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Magnesium in PDB 5wve: Apaf-1-Caspase-9 Holoenzyme

Other elements in 5wve:

The structure of Apaf-1-Caspase-9 Holoenzyme also contains other interesting chemical elements:

Iron (Fe) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Apaf-1-Caspase-9 Holoenzyme (pdb code 5wve). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Apaf-1-Caspase-9 Holoenzyme, PDB code: 5wve:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 1 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:30.0
occ:1.00
 O2B A:DTP1301 2.2 20.0 1.0
OG A:SER161 2.4 0.0 1.0
O3G A:DTP1301 2.4 20.0 1.0
PB A:DTP1301 3.5 20.0 1.0
OD2 A:ASP243 3.6 0.0 1.0
CB A:SER161 3.7 0.0 1.0
CG A:ASP243 3.8 0.0 1.0
OD1 A:ASP243 3.8 0.0 1.0
PG A:DTP1301 3.8 20.0 1.0
O3B A:DTP1301 4.0 20.0 1.0
OD2 A:ASP244 4.1 0.0 1.0
O1B A:DTP1301 4.1 20.0 1.0
O2A A:DTP1301 4.3 20.0 1.0
N A:ASP244 4.6 0.0 1.0
CB A:ASP243 4.7 0.0 1.0
O2G A:DTP1301 4.7 20.0 1.0
O3A A:DTP1301 4.7 20.0 1.0
CA A:SER161 4.7 0.0 1.0
N A:SER161 4.8 0.0 1.0
O1G A:DTP1301 4.8 20.0 1.0
CG A:ASP244 4.8 0.0 1.0

Magnesium binding site 2 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 2 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1302

b:30.0
occ:1.00
 O2B C:DTP1301 2.2 20.0 1.0
OG C:SER161 2.4 0.0 1.0
O3G C:DTP1301 2.4 20.0 1.0
PB C:DTP1301 3.5 20.0 1.0
OD2 C:ASP243 3.6 0.0 1.0
CB C:SER161 3.7 0.0 1.0
CG C:ASP243 3.8 0.0 1.0
OD1 C:ASP243 3.8 0.0 1.0
PG C:DTP1301 3.8 20.0 1.0
O3B C:DTP1301 4.0 20.0 1.0
OD2 C:ASP244 4.1 0.0 1.0
O1B C:DTP1301 4.1 20.0 1.0
O2A C:DTP1301 4.3 20.0 1.0
N C:ASP244 4.6 0.0 1.0
CB C:ASP243 4.7 0.0 1.0
O2G C:DTP1301 4.7 20.0 1.0
O3A C:DTP1301 4.7 20.0 1.0
CA C:SER161 4.7 0.0 1.0
N C:SER161 4.8 0.0 1.0
O1G C:DTP1301 4.8 20.0 1.0
CG C:ASP244 4.8 0.0 1.0

Magnesium binding site 3 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 3 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1302

b:30.0
occ:1.00
 O2B E:DTP1301 2.2 20.0 1.0
OG E:SER161 2.4 0.0 1.0
O3G E:DTP1301 2.4 20.0 1.0
PB E:DTP1301 3.5 20.0 1.0
OD2 E:ASP243 3.6 0.0 1.0
CB E:SER161 3.7 0.0 1.0
CG E:ASP243 3.8 0.0 1.0
OD1 E:ASP243 3.8 0.0 1.0
PG E:DTP1301 3.8 20.0 1.0
O3B E:DTP1301 4.0 20.0 1.0
OD2 E:ASP244 4.1 0.0 1.0
O1B E:DTP1301 4.1 20.0 1.0
O2A E:DTP1301 4.3 20.0 1.0
N E:ASP244 4.6 0.0 1.0
CB E:ASP243 4.7 0.0 1.0
O2G E:DTP1301 4.7 20.0 1.0
O3A E:DTP1301 4.7 20.0 1.0
CA E:SER161 4.7 0.0 1.0
N E:SER161 4.8 0.0 1.0
O1G E:DTP1301 4.8 20.0 1.0
CG E:ASP244 4.8 0.0 1.0

Magnesium binding site 4 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 4 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1302

b:30.0
occ:1.00
 O2B G:DTP1301 2.2 20.0 1.0
OG G:SER161 2.4 0.0 1.0
O3G G:DTP1301 2.4 20.0 1.0
PB G:DTP1301 3.5 20.0 1.0
OD2 G:ASP243 3.6 0.0 1.0
CB G:SER161 3.7 0.0 1.0
CG G:ASP243 3.8 0.0 1.0
OD1 G:ASP243 3.8 0.0 1.0
PG G:DTP1301 3.8 20.0 1.0
O3B G:DTP1301 4.0 20.0 1.0
OD2 G:ASP244 4.1 0.0 1.0
O1B G:DTP1301 4.1 20.0 1.0
O2A G:DTP1301 4.3 20.0 1.0
N G:ASP244 4.6 0.0 1.0
CB G:ASP243 4.7 0.0 1.0
O2G G:DTP1301 4.7 20.0 1.0
O3A G:DTP1301 4.7 20.0 1.0
CA G:SER161 4.7 0.0 1.0
N G:SER161 4.8 0.0 1.0
O1G G:DTP1301 4.8 20.0 1.0
CG G:ASP244 4.8 0.0 1.0

Magnesium binding site 5 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 5 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1302

b:30.0
occ:1.00
 O2B I:DTP1301 2.2 20.0 1.0
OG I:SER161 2.4 0.0 1.0
O3G I:DTP1301 2.4 20.0 1.0
PB I:DTP1301 3.5 20.0 1.0
OD2 I:ASP243 3.6 0.0 1.0
CB I:SER161 3.7 0.0 1.0
CG I:ASP243 3.8 0.0 1.0
OD1 I:ASP243 3.8 0.0 1.0
PG I:DTP1301 3.8 20.0 1.0
O3B I:DTP1301 4.0 20.0 1.0
OD2 I:ASP244 4.1 0.0 1.0
O1B I:DTP1301 4.1 20.0 1.0
O2A I:DTP1301 4.3 20.0 1.0
N I:ASP244 4.6 0.0 1.0
CB I:ASP243 4.7 0.0 1.0
O2G I:DTP1301 4.7 20.0 1.0
O3A I:DTP1301 4.7 20.0 1.0
CA I:SER161 4.7 0.0 1.0
N I:SER161 4.8 0.0 1.0
O1G I:DTP1301 4.8 20.0 1.0
CG I:ASP244 4.8 0.0 1.0

Magnesium binding site 6 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 6 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1302

b:30.0
occ:1.00
 O2B K:DTP1301 2.2 20.0 1.0
O3G K:DTP1301 2.4 20.0 1.0
OG K:SER161 2.4 0.0 1.0
PB K:DTP1301 3.5 20.0 1.0
OD2 K:ASP243 3.6 0.0 1.0
CB K:SER161 3.7 0.0 1.0
CG K:ASP243 3.8 0.0 1.0
OD1 K:ASP243 3.8 0.0 1.0
PG K:DTP1301 3.8 20.0 1.0
O3B K:DTP1301 4.0 20.0 1.0
OD2 K:ASP244 4.1 0.0 1.0
O1B K:DTP1301 4.1 20.0 1.0
O2A K:DTP1301 4.3 20.0 1.0
N K:ASP244 4.6 0.0 1.0
CB K:ASP243 4.7 0.0 1.0
O2G K:DTP1301 4.7 20.0 1.0
O3A K:DTP1301 4.7 20.0 1.0
CA K:SER161 4.7 0.0 1.0
N K:SER161 4.8 0.0 1.0
O1G K:DTP1301 4.8 20.0 1.0
CG K:ASP244 4.8 0.0 1.0

Magnesium binding site 7 out of 7 in 5wve

Go back to Magnesium Binding Sites List in 5wve
Magnesium binding site 7 out of 7 in the Apaf-1-Caspase-9 Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Apaf-1-Caspase-9 Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1302

b:30.0
occ:1.00
 O2B M:DTP1301 2.2 20.0 1.0
OG M:SER161 2.4 0.0 1.0
O3G M:DTP1301 2.4 20.0 1.0
PB M:DTP1301 3.5 20.0 1.0
OD2 M:ASP243 3.6 0.0 1.0
CB M:SER161 3.7 0.0 1.0
CG M:ASP243 3.8 0.0 1.0
OD1 M:ASP243 3.8 0.0 1.0
PG M:DTP1301 3.8 20.0 1.0
O3B M:DTP1301 4.0 20.0 1.0
OD2 M:ASP244 4.1 0.0 1.0
O1B M:DTP1301 4.1 20.0 1.0
O2A M:DTP1301 4.3 20.0 1.0
N M:ASP244 4.6 0.0 1.0
CB M:ASP243 4.7 0.0 1.0
O2G M:DTP1301 4.7 20.0 1.0
O3A M:DTP1301 4.7 20.0 1.0
CA M:SER161 4.7 0.0 1.0
N M:SER161 4.8 0.0 1.0
O1G M:DTP1301 4.8 20.0 1.0
CG M:ASP244 4.8 0.0 1.0

Reference:

Y.Li, M.Zhou, Q.Hu, X.-C.Bai, W.Huang, S.H.W.Scheres, Y.Shi. Mechanistic Insights Into Caspase-9 Activation By the Structure of the Apoptosome Holoenzyme Proc. Natl. Acad. Sci. V. 114 1542 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28143931
DOI: 10.1073/PNAS.1620626114
Page generated: Mon Sep 30 08:56:36 2024

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