Magnesium in PDB 8e7v: Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles

All present enzymatic activity of Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles:
3.4.21.92;

The binding sites of Magnesium atom in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles (pdb code 8e7v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles, PDB code: 8e7v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles


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 Substrate-Free Dnclpx.Clpp From Singly Capped Particles within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:136.7 occ:1.00 O2G B:ATP501 2.0 137.3 1.0 O2B B:ATP501 2.0 137.3 1.0 OG1 B:THR126 2.1 137.8 1.0 OD2 B:ASP184 2.8 139.2 1.0 HH22 C:ARG307 2.9 137.6 1.0 PG B:ATP501 3.3 137.3 1.0 PB B:ATP501 3.3 137.3 1.0 CB B:THR126 3.4 137.8 1.0 OE2 B:GLU185 3.4 138.7 1.0 CG B:ASP184 3.6 139.2 1.0 OD1 B:ASP184 3.6 139.2 1.0 O3B B:ATP501 3.6 137.3 1.0 NH2 C:ARG307 3.7 137.6 1.0 HB B:THR126 3.7 137.8 1.0 HG21 B:THR126 3.8 137.8 1.0 HH21 C:ARG307 3.9 137.6 1.0 O1G B:ATP501 3.9 137.3 1.0 H B:THR126 3.9 137.8 1.0 O1A B:ATP501 4.0 137.3 1.0 HH22 B:ARG370 4.0 137.3 1.0 CG2 B:THR126 4.1 137.8 1.0 O1B B:ATP501 4.3 137.3 1.0 HE3 C:LYS213 4.3 139.8 1.0 HG23 B:THR126 4.4 137.8 1.0 N B:THR126 4.4 137.8 1.0 HE2 B:LYS125 4.4 136.7 1.0 O3A B:ATP501 4.5 137.3 1.0 CA B:THR126 4.5 137.8 1.0 HB2 B:LYS125 4.5 136.7 1.0 HH12 C:ARG307 4.5 137.6 1.0 O3G B:ATP501 4.5 137.3 1.0 CD B:GLU185 4.5 138.7 1.0 HH21 B:ARG370 4.6 137.3 1.0 HH B:TYR182 4.6 139.4 1.0 NH2 B:ARG370 4.6 137.3 1.0 HA B:THR126 4.7 137.8 1.0 HD3 C:LYS213 4.7 139.8 1.0 PA B:ATP501 4.7 137.3 1.0 HD2 C:LYS213 4.7 139.8 1.0 CZ C:ARG307 4.8 137.6 1.0 HG22 B:THR126 5.0 137.8 1.0 HG2 B:GLU185 5.0 138.7 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles


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 Substrate-Free Dnclpx.Clpp From Singly Capped Particles within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:140.6 occ:1.00 OG1 C:THR126 2.0 141.7 1.0 O2B C:ATP501 2.0 141.6 1.0 OD2 C:ASP184 3.1 140.3 1.0 O2G C:ATP501 3.2 141.6 1.0 PB C:ATP501 3.2 141.6 1.0 O1G C:ATP501 3.2 141.6 1.0 OD1 C:ASP184 3.4 140.3 1.0 HH22 D:ARG307 3.4 139.4 1.0 CB C:THR126 3.4 141.7 1.0 CG C:ASP184 3.6 140.3 1.0 PG C:ATP501 3.6 141.6 1.0 HB C:THR126 3.7 141.7 1.0 O1B C:ATP501 3.7 141.6 1.0 OE2 C:GLU185 3.8 138.9 1.0 H C:THR126 3.9 141.7 1.0 HG21 C:THR126 3.9 141.7 1.0 O3B C:ATP501 3.9 141.6 1.0 OE2 D:GLU216 3.9 140.6 1.0 NH2 D:ARG307 4.0 139.4 1.0 HH21 D:ARG307 4.1 139.4 1.0 HH22 C:ARG370 4.1 139.8 1.0 CG2 C:THR126 4.2 141.7 1.0 HH C:TYR182 4.3 142.1 1.0 N C:THR126 4.3 141.7 1.0 HB2 C:LYS125 4.4 140.1 1.0 O1A C:ATP501 4.4 141.6 1.0 HE2 C:LYS125 4.4 140.1 1.0 CA C:THR126 4.4 141.7 1.0 HA C:THR126 4.5 141.7 1.0 O3A C:ATP501 4.5 141.6 1.0 HG23 C:THR126 4.5 141.7 1.0 CD C:GLU185 4.8 138.9 1.0 CD D:GLU216 4.8 140.6 1.0 NH2 C:ARG370 4.9 139.8 1.0 PA C:ATP501 4.9 141.6 1.0 OE1 D:GLU216 5.0 140.6 1.0 HE2 C:TYR182 5.0 142.1 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp From Singly Capped Particles


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 Substrate-Free Dnclpx.Clpp From Singly Capped Particles within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:137.1 occ:1.00 O2G D:ATP501 2.0 138.0 1.0 OG1 D:THR126 2.0 137.6 1.0 O2B D:ATP501 2.3 138.0 1.0 OE2 D:GLU185 3.1 137.9 1.0 OD1 D:ASP184 3.1 138.6 1.0 OD2 D:ASP184 3.2 138.6 1.0 CB D:THR126 3.4 137.6 1.0 PG D:ATP501 3.4 138.0 1.0 PB D:ATP501 3.5 138.0 1.0 CG D:ASP184 3.5 138.6 1.0 HB D:THR126 3.6 137.6 1.0 O3B D:ATP501 3.7 138.0 1.0 H D:THR126 3.7 137.6 1.0 HG21 D:THR126 3.9 137.6 1.0 HH22 E:ARG307 4.0 138.6 1.0 HD3 E:LYS213 4.0 139.3 1.0 HH22 D:ARG370 4.1 138.0 1.0 HE2 D:LYS125 4.1 136.7 1.0 CD D:GLU185 4.2 137.9 1.0 CG2 D:THR126 4.2 137.6 1.0 HB2 D:LYS125 4.2 136.7 1.0 N D:THR126 4.3 137.6 1.0 HH21 E:ARG307 4.3 138.6 1.0 CA D:THR126 4.3 137.6 1.0 O3G D:ATP501 4.3 138.0 1.0 O1B D:ATP501 4.4 138.0 1.0 O1A D:ATP501 4.4 138.0 1.0 NH2 E:ARG307 4.4 138.6 1.0 O1G D:ATP501 4.4 138.0 1.0 HH D:TYR182 4.4 138.3 1.0 HA D:THR126 4.5 137.6 1.0 HG23 D:THR126 4.6 137.6 1.0 HZ2 E:LYS213 4.6 139.3 1.0 O3A D:ATP501 4.7 138.0 1.0 HZ1 D:LYS125 4.7 136.7 1.0 NH2 D:ARG370 4.8 138.0 1.0 OE1 D:GLU185 4.8 137.9 1.0 HD2 E:LYS213 4.8 139.3 1.0 CD E:LYS213 4.9 139.3 1.0 H D:GLU185 4.9 137.9 1.0 CB D:ASP184 4.9 138.6 1.0 HZ3 D:LYS125 4.9 136.7 1.0 HG2 D:GLU185 4.9 137.9 1.0 HH21 D:ARG370 4.9 138.0 1.0 HB3 D:ASP184 5.0 138.6 1.0

A.Ghanbarpour, S.Cohen, J.H.Davis, R.T.Sauer. Cryo-Em Structure of Substrate-Free Dnclpx.Clpp Nat Commun 2023.
ISSN: ESSN 2041-1723