:ASP214 4.6 17.4 1.0 N B:SER247 4.6 10.3 1.0 O3G B:ATP501 4.6 12.1 1.0 C B:SER246 4.7 17.3 1.0 O2G B:ATP501 4.7 12.1 1.0 C B:ASP214 4.7 17.4 1.0 O2B B:ATP501 4.7 12.1 1.0 CA B:ASP214 4.8 17.4 1.0 O B:SER247 4.9 10.3 1.0 CG B:LYS157 4.9 9.6 1.0 CA B:SER246 4.9 17.3 1.0 N B:THR158 5.0 9.9 1.0

Magnesium binding site 3 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:49.1 occ:1.00 O2G C:ATP501 2.0 17.2 1.0 O1G C:ATP501 2.6 17.2 1.0 PG C:ATP501 2.7 17.2 1.0 OD1 C:ASP214 3.1 12.1 1.0 CE C:LYS157 3.5 12.9 1.0 O3B C:ATP501 3.8 17.2 1.0 OG C:SER246 3.8 14.5 1.0 CG C:ASP214 3.9 12.1 1.0 CB C:ASP215 4.0 15.0 1.0 O3G C:ATP501 4.0 17.2 1.0 OD2 C:ASP214 4.0 12.1 1.0 N C:ASP215 4.2 15.0 1.0 NZ C:LYS157 4.2 12.9 1.0 CA C:ASP215 4.3 15.0 1.0 OG1 C:THR158 4.3 12.5 1.0 CD C:LYS157 4.6 12.9 1.0 O2B C:ATP501 4.7 17.2 1.0 CB C:LYS157 4.7 12.9 1.0 CB C:SER246 4.7 14.5 1.0 PB C:ATP501 4.8 17.2 1.0

Magnesium binding site 4 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg500 b:53.4 occ:1.00 O1G D:ATP501 2.2 13.3 1.0 O3G D:ATP501 2.2 13.3 1.0 OD1 D:ASP215 2.2 15.9 1.0 PG D:ATP501 2.6 13.3 1.0 OD1 D:ASP214 2.6 17.9 1.0 CG D:ASP215 2.8 15.9 1.0 OD2 D:ASP215 3.1 15.9 1.0 OG D:SER246 3.3 21.8 1.0 CE D:LYS157 3.6 12.2 1.0 CG D:ASP214 3.7 17.9 1.0 O3B D:ATP501 3.8 13.3 1.0 O2G D:ATP501 3.8 13.3 1.0 NZ D:LYS157 3.9 12.2 1.0 N D:ASP215 4.0 15.9 1.0 CB D:ASP215 4.1 15.9 1.0 CB D:SER246 4.1 21.8 1.0 CA D:ASP215 4.3 15.9 1.0 OD2 D:ASP214 4.3 17.9 1.0 OG1 D:THR158 4.3 11.5 1.0 CB D:LYS157 4.6 12.2 1.0 CB D:ASP214 4.7 17.9 1.0 CD D:LYS157 4.7 12.2 1.0 C D:ASP214 4.8 17.9 1.0 CA D:ASP214 4.9 17.9 1.0 N D:SER247 4.9 18.7 1.0

Magnesium binding site 5 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:33.1 occ:1.00 O2G E:ATP502 2.8 14.8 1.0 O1A E:ATP502 2.9 14.8 1.0 NH2 E:ARG313 3.3 11.7 1.0 NH2 D:ARG264 3.9 15.2 1.0 PA E:ATP502 4.1 14.8 1.0 PG E:ATP502 4.1 14.8 1.0 OH E:TYR115 4.4 17.3 1.0 CZ E:ARG313 4.4 11.7 1.0 O3A E:ATP502 4.4 14.8 1.0 OG1 E:THR158 4.5 9.8 1.0 O3G E:ATP502 4.5 14.8 1.0 O3B E:ATP502 4.5 14.8 1.0 CB E:THR158 4.6 9.8 1.0 O5' E:ATP502 4.6 14.8 1.0 CG2 E:THR158 4.7 9.8 1.0 NE E:ARG313 4.7 11.7 1.0 CZ D:ARG264 4.7 15.2 1.0 NE D:ARG264 4.9 15.2 1.0

Magnesium binding site 6 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg503 b:13.6 occ:1.00 O1G F:ATP501 2.1 13.7 1.0 O1A F:ATP501 3.1 13.7 1.0 NH2 F:ARG313 3.1 13.6 1.0 NH2 E:ARG264 3.2 17.6 1.0 PG F:ATP501 3.5 13.7 1.0 CZ E:ARG264 4.0 17.6 1.0 O2G F:ATP501 4.2 13.7 1.0 PA F:ATP501 4.2 13.7 1.0 OG1 F:THR158 4.3 11.9 1.0 O3G F:ATP501 4.3 13.7 1.0 CZ F:ARG313 4.4 13.6 1.0 O3A F:ATP501 4.4 13.7 1.0 NE E:ARG264 4.5 17.6 1.0 O3B F:ATP501 4.5 13.7 1.0 CB F:THR158 4.6 11.9 1.0 CH2 E:TRP267 4.7 14.2 1.0 NH1 E:ARG264 4.7 17.6 1.0 CZ3 E:TRP267 4.8 14.2 1.0 CG2 F:THR158 4.8 11.9 1.0

Magnesium binding site 7 out of 7 in the Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Bacterial Replication Origin Opening Basal Unwinding System within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg500 b:33.1 occ:1.00 O2G G:ATP501 2.8 14.8 1.0 O1A G:ATP501 2.9 14.8 1.0 NH2 G:ARG313 3.3 11.7 1.0 CH2 F:TRP267 3.9 49.6 1.0 PA G:ATP501 4.1 14.8 1.0 PG G:ATP501 4.1 14.8 1.0 CZ3 F:TRP267 4.1 49.6 1.0 NH1 F:ARG264 4.2 19.9 1.0 OH G:TYR115 4.4 17.3 1.0 CZ F:ARG264 4.4 19.9 1.0 CZ G:ARG313 4.4 11.7 1.0 O3A G:ATP501 4.4 14.8 1.0 OG1 G:THR158 4.5 9.8 1.0 O3G G:ATP501 4.5 14.8 1.0 O3B G:ATP501 4.5 14.8 1.0 NH2 F:ARG264 4.5 19.9 1.0 CB G:THR158 4.6 9.8 1.0 O5' G:ATP501 4.6 14.8 1.0 CG2 G:THR158 4.7 9.8 1.0 NE G:ARG313 4.7 11.7 1.0 CZ2 F:TRP267 4.7 49.6 1.0 OD1 F:ASN234 4.8 18.8 1.0

S.Pelliciari, S.Bodet-Lefevre, S.Fenyk, D.Stevens, C.Winterhalter, F.D.Schramm, S.Pintar, D.R.Burnham, G.Merces, T.T.Richardson, Y.Tashiro, J.Hubbard, H.Yardimci, A.Ilangovan, H.Murray. The Bacterial Replication Origin Bus Promotes Nucleobase Capture. Nat Commun V. 14 8339 2023.
ISSN: ESSN 2041-1723
PubMed: 38097584
DOI: 10.1093/NAR/GKAC1060