Magnesium in PDB 8dck: Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound

The binding sites of Magnesium atom in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound (pdb code 8dck). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound, PDB code: 8dck:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:54.7 occ:1.00 O2B A:ATP801 2.1 61.3 1.0 OG A:SER509 2.1 56.2 1.0 O3G A:ATP801 2.3 61.3 1.0 OE1 A:GLN550 2.4 55.9 1.0 O3B A:ATP801 2.8 61.3 1.0 NE2 A:GLN631 2.8 57.1 1.0 PB A:ATP801 3.0 61.3 1.0 PG A:ATP801 3.0 61.3 1.0 O2G A:ATP801 3.3 61.3 1.0 CB A:SER509 3.4 56.2 1.0 CD A:GLN550 3.4 55.9 1.0 NE2 A:GLN550 3.6 55.9 1.0 O1A A:ATP801 3.8 61.3 1.0 O3A A:ATP801 3.8 61.3 1.0 OG B:SER607 3.9 61.4 1.0 CD A:GLN631 4.0 57.1 1.0 O1B A:ATP801 4.2 61.3 1.0 OD1 A:ASP630 4.2 55.0 1.0 PA A:ATP801 4.3 61.3 1.0 O1G A:ATP801 4.4 61.3 1.0 CA A:SER509 4.4 56.2 1.0 N A:SER509 4.4 56.2 1.0 N B:GLY608 4.5 58.9 1.0 OE1 A:GLN631 4.5 57.1 1.0 CG A:LYS508 4.7 57.9 1.0 OD2 A:ASP630 4.8 55.0 1.0 CG A:GLN550 4.8 55.9 1.0 O2A A:ATP801 4.8 61.3 1.0 CG A:ASP630 4.9 55.0 1.0

Magnesium binding site 2 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:69.1 occ:1.00 OE1 B:GLN550 2.0 68.6 1.0 O2B B:ATP801 2.0 73.6 1.0 O3G B:ATP801 2.2 73.6 1.0 OG B:SER509 2.4 72.5 1.0 CD B:GLN550 2.7 68.6 1.0 NE2 B:GLN550 2.8 68.6 1.0 O3B B:ATP801 2.9 73.6 1.0 PB B:ATP801 3.0 73.6 1.0 PG B:ATP801 3.1 73.6 1.0 CB B:SER509 3.7 72.5 1.0 O2G B:ATP801 3.9 73.6 1.0 O3A B:ATP801 3.9 73.6 1.0 CG B:GLN550 4.2 68.6 1.0 O1B B:ATP801 4.2 73.6 1.0 O1A B:ATP801 4.3 73.6 1.0 CG B:LYS508 4.3 76.1 1.0 O1G B:ATP801 4.4 73.6 1.0 CB A:SER607 4.4 69.3 1.0 N A:GLY608 4.4 67.0 1.0 N B:SER509 4.5 72.5 1.0 CA B:SER509 4.6 72.5 1.0 PA B:ATP801 4.6 73.6 1.0 CB B:GLN550 4.8 68.6 1.0 OG A:SER607 4.8 69.3 1.0 OD1 B:ASP630 4.8 73.3 1.0 CD B:LYS508 4.8 76.1 1.0 OD2 B:ASP630 4.9 73.3 1.0

Magnesium binding site 3 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg802 b:55.7 occ:1.00 O2B I:ATP801 2.1 62.0 1.0 OG I:SER509 2.1 57.7 1.0 O3G I:ATP801 2.3 62.0 1.0 OE1 I:GLN550 2.4 57.9 1.0 O3B I:ATP801 2.8 62.0 1.0 NE2 I:GLN631 2.8 58.7 1.0 PB I:ATP801 3.0 62.0 1.0 PG I:ATP801 3.0 62.0 1.0 O2G I:ATP801 3.3 62.0 1.0 CB I:SER509 3.4 57.7 1.0 CD I:GLN550 3.4 57.9 1.0 NE2 I:GLN550 3.6 57.9 1.0 O1A I:ATP801 3.8 62.0 1.0 O3A I:ATP801 3.8 62.0 1.0 OG J:SER607 3.9 60.8 1.0 CD I:GLN631 4.0 58.7 1.0 O1B I:ATP801 4.2 62.0 1.0 OD1 I:ASP630 4.2 56.9 1.0 PA I:ATP801 4.3 62.0 1.0 O1G I:ATP801 4.4 62.0 1.0 CA I:SER509 4.4 57.7 1.0 N I:SER509 4.4 57.7 1.0 N J:GLY608 4.5 59.4 1.0 OE1 I:GLN631 4.5 58.7 1.0 CG I:LYS508 4.7 58.7 1.0 OD2 I:ASP630 4.8 56.9 1.0 CG I:GLN550 4.8 57.9 1.0 O2A I:ATP801 4.8 62.0 1.0 CG I:ASP630 4.9 56.9 1.0

Magnesium binding site 4 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg802 b:67.5 occ:1.00 OE1 J:GLN550 2.0 67.0 1.0 O2B J:ATP801 2.0 71.3 1.0 O3G J:ATP801 2.2 71.3 1.0 OG J:SER509 2.4 70.6 1.0 CD J:GLN550 2.7 67.0 1.0 NE2 J:GLN550 2.8 67.0 1.0 O3B J:ATP801 2.9 71.3 1.0 PB J:ATP801 3.0 71.3 1.0 PG J:ATP801 3.1 71.3 1.0 CB J:SER509 3.7 70.6 1.0 O2G J:ATP801 3.9 71.3 1.0 O3A J:ATP801 3.9 71.3 1.0 CG J:GLN550 4.2 67.0 1.0 O1B J:ATP801 4.2 71.3 1.0 O1A J:ATP801 4.3 71.3 1.0 CG J:LYS508 4.3 72.9 1.0 O1G J:ATP801 4.4 71.3 1.0 CB I:SER607 4.4 67.0 1.0 N I:GLY608 4.4 66.3 1.0 N J:SER509 4.5 70.6 1.0 CA J:SER509 4.6 70.6 1.0 PA J:ATP801 4.6 71.3 1.0 CB J:GLN550 4.8 67.0 1.0 OG I:SER607 4.8 67.0 1.0 OD1 J:ASP630 4.8 70.6 1.0 CD J:LYS508 4.8 72.9 1.0 OD2 J:ASP630 4.9 70.6 1.0

Magnesium binding site 5 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg802 b:55.7 occ:1.00 O2B E:ATP801 2.1 62.0 1.0 OG E:SER509 2.1 57.5 1.0 O3G E:ATP801 2.3 62.0 1.0 OE1 E:GLN550 2.4 57.3 1.0 O3B E:ATP801 2.8 62.0 1.0 NE2 E:GLN631 2.8 58.2 1.0 PB E:ATP801 3.0 62.0 1.0 PG E:ATP801 3.0 62.0 1.0 O2G E:ATP801 3.3 62.0 1.0 CB E:SER509 3.4 57.5 1.0 CD E:GLN550 3.4 57.3 1.0 NE2 E:GLN550 3.6 57.3 1.0 O1A E:ATP801 3.8 62.0 1.0 O3A E:ATP801 3.8 62.0 1.0 OG F:SER607 3.9 61.0 1.0 CD E:GLN631 4.0 58.2 1.0 O1B E:ATP801 4.2 62.0 1.0 OD1 E:ASP630 4.2 56.5 1.0 PA E:ATP801 4.3 62.0 1.0 O1G E:ATP801 4.4 62.0 1.0 CA E:SER509 4.4 57.5 1.0 N E:SER509 4.4 57.5 1.0 N F:GLY608 4.5 59.8 1.0 OE1 E:GLN631 4.5 58.2 1.0 CG E:LYS508 4.7 58.4 1.0 OD2 E:ASP630 4.8 56.5 1.0 CG E:GLN550 4.8 57.3 1.0 O2A E:ATP801 4.8 62.0 1.0 CG E:ASP630 4.9 56.5 1.0

Magnesium binding site 6 out of 6 in the Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Hemolysin A Secretion System Hlyb/D Complex, Atp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg802 b:66.3 occ:1.00 OE1 F:GLN550 2.0 68.6 1.0 O2B F:ATP801 2.0 73.0 1.0 O3G F:ATP801 2.2 73.0 1.0 OG F:SER509 2.4 71.5 1.0 CD F:GLN550 2.7 68.6 1.0 NE2 F:GLN550 2.8 68.6 1.0 O3B F:ATP801 2.9 73.0 1.0 PB F:ATP801 3.0 73.0 1.0 PG F:ATP801 3.1 73.0 1.0 CB F:SER509 3.7 71.5 1.0 O2G F:ATP801 3.9 73.0 1.0 O3A F:ATP801 3.9 73.0 1.0 CG F:GLN550 4.2 68.6 1.0 O1B F:ATP801 4.2 73.0 1.0 O1A F:ATP801 4.3 73.0 1.0 CG F:LYS508 4.3 73.5 1.0 O1G F:ATP801 4.4 73.0 1.0 CB E:SER607 4.4 68.1 1.0 N E:GLY608 4.4 67.2 1.0 N F:SER509 4.5 71.5 1.0 CA F:SER509 4.6 71.5 1.0 PA F:ATP801 4.6 73.0 1.0 CB F:GLN550 4.8 68.6 1.0 OG E:SER607 4.8 68.1 1.0 OD1 F:ASP630 4.8 72.8 1.0 CD F:LYS508 4.8 73.5 1.0 OD2 F:ASP630 4.9 72.8 1.0

H.Zhao, J.Lee, J.Chen. The Hemolysin A Secretion System Is A Multi-Engine Pump Containing Three Abc Transporters. Cell V. 185 3329 2022.
ISSN: ISSN 1097-4172
PubMed: 36055198
DOI: 10.1016/J.CELL.2022.07.017