Magnesium in PDB 8e9b: Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction (pdb code 8e9b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction, PDB code: 8e9b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8e9b

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Magnesium binding site 1 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:96.9
occ:1.00
 O3B A:ADP902 2.2 100.0 1.0
O1B A:ADP902 2.7 100.0 1.0
PB A:ADP902 2.9 100.0 1.0
O2B A:ADP902 3.8 100.0 1.0
OE1 A:GLN160 4.1 96.7 1.0
NE2 A:GLN160 4.2 96.7 1.0
O3A A:ADP902 4.2 100.0 1.0
O2A A:ADP902 4.3 100.0 1.0
CA A:GLY187 4.3 95.7 1.0
CD A:GLN160 4.3 96.7 1.0
CA A:GLY13 4.4 96.1 1.0
OD1 A:ASP185 4.5 98.1 1.0
N A:THR14 4.5 92.1 1.0
N A:ASP188 4.6 99.2 1.0
PA A:ADP902 5.0 100.0 1.0
O A:VAL190 5.0 95.0 1.0

Magnesium binding site 2 out of 10 in 8e9b

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Magnesium binding site 2 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:103.5
occ:1.00
 O2B B:ATP902 2.3 92.9 1.0
O1G B:ATP902 2.6 92.9 1.0
O3B B:ATP902 3.2 92.9 1.0
PB B:ATP902 3.2 92.9 1.0
PG B:ATP902 3.6 92.9 1.0
O3A B:ATP902 3.8 92.9 1.0
OD2 B:ASP9 3.9 100.6 1.0
CG2 B:VAL350 4.0 89.2 1.0
OD2 B:ASP154 4.2 92.4 1.0
CG B:GLN137 4.3 95.5 1.0
NZ B:LYS16 4.3 94.3 1.0
O2A B:ATP902 4.4 92.9 1.0
CB B:VAL350 4.4 89.2 1.0
OD1 B:ASP9 4.5 100.6 1.0
O3G B:ATP902 4.5 92.9 1.0
CG B:ASP9 4.6 100.6 1.0
O1B B:ATP902 4.6 92.9 1.0
O2G B:ATP902 4.6 92.9 1.0
CG1 B:VAL350 4.7 89.2 1.0
PA B:ATP902 4.7 92.9 1.0
CD B:GLN137 4.7 95.5 1.0
NE2 B:GLN137 4.9 95.5 1.0
CA B:GLY11 5.0 98.2 1.0

Magnesium binding site 3 out of 10 in 8e9b

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Magnesium binding site 3 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg801

b:84.8
occ:1.00
 O3B M:ADP802 2.0 82.8 1.0
OE1 M:GLN137 2.4 89.1 1.0
O2B M:ADP802 2.8 82.8 1.0
PB M:ADP802 2.9 82.8 1.0
CD M:GLN137 3.3 89.1 1.0
NE2 M:GLN137 3.5 89.1 1.0
O3A M:ADP802 3.9 82.8 1.0
O1B M:ADP802 4.1 82.8 1.0
OD1 M:ASP11 4.4 98.6 1.0
CA M:GLY13 4.5 88.8 1.0
CG M:GLN137 4.7 89.1 1.0
OD1 M:ASP154 4.7 80.8 1.0
CG2 M:VAL339 4.8 89.0 1.0
OD2 M:ASP11 4.8 98.6 1.0
CA M:GLY156 4.8 81.0 1.0

Magnesium binding site 4 out of 10 in 8e9b

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Magnesium binding site 4 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg801

b:81.6
occ:1.00
 O3B N:ADP802 2.1 78.5 1.0
PB N:ADP802 3.1 78.5 1.0
O1B N:ADP802 3.3 78.5 1.0
OD1 N:ASP154 3.5 82.4 1.0
O3A N:ADP802 3.5 78.5 1.0
CG2 N:VAL339 4.3 86.6 1.0
CA N:GLY156 4.4 81.3 1.0
CG N:ASP154 4.4 82.4 1.0
O2B N:ADP802 4.5 78.5 1.0
OD2 N:ASP154 4.6 82.4 1.0
N N:GLY156 4.7 81.3 1.0
CG N:GLN137 4.8 87.0 1.0
PA N:ADP802 4.8 78.5 1.0
O1A N:ADP802 4.8 78.5 1.0
OD1 N:ASP11 4.9 94.2 1.0

Magnesium binding site 5 out of 10 in 8e9b

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Magnesium binding site 5 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg801

b:76.8
occ:1.00
 O3B O:ADP802 2.1 74.2 1.0
PB O:ADP802 3.2 74.2 1.0
O2B O:ADP802 3.5 74.2 1.0
O3A O:ADP802 3.6 74.2 1.0
OD1 O:ASP154 3.7 75.6 1.0
CG O:GLN137 4.1 79.5 1.0
CA O:GLY156 4.1 75.5 1.0
CG O:ASP154 4.5 75.6 1.0
O1B O:ADP802 4.5 74.2 1.0
N O:GLY156 4.6 75.5 1.0
OD2 O:ASP154 4.7 75.6 1.0
CG2 O:VAL339 4.7 73.8 1.0
CD O:GLN137 4.8 79.5 1.0
CB O:GLN137 4.9 79.5 1.0
PA O:ADP802 4.9 74.2 1.0
O2A O:ADP802 5.0 74.2 1.0
NE2 O:GLN137 5.0 79.5 1.0

Magnesium binding site 6 out of 10 in 8e9b

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Magnesium binding site 6 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg801

b:77.1
occ:1.00
 O3B P:ADP802 2.1 79.0 1.0
PB P:ADP802 3.0 79.0 1.0
O1B P:ADP802 3.1 79.0 1.0
O3A P:ADP802 3.5 79.0 1.0
OD1 P:ASP154 3.5 78.4 1.0
NE2 P:GLN137 3.6 85.0 1.0
OE1 P:GLN137 3.9 85.0 1.0
CD P:GLN137 4.0 85.0 1.0
OD2 P:ASP154 4.0 78.4 1.0
CG P:ASP154 4.2 78.4 1.0
O2B P:ADP802 4.4 79.0 1.0
CG2 P:VAL339 4.4 80.6 1.0
O1A P:ADP802 4.7 79.0 1.0
PA P:ADP802 4.7 79.0 1.0
CA P:GLY156 4.8 82.3 1.0
NZ P:LYS18 5.0 89.1 1.0

Magnesium binding site 7 out of 10 in 8e9b

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Magnesium binding site 7 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


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 S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg801

b:85.0
occ:1.00
 O3B Q:ADP802 2.0 77.7 1.0
O1B Q:ADP802 2.4 77.7 1.0
PB Q:ADP802 2.5 77.7 1.0
O2B Q:ADP802 3.2 77.7 1.0
NE2 Q:GLN137 3.8 82.5 1.0
O3A Q:ADP802 3.9 77.7 1.0
CG Q:GLN137 4.1 82.5 1.0
OD2 Q:ASP154 4.3 82.1 1.0
CA Q:GLY13 4.4 78.9 1.0
OD2 Q:ASP11 4.5 83.3 1.0
CD Q:GLN137 4.5 82.5 1.0
OD1 Q:ASP11 4.7 83.3 1.0
O2A Q:ADP802 4.9 77.7 1.0
PA Q:ADP802 5.0 77.7 1.0

Magnesium binding site 8 out of 10 in 8e9b

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Magnesium binding site 8 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg801

b:93.1
occ:1.00
 O3B R:ADP802 2.0 84.3 1.0
O1B R:ADP802 2.3 84.3 1.0
PB R:ADP802 2.5 84.3 1.0
O3A R:ADP802 3.3 84.3 1.0
NE2 R:GLN137 3.9 98.3 1.0
O2B R:ADP802 3.9 84.3 1.0
OE1 R:GLN137 4.0 98.3 1.0
CD R:GLN137 4.1 98.3 1.0
OD2 R:ASP11 4.1 100.8 1.0
OD1 R:ASP154 4.2 94.3 1.0
O1A R:ADP802 4.4 84.3 1.0
PA R:ADP802 4.5 84.3 1.0
CA R:GLY13 4.6 90.8 1.0
CG2 R:VAL339 4.7 92.9 1.0
CG R:ASP11 4.8 100.8 1.0
OD1 R:ASP11 4.8 100.8 1.0
NZ R:LYS18 4.9 94.8 1.0

Magnesium binding site 9 out of 10 in 8e9b

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Magnesium binding site 9 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg801

b:105.2
occ:1.00
 O3B H:ADP802 2.9 94.7 1.0
O1B H:ADP802 3.5 94.7 1.0
OD1 H:ASP11 3.5 104.2 1.0
CG H:GLN137 3.6 101.5 1.0
PB H:ADP802 3.7 94.7 1.0
OD2 H:ASP11 4.1 104.2 1.0
CG H:ASP11 4.2 104.2 1.0
CD H:GLN137 4.3 101.5 1.0
CA H:GLY13 4.5 96.7 1.0
O3A H:ADP802 4.6 94.7 1.0
OD1 H:ASP154 4.6 101.7 1.0
NE2 H:GLN137 4.7 101.5 1.0
CB H:GLN137 4.7 101.5 1.0
OD2 H:ASP154 4.8 101.7 1.0
OE1 H:GLN137 4.9 101.5 1.0

Magnesium binding site 10 out of 10 in 8e9b

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Magnesium binding site 10 out of 10 in the Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of S. Pombe ARP2/3 Complex in the Branch Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg801

b:131.9
occ:1.00
 OE1 I:GLN137 2.6 128.9 1.0
CD I:GLN137 2.6 128.9 1.0
NE2 I:GLN137 2.7 128.9 1.0
O1B I:ADP802 2.9 109.5 1.0
OD2 I:ASP11 3.5 128.8 1.0
OD2 I:ASP154 3.5 124.6 1.0
CG I:GLN137 3.7 128.9 1.0
O3B I:ADP802 3.8 109.5 1.0
PB I:ADP802 3.9 109.5 1.0
OD1 I:ASP11 4.0 128.8 1.0
CG I:ASP11 4.1 128.8 1.0
CB I:GLN137 4.2 128.9 1.0
CG2 I:VAL339 4.2 121.0 1.0
CG I:ASP154 4.6 124.6 1.0
CG1 I:VAL339 4.6 121.0 1.0
O3A I:ADP802 4.7 109.5 1.0
CB I:VAL339 4.8 121.0 1.0
OD1 I:ASP154 4.9 124.6 1.0

Reference:

S.Z.Chou, M.Chatterjee, T.D.Pollard. Mechanism of Actin Filament Branch Formation By ARP2/3 Complex Revealed By A High-Resolution Cryo-Em Structureof the Branch Junction. Proc.Natl.Acad.Sci.Usa V. 119 22119 2022.
ISSN: ESSN 1091-6490
PubMed: 36442092
DOI: 10.1073/PNAS.2206722119
Page generated: Fri Oct 4 01:06:46 2024

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