Magnesium in PDB 8e91: Cryo-Em Structure of Substrate-Free Clpx.Clpp

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

The binding sites of Magnesium atom in the Cryo-Em Structure of Substrate-Free Clpx.Clpp (pdb code 8e91). 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 Clpx.Clpp, PDB code: 8e91:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of Substrate-Free Clpx.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 Clpx.Clpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:114.3 occ:1.00 O2G B:AGS501 2.0 125.1 1.0 OG1 B:THR126 2.0 125.0 1.0 O2B B:AGS501 2.1 125.1 1.0 PG B:AGS501 2.9 125.1 1.0 S1G B:AGS501 3.0 125.1 1.0 OD2 B:ASP184 3.1 124.7 1.0 HH22 C:ARG307 3.2 123.8 1.0 PB B:AGS501 3.3 125.1 1.0 CB B:THR126 3.4 125.0 1.0 H B:THR126 3.6 125.0 1.0 O3B B:AGS501 3.6 125.1 1.0 OE2 B:GLU185 3.6 121.2 1.0 HB B:THR126 3.6 125.0 1.0 OD1 B:ASP184 3.6 124.7 1.0 CG B:ASP184 3.8 124.7 1.0 O1A B:AGS501 4.0 125.1 1.0 HE2 B:LYS125 4.0 123.0 1.0 NH2 C:ARG307 4.0 123.8 1.0 HB2 B:LYS125 4.0 123.0 1.0 HH22 B:ARG370 4.0 123.6 1.0 HG21 B:THR126 4.0 125.0 1.0 O1B B:AGS501 4.1 125.1 1.0 N B:THR126 4.2 125.0 1.0 HH21 C:ARG307 4.2 123.8 1.0 O3G B:AGS501 4.2 125.1 1.0 CG2 B:THR126 4.3 125.0 1.0 CA B:THR126 4.3 125.0 1.0 HH B:TYR182 4.5 125.7 1.0 O3A B:AGS501 4.5 125.1 1.0 HG23 B:THR126 4.5 125.0 1.0 HA B:THR126 4.5 125.0 1.0 PA B:AGS501 4.6 125.1 1.0 CD B:GLU185 4.7 121.2 1.0 HH12 C:ARG307 4.7 123.8 1.0 NH2 B:ARG370 4.8 123.6 1.0 HZ2 B:LYS125 4.8 123.0 1.0 HH21 B:ARG370 4.9 123.6 1.0 CE B:LYS125 4.9 123.0 1.0 HZ1 B:LYS125 4.9 123.0 1.0 O2A B:AGS501 4.9 125.1 1.0 HE3 C:LYS213 4.9 127.3 1.0 CB B:LYS125 4.9 123.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of Substrate-Free Clpx.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 Clpx.Clpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:120.9 occ:1.00 OG1 C:THR126 2.0 132.2 1.0 O2B C:AGS501 2.0 130.1 1.0 S1G C:AGS501 2.4 130.1 1.0 HH22 D:ARG307 3.2 127.2 1.0 OD2 C:ASP184 3.2 127.5 1.0 CB C:THR126 3.3 132.2 1.0 HB C:THR126 3.4 132.2 1.0 PB C:AGS501 3.5 130.1 1.0 OE2 D:GLU216 3.5 126.9 1.0 HG21 C:THR126 3.6 132.2 1.0 PG C:AGS501 3.6 130.1 1.0 HH21 D:ARG307 3.6 127.2 1.0 NH2 D:ARG307 3.7 127.2 1.0 O2G C:AGS501 3.7 130.1 1.0 OD1 C:ASP184 3.8 127.5 1.0 OE2 C:GLU185 3.8 126.0 1.0 CG C:ASP184 3.9 127.5 1.0 HH22 C:ARG370 3.9 129.6 1.0 CG2 C:THR126 4.0 132.2 1.0 H C:THR126 4.0 132.2 1.0 O3B C:AGS501 4.1 130.1 1.0 O1B C:AGS501 4.3 130.1 1.0 CD D:GLU216 4.4 126.9 1.0 HG23 C:THR126 4.4 132.2 1.0 OE1 D:GLU216 4.4 126.9 1.0 CA C:THR126 4.4 132.2 1.0 O3A C:AGS501 4.4 130.1 1.0 N C:THR126 4.5 132.2 1.0 O1A C:AGS501 4.5 130.1 1.0 NH2 C:ARG370 4.6 129.6 1.0 HB2 C:LYS125 4.6 126.7 1.0 HH C:TYR182 4.6 131.3 1.0 HH21 C:ARG370 4.6 129.6 1.0 HA C:THR126 4.6 132.2 1.0 HE2 C:LYS125 4.7 126.7 1.0 HG22 C:THR126 4.7 132.2 1.0 HG3 D:LYS213 4.9 128.9 1.0 CZ D:ARG307 4.9 127.2 1.0 CD C:GLU185 4.9 126.0 1.0 PA C:AGS501 5.0 130.1 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of Substrate-Free Clpx.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 Clpx.Clpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:119.8 occ:1.00 O2B D:AGS501 2.0 128.5 1.0 OG1 D:THR126 2.0 130.4 1.0 O2G D:AGS501 2.0 128.5 1.0 PG D:AGS501 3.1 128.5 1.0 HB D:THR126 3.2 130.4 1.0 CB D:THR126 3.2 130.4 1.0 O3G D:AGS501 3.2 128.5 1.0 PB D:AGS501 3.4 128.5 1.0 OD2 D:ASP184 3.4 126.4 1.0 HH22 D:ARG370 3.5 129.7 1.0 O3B D:AGS501 3.7 128.5 1.0 H D:THR126 3.7 130.4 1.0 HG21 D:THR126 3.7 130.4 1.0 OE2 E:GLU216 3.8 128.2 1.0 OD1 D:ASP184 3.8 126.4 1.0 HH22 E:ARG307 3.8 129.7 1.0 OE2 D:GLU185 3.8 124.4 1.0 HH21 E:ARG307 3.9 129.7 1.0 CG D:ASP184 4.0 126.4 1.0 CG2 D:THR126 4.0 130.4 1.0 O1A D:AGS501 4.0 128.5 1.0 OE1 E:GLU216 4.1 128.2 1.0 NH2 E:ARG307 4.1 129.7 1.0 NH2 D:ARG370 4.1 129.7 1.0 HH21 D:ARG370 4.2 129.7 1.0 O1B D:AGS501 4.2 128.5 1.0 N D:THR126 4.3 130.4 1.0 CA D:THR126 4.3 130.4 1.0 CD E:GLU216 4.4 128.2 1.0 HD3 E:LYS213 4.4 127.8 1.0 O3A D:AGS501 4.4 128.5 1.0 HB2 D:LYS125 4.4 127.0 1.0 HE2 D:LYS125 4.5 127.0 1.0 HA D:THR126 4.6 130.4 1.0 HG23 D:THR126 4.6 130.4 1.0 HH D:TYR182 4.7 127.5 1.0 HG22 D:THR126 4.7 130.4 1.0 PA D:AGS501 4.7 128.5 1.0 S1G D:AGS501 4.8 128.5 1.0 CD D:GLU185 4.9 124.4 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