Magnesium in PDB 8e8q: Cryo-Em Structure of Substrate-Free Dnclpx.Clpp

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

The binding sites of Magnesium atom in the Cryo-Em Structure of Substrate-Free Dnclpx.Clpp (pdb code 8e8q). 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, PDB code: 8e8q:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:101.6 occ:1.00 OG1 B:THR126 2.1 104.9 1.0 O2G B:ATP501 2.1 105.9 1.0 O2B B:ATP501 2.1 105.9 1.0 PG B:ATP501 3.0 105.9 1.0 HH22 C:ARG307 3.1 102.9 1.0 OD2 B:ASP184 3.1 107.8 1.0 O3B B:ATP501 3.1 105.9 1.0 PB B:ATP501 3.1 105.9 1.0 CB B:THR126 3.4 104.9 1.0 O1G B:ATP501 3.5 105.9 1.0 HB B:THR126 3.6 104.9 1.0 OE2 B:GLU185 3.6 109.0 1.0 H B:THR126 3.7 104.9 1.0 OD1 B:ASP184 3.8 107.8 1.0 NH2 C:ARG307 3.8 102.9 1.0 HH22 B:ARG370 3.8 105.4 1.0 CG B:ASP184 3.8 107.8 1.0 O1A B:ATP501 3.8 105.9 1.0 HG21 B:THR126 3.9 104.9 1.0 HH21 C:ARG307 4.0 102.9 1.0 O3A B:ATP501 4.2 105.9 1.0 CG2 B:THR126 4.2 104.9 1.0 O1B B:ATP501 4.2 105.9 1.0 HE2 B:LYS125 4.2 104.8 1.0 HB2 B:LYS125 4.2 104.8 1.0 N B:THR126 4.3 104.9 1.0 O3G B:ATP501 4.3 105.9 1.0 CA B:THR126 4.4 104.9 1.0 PA B:ATP501 4.5 105.9 1.0 HG23 B:THR126 4.5 104.9 1.0 HH12 C:ARG307 4.5 102.9 1.0 NH2 B:ARG370 4.5 105.4 1.0 HH21 B:ARG370 4.6 105.4 1.0 HH B:TYR182 4.6 106.3 1.0 HA B:THR126 4.6 104.9 1.0 HE3 C:LYS213 4.7 108.2 1.0 CD B:GLU185 4.7 109.0 1.0 O2A B:ATP501 4.8 105.9 1.0 CZ C:ARG307 4.9 102.9 1.0 HZ2 B:LYS125 4.9 104.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:99.2 occ:1.00 O2B C:ATP501 2.0 102.6 1.0 OG1 C:THR126 2.1 100.0 1.0 OD2 C:ASP184 2.8 99.6 1.0 O1G C:ATP501 3.1 102.6 1.0 PB C:ATP501 3.3 102.6 1.0 HH22 D:ARG307 3.3 99.2 1.0 CB C:THR126 3.4 100.0 1.0 OD1 C:ASP184 3.4 99.6 1.0 CG C:ASP184 3.5 99.6 1.0 OE2 C:GLU185 3.6 100.5 1.0 HG21 C:THR126 3.6 100.0 1.0 HB C:THR126 3.6 100.0 1.0 O3B C:ATP501 3.7 102.6 1.0 PG C:ATP501 3.8 102.6 1.0 HH21 D:ARG307 3.9 99.2 1.0 NH2 D:ARG307 3.9 99.2 1.0 OE2 D:GLU216 3.9 102.8 1.0 O2G C:ATP501 3.9 102.6 1.0 CG2 C:THR126 4.0 100.0 1.0 O1B C:ATP501 4.0 102.6 1.0 H C:THR126 4.1 100.0 1.0 HH22 C:ARG370 4.3 102.2 1.0 OE1 D:GLU216 4.4 102.8 1.0 HG23 C:THR126 4.4 100.0 1.0 HH C:TYR182 4.4 100.5 1.0 CA C:THR126 4.5 100.0 1.0 O3A C:ATP501 4.5 102.6 1.0 HE2 C:LYS125 4.5 98.9 1.0 CD D:GLU216 4.5 102.8 1.0 N C:THR126 4.5 100.0 1.0 HG3 D:LYS213 4.6 103.6 1.0 HB2 C:LYS125 4.6 98.9 1.0 HA C:THR126 4.6 100.0 1.0 CD C:GLU185 4.7 100.5 1.0 HG22 C:THR126 4.8 100.0 1.0 CB C:ASP184 4.9 99.6 1.0 HG2 C:GLU185 4.9 100.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:99.8 occ:1.00 O2B D:ATP501 2.0 102.9 1.0 OG1 D:THR126 2.4 99.8 1.0 O2G D:ATP501 2.8 102.9 1.0 O3G D:ATP501 3.0 102.9 1.0 PB D:ATP501 3.2 102.9 1.0 PG D:ATP501 3.3 102.9 1.0 OE2 D:GLU185 3.3 101.5 1.0 OD2 D:ASP184 3.4 99.6 1.0 O3B D:ATP501 3.5 102.9 1.0 OD1 D:ASP184 3.5 99.6 1.0 CB D:THR126 3.6 99.8 1.0 HH22 E:ARG307 3.7 106.5 1.0 HB D:THR126 3.7 99.8 1.0 CG D:ASP184 3.8 99.6 1.0 HH22 D:ARG370 3.8 104.6 1.0 OE2 E:GLU216 3.9 108.1 1.0 HH21 E:ARG307 3.9 106.5 1.0 HG21 D:THR126 3.9 99.8 1.0 NH2 E:ARG307 4.0 106.5 1.0 O1B D:ATP501 4.0 102.9 1.0 HD3 E:LYS213 4.1 105.5 1.0 H D:THR126 4.2 99.8 1.0 OE1 E:GLU216 4.2 108.1 1.0 CG2 D:THR126 4.4 99.8 1.0 O3A D:ATP501 4.4 102.9 1.0 CD D:GLU185 4.4 101.5 1.0 CD E:GLU216 4.5 108.1 1.0 NH2 D:ARG370 4.5 104.6 1.0 HH21 D:ARG370 4.6 104.6 1.0 HE2 D:LYS125 4.6 99.7 1.0 O1G D:ATP501 4.7 102.9 1.0 CA D:THR126 4.8 99.8 1.0 HB2 D:LYS125 4.8 99.7 1.0 N D:THR126 4.8 99.8 1.0 HH D:TYR182 4.8 97.8 1.0 HZ1 D:LYS125 4.8 99.7 1.0 HG23 D:THR126 4.9 99.8 1.0 HG2 D:GLU185 4.9 101.5 1.0 HD2 E:LYS213 4.9 105.5 1.0 CD E:LYS213 5.0 105.5 1.0 HA D:THR126 5.0 99.8 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