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Magnesium in PDB 8jo0: The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex (pdb code 8jo0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex, PDB code: 8jo0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8jo0

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Magnesium binding site 1 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:313.4
occ:1.00
 O2G A:ATP602 2.8 143.5 1.0
OG A:SER166 2.9 108.8 1.0
NZ A:LYS191 3.0 155.1 1.0
O2A A:ATP602 3.1 117.0 1.0
CB A:SER166 3.3 128.2 1.0
O1B A:ATP602 3.4 120.0 1.0
OD2 A:ASP250 3.6 136.1 1.0
OD1 A:ASP250 4.2 119.4 1.0
PG A:ATP602 4.2 149.2 1.0
CE A:LYS191 4.3 145.6 1.0
CG A:ASP250 4.3 123.2 1.0
PA A:ATP602 4.6 116.1 1.0
O3B A:ATP602 4.7 313.5 1.0
PB A:ATP602 4.7 109.9 1.0
CE1 A:TYR369 4.8 114.1 1.0
CA A:SER166 4.8 109.8 1.0
O3G A:ATP602 5.0 92.3 1.0

Magnesium binding site 2 out of 7 in 8jo0

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Magnesium binding site 2 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:313.4
occ:1.00
 O2G B:ATP602 2.8 143.5 1.0
OG B:SER166 2.9 108.8 1.0
NZ B:LYS191 3.0 155.1 1.0
O2A B:ATP602 3.1 117.0 1.0
CB B:SER166 3.3 128.2 1.0
O1B B:ATP602 3.4 120.0 1.0
OD2 B:ASP250 3.6 136.1 1.0
OD1 B:ASP250 4.2 119.4 1.0
PG B:ATP602 4.2 149.2 1.0
CE B:LYS191 4.3 145.6 1.0
CG B:ASP250 4.3 123.2 1.0
PA B:ATP602 4.6 116.1 1.0
O3B B:ATP602 4.7 313.5 1.0
PB B:ATP602 4.7 109.9 1.0
CA B:SER166 4.8 109.8 1.0
CE1 B:TYR369 4.9 114.1 1.0
O3G B:ATP602 5.0 92.3 1.0

Magnesium binding site 3 out of 7 in 8jo0

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Magnesium binding site 3 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:313.4
occ:1.00
 O2G C:ATP602 2.8 143.5 1.0
OG C:SER166 2.9 108.8 1.0
NZ C:LYS191 3.0 155.1 1.0
O2A C:ATP602 3.1 117.0 1.0
CB C:SER166 3.3 128.2 1.0
O1B C:ATP602 3.4 120.0 1.0
OD2 C:ASP250 3.6 136.1 1.0
OD1 C:ASP250 4.2 119.4 1.0
PG C:ATP602 4.2 149.2 1.0
CE C:LYS191 4.3 145.6 1.0
CG C:ASP250 4.3 123.2 1.0
PA C:ATP602 4.6 116.1 1.0
O3B C:ATP602 4.7 313.5 1.0
PB C:ATP602 4.7 109.9 1.0
CA C:SER166 4.8 109.8 1.0
CE1 C:TYR369 4.9 114.1 1.0
O3G C:ATP602 5.0 92.3 1.0

Magnesium binding site 4 out of 7 in 8jo0

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Magnesium binding site 4 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:313.4
occ:1.00
 O2G D:ATP602 2.8 143.5 1.0
OG D:SER166 2.9 108.8 1.0
NZ D:LYS191 3.0 155.1 1.0
O2A D:ATP602 3.1 117.0 1.0
CB D:SER166 3.3 128.2 1.0
O1B D:ATP602 3.4 120.0 1.0
OD2 D:ASP250 3.6 136.1 1.0
OD1 D:ASP250 4.2 119.4 1.0
PG D:ATP602 4.2 149.2 1.0
CE D:LYS191 4.3 145.6 1.0
CG D:ASP250 4.3 123.2 1.0
PA D:ATP602 4.6 116.1 1.0
O3B D:ATP602 4.7 313.5 1.0
PB D:ATP602 4.7 109.9 1.0
CA D:SER166 4.8 109.8 1.0
O3G D:ATP602 5.0 92.3 1.0

Magnesium binding site 5 out of 7 in 8jo0

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Magnesium binding site 5 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:313.4
occ:1.00
 O2G E:ATP602 2.8 143.5 1.0
OG E:SER166 2.9 108.8 1.0
NZ E:LYS191 3.0 155.1 1.0
O2A E:ATP602 3.1 117.0 1.0
CB E:SER166 3.3 128.2 1.0
O1B E:ATP602 3.4 120.0 1.0
OD2 E:ASP250 3.6 136.1 1.0
OD1 E:ASP250 4.2 119.4 1.0
PG E:ATP602 4.2 149.2 1.0
CE E:LYS191 4.3 145.6 1.0
CG E:ASP250 4.3 123.2 1.0
OG E:SER370 4.4 99.2 1.0
PA E:ATP602 4.6 116.1 1.0
O3B E:ATP602 4.7 313.5 1.0
PB E:ATP602 4.7 109.9 1.0
CA E:SER166 4.8 109.8 1.0
O3G E:ATP602 5.0 92.3 1.0

Magnesium binding site 6 out of 7 in 8jo0

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Magnesium binding site 6 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:313.4
occ:1.00
 O2G F:ATP602 2.8 143.5 1.0
OG F:SER166 2.9 108.8 1.0
NZ F:LYS191 3.0 155.1 1.0
O2A F:ATP602 3.1 117.0 1.0
CB F:SER166 3.3 128.2 1.0
O1B F:ATP602 3.4 120.0 1.0
OD2 F:ASP250 3.6 136.1 1.0
OD1 F:ASP250 4.2 119.4 1.0
PG F:ATP602 4.2 149.2 1.0
CE F:LYS191 4.3 145.6 1.0
CG F:ASP250 4.3 123.2 1.0
PA F:ATP602 4.6 116.1 1.0
O3B F:ATP602 4.7 313.5 1.0
PB F:ATP602 4.7 109.9 1.0
CA F:SER166 4.8 109.8 1.0
CE1 F:TYR369 4.9 114.1 1.0
O3G F:ATP602 5.0 92.3 1.0

Magnesium binding site 7 out of 7 in 8jo0

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Magnesium binding site 7 out of 7 in the The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Cryo-Em Structure of A Heptameric Ced-4/Ced-3 Catalytic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:313.4
occ:1.00
 O2G G:ATP602 2.8 143.5 1.0
OG G:SER166 2.9 108.8 1.0
NZ G:LYS191 3.0 155.1 1.0
O2A G:ATP602 3.1 117.0 1.0
CB G:SER166 3.3 128.2 1.0
O1B G:ATP602 3.4 120.0 1.0
OD2 G:ASP250 3.6 136.1 1.0
OD1 G:ASP250 4.2 119.4 1.0
PG G:ATP602 4.2 149.2 1.0
CE G:LYS191 4.3 145.6 1.0
CG G:ASP250 4.3 123.2 1.0
PA G:ATP602 4.6 116.1 1.0
O3B G:ATP602 4.7 313.5 1.0
PB G:ATP602 4.7 109.9 1.0
CA G:SER166 4.8 109.8 1.0
CE1 G:TYR369 4.9 114.1 1.0
O3G G:ATP602 5.0 92.3 1.0

Reference:

Y.Li, L.Tian, Y.Zhang, Y.Shi. Structural Insights Into Ced-3 Activation To Be Published.
Page generated: Fri Oct 4 13:13:41 2024

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