Magnesium in PDB 6d8c: Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin

The binding sites of Magnesium atom in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin (pdb code 6d8c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin, PDB code: 6d8c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin


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 Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:42.2 occ:1.00 O3B H:ADP401 2.0 46.1 1.0 OE1 H:GLN137 2.4 47.3 1.0 PB H:ADP401 2.4 46.1 1.0 O2B H:ADP401 2.5 46.1 1.0 O3A H:ADP401 2.6 46.1 1.0 HA3 H:GLY156 3.4 46.6 1.0 HA2 H:GLY156 3.4 46.6 1.0 OD2 H:ASP154 3.6 46.9 1.0 CD H:GLN137 3.6 47.3 1.0 HG21 H:VAL339 3.6 46.4 1.0 H H:GLY302 3.7 45.6 1.0 HA3 H:GLY301 3.7 45.4 1.0 OD1 H:ASP154 3.8 46.9 1.0 HA2 H:GLY301 3.8 45.4 1.0 PA H:ADP401 3.8 46.1 1.0 CA H:GLY156 3.8 46.6 1.0 HG11 H:VAL339 3.8 46.4 1.0 O2A H:ADP401 3.9 46.1 1.0 CG H:ASP154 3.9 46.9 1.0 O1B H:ADP401 3.9 46.1 1.0 HZ1 H:LYS18 3.9 46.3 1.0 CA H:GLY301 4.2 45.4 1.0 HE22 H:GLN137 4.2 47.3 1.0 H H:GLY156 4.3 46.6 1.0 NE2 H:GLN137 4.4 47.3 1.0 N H:GLY156 4.4 46.6 1.0 N H:GLY302 4.4 45.6 1.0 CG2 H:VAL339 4.5 46.4 1.0 HG2 H:GLN137 4.6 47.3 1.0 HG22 H:VAL339 4.6 46.4 1.0 O H:ASP154 4.6 46.9 1.0 OD2 H:ASP11 4.6 48.5 1.0 O1A H:ADP401 4.6 46.1 1.0 HG13 H:VAL339 4.6 46.4 1.0 CG H:GLN137 4.6 47.3 1.0 CG1 H:VAL339 4.6 46.4 1.0 HG3 H:GLN137 4.8 47.3 1.0 NZ H:LYS18 4.8 46.3 1.0 H H:ASP157 4.8 45.1 1.0 O5' H:ADP401 4.9 46.1 1.0 C H:GLY301 4.9 45.4 1.0 HZ2 H:LYS18 5.0 46.3 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin


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 Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg402 b:42.2 occ:1.00 O3B J:ADP401 2.0 46.1 1.0 OE1 J:GLN137 2.4 47.3 1.0 PB J:ADP401 2.4 46.1 1.0 O2B J:ADP401 2.5 46.1 1.0 O3A J:ADP401 2.6 46.1 1.0 HA3 J:GLY156 3.4 46.6 1.0 HA2 J:GLY156 3.4 46.6 1.0 OD2 J:ASP154 3.6 46.9 1.0 CD J:GLN137 3.6 47.3 1.0 HG21 J:VAL339 3.6 46.4 1.0 H J:GLY302 3.7 45.6 1.0 HA3 J:GLY301 3.7 45.4 1.0 OD1 J:ASP154 3.8 46.9 1.0 HA2 J:GLY301 3.8 45.4 1.0 PA J:ADP401 3.8 46.1 1.0 CA J:GLY156 3.8 46.6 1.0 HG11 J:VAL339 3.8 46.4 1.0 O2A J:ADP401 3.9 46.1 1.0 CG J:ASP154 3.9 46.9 1.0 O1B J:ADP401 3.9 46.1 1.0 HZ1 J:LYS18 3.9 46.3 1.0 CA J:GLY301 4.2 45.4 1.0 HE22 J:GLN137 4.2 47.3 1.0 H J:GLY156 4.3 46.6 1.0 NE2 J:GLN137 4.4 47.3 1.0 N J:GLY156 4.4 46.6 1.0 N J:GLY302 4.4 45.6 1.0 CG2 J:VAL339 4.5 46.4 1.0 HG2 J:GLN137 4.6 47.3 1.0 HG22 J:VAL339 4.6 46.4 1.0 O J:ASP154 4.6 46.9 1.0 OD2 J:ASP11 4.6 48.5 1.0 O1A J:ADP401 4.6 46.1 1.0 HG13 J:VAL339 4.6 46.4 1.0 CG J:GLN137 4.6 47.3 1.0 CG1 J:VAL339 4.6 46.4 1.0 HG3 J:GLN137 4.8 47.3 1.0 NZ J:LYS18 4.8 46.3 1.0 H J:ASP157 4.8 45.1 1.0 O5' J:ADP401 4.9 46.1 1.0 C J:GLY301 4.9 45.4 1.0 HZ2 J:LYS18 5.0 46.3 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin


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 Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg402 b:42.2 occ:1.00 O3B K:ADP401 2.0 46.1 1.0 OE1 K:GLN137 2.4 47.3 1.0 PB K:ADP401 2.4 46.1 1.0 O2B K:ADP401 2.5 46.1 1.0 O3A K:ADP401 2.6 46.1 1.0 HA3 K:GLY156 3.4 46.6 1.0 HA2 K:GLY156 3.4 46.6 1.0 OD2 K:ASP154 3.6 46.9 1.0 CD K:GLN137 3.6 47.3 1.0 HG21 K:VAL339 3.6 46.4 1.0 H K:GLY302 3.7 45.6 1.0 HA3 K:GLY301 3.7 45.4 1.0 OD1 K:ASP154 3.8 46.9 1.0 HA2 K:GLY301 3.8 45.4 1.0 PA K:ADP401 3.8 46.1 1.0 CA K:GLY156 3.8 46.6 1.0 HG11 K:VAL339 3.8 46.4 1.0 O2A K:ADP401 3.9 46.1 1.0 CG K:ASP154 3.9 46.9 1.0 O1B K:ADP401 3.9 46.1 1.0 HZ1 K:LYS18 3.9 46.3 1.0 CA K:GLY301 4.2 45.4 1.0 HE22 K:GLN137 4.2 47.3 1.0 H K:GLY156 4.3 46.6 1.0 NE2 K:GLN137 4.4 47.3 1.0 N K:GLY156 4.4 46.6 1.0 N K:GLY302 4.4 45.6 1.0 CG2 K:VAL339 4.5 46.4 1.0 HG2 K:GLN137 4.6 47.3 1.0 HG22 K:VAL339 4.6 46.4 1.0 O K:ASP154 4.6 46.9 1.0 OD2 K:ASP11 4.6 48.5 1.0 O1A K:ADP401 4.6 46.1 1.0 HG13 K:VAL339 4.6 46.4 1.0 CG K:GLN137 4.6 47.3 1.0 CG1 K:VAL339 4.6 46.4 1.0 HG3 K:GLN137 4.8 47.3 1.0 NZ K:LYS18 4.8 46.3 1.0 H K:ASP157 4.8 45.1 1.0 O5' K:ADP401 4.9 46.1 1.0 C K:GLY301 4.9 45.4 1.0 HZ2 K:LYS18 5.0 46.3 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin


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 Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg402 b:42.2 occ:1.00 O3B L:ADP401 2.0 46.1 1.0 OE1 L:GLN137 2.4 47.3 1.0 PB L:ADP401 2.4 46.1 1.0 O2B L:ADP401 2.5 46.1 1.0 O3A L:ADP401 2.6 46.1 1.0 HA3 L:GLY156 3.4 46.6 1.0 HA2 L:GLY156 3.4 46.6 1.0 OD2 L:ASP154 3.6 46.9 1.0 CD L:GLN137 3.6 47.3 1.0 HG21 L:VAL339 3.6 46.4 1.0 H L:GLY302 3.7 45.6 1.0 HA3 L:GLY301 3.7 45.4 1.0 OD1 L:ASP154 3.8 46.9 1.0 HA2 L:GLY301 3.8 45.4 1.0 PA L:ADP401 3.8 46.1 1.0 CA L:GLY156 3.8 46.6 1.0 HG11 L:VAL339 3.8 46.4 1.0 O2A L:ADP401 3.9 46.1 1.0 CG L:ASP154 3.9 46.9 1.0 HZ1 L:LYS18 3.9 46.3 1.0 O1B L:ADP401 3.9 46.1 1.0 CA L:GLY301 4.2 45.4 1.0 HE22 L:GLN137 4.2 47.3 1.0 H L:GLY156 4.3 46.6 1.0 NE2 L:GLN137 4.4 47.3 1.0 N L:GLY156 4.4 46.6 1.0 N L:GLY302 4.4 45.6 1.0 CG2 L:VAL339 4.5 46.4 1.0 HG2 L:GLN137 4.6 47.3 1.0 HG22 L:VAL339 4.6 46.4 1.0 O L:ASP154 4.6 46.9 1.0 OD2 L:ASP11 4.6 48.5 1.0 O1A L:ADP401 4.6 46.1 1.0 HG13 L:VAL339 4.6 46.4 1.0 CG L:GLN137 4.6 47.3 1.0 CG1 L:VAL339 4.6 46.4 1.0 HG3 L:GLN137 4.8 47.3 1.0 NZ L:LYS18 4.8 46.3 1.0 H L:ASP157 4.8 45.1 1.0 O5' L:ADP401 4.9 46.1 1.0 C L:GLY301 4.9 45.4 1.0 HZ2 L:LYS18 5.0 46.3 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin


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 Flnaabd E254K Bound to Phalloidin-Stabilized F- Actin within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg402 b:42.2 occ:1.00 O3B M:ADP401 2.0 46.1 1.0 OE1 M:GLN137 2.4 47.3 1.0 PB M:ADP401 2.4 46.1 1.0 O2B M:ADP401 2.5 46.1 1.0 O3A M:ADP401 2.6 46.1 1.0 HA3 M:GLY156 3.4 46.6 1.0 HA2 M:GLY156 3.4 46.6 1.0 OD2 M:ASP154 3.6 46.9 1.0 CD M:GLN137 3.6 47.3 1.0 HG21 M:VAL339 3.6 46.4 1.0 H M:GLY302 3.7 45.6 1.0 HA3 M:GLY301 3.7 45.4 1.0 OD1 M:ASP154 3.8 46.9 1.0 HA2 M:GLY301 3.8 45.4 1.0 PA M:ADP401 3.8 46.1 1.0 CA M:GLY156 3.8 46.6 1.0 HG11 M:VAL339 3.8 46.4 1.0 O2A M:ADP401 3.9 46.1 1.0 CG M:ASP154 3.9 46.9 1.0 HZ1 M:LYS18 3.9 46.3 1.0 O1B M:ADP401 3.9 46.1 1.0 CA M:GLY301 4.2 45.4 1.0 HE22 M:GLN137 4.2 47.3 1.0 H M:GLY156 4.3 46.6 1.0 NE2 M:GLN137 4.4 47.3 1.0 N M:GLY156 4.4 46.6 1.0 N M:GLY302 4.4 45.6 1.0 CG2 M:VAL339 4.5 46.4 1.0 HG2 M:GLN137 4.6 47.3 1.0 HG22 M:VAL339 4.6 46.4 1.0 O M:ASP154 4.6 46.9 1.0 OD2 M:ASP11 4.6 48.5 1.0 O1A M:ADP401 4.6 46.1 1.0 HG13 M:VAL339 4.6 46.4 1.0 CG M:GLN137 4.6 47.3 1.0 CG1 M:VAL339 4.6 46.4 1.0 HG3 M:GLN137 4.8 47.3 1.0 NZ M:LYS18 4.8 46.3 1.0 H M:ASP157 4.8 45.1 1.0 O5' M:ADP401 4.9 46.1 1.0 C M:GLY301 4.9 45.4 1.0 HZ2 M:LYS18 5.0 46.3 1.0

D.V.Iwamoto, A.Huehn, B.Simon, C.Huet-Calderwood, M.Baldassarre, C.V.Sindelar, D.A.Calderwood. Structural Basis of the Filamin A Actin-Binding Domain Interaction with F-Actin. Nat. Struct. Mol. Biol. V. 25 918 2018.
ISSN: ESSN 1545-9985
PubMed: 30224736
DOI: 10.1038/S41594-018-0128-3