Magnesium in PDB 6w17: Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament

The binding sites of Magnesium atom in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament (pdb code 6w17). 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 DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament, PDB code: 6w17:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:0.7 occ:1.00 O1G A:ATP501 2.0 0.8 1.0 O3B A:ATP501 2.1 0.8 1.0 O2B A:ATP501 2.2 0.8 1.0 PG A:ATP501 2.4 0.8 1.0 PB A:ATP501 2.7 0.8 1.0 O3G A:ATP501 3.0 0.8 1.0 O1B A:ATP501 3.8 0.8 1.0 OE1 A:GLN160 3.8 94.5 1.0 O3A A:ATP501 3.8 0.8 1.0 O2G A:ATP501 3.8 0.8 1.0 CA A:GLY187 4.1 0.3 1.0 NE2 A:GLN160 4.4 94.5 1.0 CD A:GLN160 4.5 94.5 1.0 N A:GLY187 4.9 0.3 1.0 NZ A:LYS18 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:88.7 occ:1.00 O1G B:ATP501 2.0 83.3 1.0 O3B B:ATP501 2.1 83.3 1.0 O2B B:ATP501 2.2 83.3 1.0 OE1 B:GLN137 2.3 82.3 1.0 PG B:ATP501 2.4 83.3 1.0 PB B:ATP501 2.7 83.3 1.0 O3G B:ATP501 3.0 83.3 1.0 CD B:GLN137 3.2 82.3 1.0 OD2 B:ASP154 3.4 78.2 1.0 NE2 B:GLN137 3.7 82.3 1.0 O1B B:ATP501 3.8 83.3 1.0 O3A B:ATP501 3.8 83.3 1.0 O2G B:ATP501 3.8 83.3 1.0 OD1 B:ASP154 4.0 78.2 1.0 CG B:ASP154 4.1 78.2 1.0 CG B:GLN137 4.5 82.3 1.0 CG2 B:VAL350 4.7 83.0 1.0 CA B:GLY156 4.7 81.7 1.0 CB B:GLN137 4.9 82.3 1.0

Magnesium binding site 3 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg402 b:70.1 occ:1.00 O3B I:ADP401 2.0 69.9 1.0 OE1 I:GLN137 2.6 73.5 1.0 O1B I:ADP401 2.6 69.9 1.0 PB I:ADP401 2.7 69.9 1.0 CA I:GLY156 3.2 71.3 1.0 O3A I:ADP401 3.3 69.9 1.0 OD2 I:ASP154 3.4 68.6 1.0 CD I:GLN137 3.5 73.5 1.0 NE2 I:GLN137 3.7 73.5 1.0 N I:GLY156 3.8 71.3 1.0 OD1 I:ASP154 4.0 68.6 1.0 O2B I:ADP401 4.1 69.9 1.0 CG I:ASP154 4.1 68.6 1.0 C I:GLY156 4.2 71.3 1.0 N I:ASP157 4.6 73.3 1.0 PA I:ADP401 4.8 69.9 1.0 CG I:GLN137 4.9 73.5 1.0 O1A I:ADP401 4.9 69.9 1.0

Magnesium binding site 4 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg402 b:78.0 occ:1.00 O3B J:ADP401 2.0 75.4 1.0 NE2 J:GLN137 2.5 80.6 1.0 O1B J:ADP401 2.6 75.4 1.0 PB J:ADP401 2.7 75.4 1.0 O3A J:ADP401 3.3 75.4 1.0 CD J:GLN137 3.4 80.6 1.0 OD2 J:ASP154 3.5 78.6 1.0 OE1 J:GLN137 3.6 80.6 1.0 CA J:GLY156 3.7 77.2 1.0 N J:GLY156 4.0 77.2 1.0 O2B J:ADP401 4.1 75.4 1.0 CG1 J:VAL159 4.2 77.1 1.0 O J:VAL159 4.5 77.1 1.0 CG J:ASP154 4.6 78.6 1.0 CG J:GLN137 4.7 80.6 1.0 PA J:ADP401 4.8 75.4 1.0 C J:GLY156 4.9 77.2 1.0 O1A J:ADP401 4.9 75.4 1.0 N J:ASP157 4.9 79.1 1.0

Magnesium binding site 5 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg402 b:84.8 occ:1.00 O3B K:ADP401 2.0 83.0 1.0 O1B K:ADP401 2.6 83.0 1.0 PB K:ADP401 2.7 83.0 1.0 O3A K:ADP401 3.3 83.0 1.0 CA K:GLY156 3.5 85.5 1.0 N K:GLY156 4.0 85.5 1.0 O2B K:ADP401 4.1 83.0 1.0 C K:GLY156 4.4 85.5 1.0 NE2 K:GLN137 4.5 91.7 1.0 N K:ASP157 4.6 87.0 1.0 PA K:ADP401 4.8 83.0 1.0 CA K:GLY13 4.8 86.8 1.0 O K:VAL159 4.8 89.0 1.0 O1A K:ADP401 4.9 83.0 1.0

Magnesium binding site 6 out of 6 in the Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of DIP1-Activated ARP2/3 Complex with Nucleated Actin Filament within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg402 b:0.1 occ:1.00 O1B L:ADP401 2.0 0.3 1.0 OE1 L:GLN137 2.2 0.8 1.0 O3B L:ADP401 2.6 0.3 1.0 PB L:ADP401 2.7 0.3 1.0 CD L:GLN137 3.1 0.8 1.0 O3A L:ADP401 3.3 0.3 1.0 NE2 L:GLN137 3.4 0.8 1.0 CA L:GLY156 3.5 0.4 1.0 N L:GLY156 3.8 0.4 1.0 O2B L:ADP401 4.1 0.3 1.0 CG L:GLN137 4.4 0.8 1.0 C L:SER155 4.7 0.3 1.0 OD2 L:ASP154 4.7 0.2 1.0 PA L:ADP401 4.8 0.3 1.0 C L:GLY156 4.8 0.4 1.0 CG1 L:VAL159 4.8 0.7 1.0 O1A L:ADP401 4.9 0.3 1.0 CB L:GLN137 5.0 0.8 1.0

M.Shaaban, S.Chowdhury, B.J.Nolen. Cryo-Em Reveals the Transition of ARP2/3 Complex From Inactive to Nucleation-Competent State. Nat.Struct.Mol.Biol. V. 27 1009 2020.
ISSN: ESSN 1545-9985
PubMed: 32839613
DOI: 10.1038/S41594-020-0481-X