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

Magnesium Binding Sites:

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 8dck

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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 8dck

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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 8dck

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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 8dck

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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 8dck

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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 8dck

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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

Reference:

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
Page generated: Fri Apr 7 08:55:04 2023

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