Magnesium in PDB 6vfs: Clpxp From Neisseria Meningitidis - Conformation A

All present enzymatic activity of Clpxp From Neisseria Meningitidis - Conformation A:
3.4.21.92;

The binding sites of Magnesium atom in the Clpxp From Neisseria Meningitidis - Conformation A (pdb code 6vfs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Clpxp From Neisseria Meningitidis - Conformation A, PDB code: 6vfs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Clpxp From Neisseria Meningitidis - Conformation A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Clpxp From Neisseria Meningitidis - Conformation A within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:50.0 occ:1.00 OG1 E:THR126 2.1 44.8 1.0 O1B E:ATP501 2.2 45.0 1.0 OD2 E:ASP184 2.7 42.8 1.0 O3G E:ATP501 3.0 45.0 1.0 CB E:THR126 3.2 44.8 1.0 HB E:THR126 3.2 44.8 1.0 HG21 E:THR126 3.4 44.8 1.0 PB E:ATP501 3.4 45.0 1.0 HH22 F:ARG306 3.5 43.8 1.0 CG E:ASP184 3.6 42.8 1.0 OD1 E:ASP184 3.8 42.8 1.0 HH21 F:ARG306 3.8 43.8 1.0 CG2 E:THR126 3.8 44.8 1.0 HZ3 F:LYS213 3.8 46.6 1.0 OE2 F:GLU216 3.8 47.0 1.0 O2B E:ATP501 3.9 45.0 1.0 HD3 F:LYS213 3.9 46.6 1.0 NH2 F:ARG306 4.0 43.8 1.0 PG E:ATP501 4.0 45.0 1.0 HE21 E:GLN185 4.0 43.0 1.0 H E:THR126 4.1 36.3 1.0 O1G E:ATP501 4.2 45.0 1.0 O3B E:ATP501 4.2 45.0 1.0 HZ2 F:LYS213 4.4 46.6 1.0 HG23 E:THR126 4.4 44.8 1.0 CA E:THR126 4.4 36.3 1.0 O1A E:ATP501 4.5 45.0 1.0 NZ F:LYS213 4.5 46.6 1.0 HG22 E:THR126 4.5 44.8 1.0 HE22 E:GLN185 4.5 43.0 1.0 HD2 F:LYS213 4.6 46.6 1.0 NE2 E:GLN185 4.6 43.0 1.0 HH E:TYR182 4.6 40.5 1.0 N E:THR126 4.6 36.3 1.0 CD F:LYS213 4.6 46.6 1.0 HA E:THR126 4.7 36.3 1.0 O3A E:ATP501 4.7 45.0 1.0 HH21 E:ARG369 4.7 42.7 1.0 HE2 E:TYR182 4.9 40.5 1.0 HE2 E:LYS125 5.0 42.0 1.0 CD F:GLU216 5.0 47.0 1.0

Magnesium binding site 2 out of 4 in the Clpxp From Neisseria Meningitidis - Conformation A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Clpxp From Neisseria Meningitidis - Conformation A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:50.0 occ:1.00 HG1 C:THR126 1.9 51.9 1.0 OG1 C:THR126 2.2 51.9 1.0 O1B C:ATP501 2.3 50.5 1.0 HB C:THR126 2.8 51.9 1.0 OD2 C:ASP184 2.8 45.2 1.0 O1G C:ATP501 2.9 50.5 1.0 CB C:THR126 3.1 51.9 1.0 PB C:ATP501 3.1 50.5 1.0 O2B C:ATP501 3.1 50.5 1.0 O3G C:ATP501 3.2 50.5 1.0 PG C:ATP501 3.5 50.5 1.0 OD1 C:ASP184 3.5 45.2 1.0 CG C:ASP184 3.5 45.2 1.0 H C:THR126 3.6 42.1 1.0 HG21 C:THR126 3.7 51.9 1.0 O3B C:ATP501 3.8 50.5 1.0 HH C:TYR182 3.8 43.6 1.0 HE21 C:GLN185 4.0 44.1 1.0 HH22 D:ARG306 4.0 41.9 1.0 HZ3 D:LYS213 4.0 45.3 1.0 CG2 C:THR126 4.0 51.9 1.0 N C:THR126 4.1 42.1 1.0 HB2 C:LYS125 4.2 46.3 1.0 CA C:THR126 4.2 42.1 1.0 HE2 C:LYS125 4.2 46.3 1.0 O1A C:ATP501 4.5 50.5 1.0 O3A C:ATP501 4.5 50.5 1.0 OH C:TYR182 4.6 43.6 1.0 HG22 C:THR126 4.6 51.9 1.0 HD3 D:LYS213 4.6 45.3 1.0 NH2 D:ARG306 4.6 41.9 1.0 NE2 C:GLN185 4.6 44.1 1.0 HA C:THR126 4.6 42.1 1.0 HH21 D:ARG306 4.6 41.9 1.0 HG23 C:THR126 4.6 51.9 1.0 HZ2 D:LYS213 4.7 45.3 1.0 HE22 C:GLN185 4.7 44.1 1.0 NZ D:LYS213 4.7 45.3 1.0 HE2 C:TYR182 4.9 43.6 1.0 O2G C:ATP501 4.9 50.5 1.0 CB C:ASP184 5.0 45.2 1.0 PA C:ATP501 5.0 50.5 1.0

Magnesium binding site 3 out of 4 in the Clpxp From Neisseria Meningitidis - Conformation A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Clpxp From Neisseria Meningitidis - Conformation A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:50.0 occ:1.00 OG1 B:THR126 2.1 54.3 1.0 O3G B:ATP501 2.2 50.5 1.0 O1B B:ATP501 2.2 50.5 1.0 OD2 B:ASP184 3.1 50.6 1.0 HB B:THR126 3.1 54.3 1.0 CB B:THR126 3.1 54.3 1.0 PG B:ATP501 3.3 50.5 1.0 O1G B:ATP501 3.5 50.5 1.0 PB B:ATP501 3.6 50.5 1.0 HG21 B:THR126 3.6 54.3 1.0 HH22 C:ARG306 3.6 43.6 1.0 H B:THR126 3.8 44.0 1.0 O3B B:ATP501 3.9 50.5 1.0 CG B:ASP184 3.9 50.6 1.0 CG2 B:THR126 3.9 54.3 1.0 OD1 B:ASP184 4.0 50.6 1.0 HZ3 C:LYS213 4.1 49.1 1.0 HE21 B:GLN185 4.2 50.5 1.0 CA B:THR126 4.3 44.0 1.0 NH2 C:ARG306 4.3 43.6 1.0 HH B:TYR182 4.3 50.6 1.0 N B:THR126 4.4 44.0 1.0 HH21 C:ARG306 4.4 43.6 1.0 HD3 C:LYS213 4.4 49.1 1.0 HG23 B:THR126 4.5 54.3 1.0 O1A B:ATP501 4.5 50.5 1.0 O3A B:ATP501 4.6 50.5 1.0 HB2 B:LYS125 4.6 49.0 1.0 O2G B:ATP501 4.6 50.5 1.0 HZ2 C:LYS213 4.6 49.1 1.0 O2B B:ATP501 4.6 50.5 1.0 HA B:THR126 4.6 44.0 1.0 HG22 B:THR126 4.7 54.3 1.0 HE2 B:LYS125 4.7 49.0 1.0 NZ C:LYS213 4.8 49.1 1.0 NE2 B:GLN185 4.9 50.5 1.0 HE22 B:GLN185 4.9 50.5 1.0 HE2 B:TYR182 4.9 50.6 1.0 HH21 B:ARG369 4.9 43.1 1.0

Magnesium binding site 4 out of 4 in the Clpxp From Neisseria Meningitidis - Conformation A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Clpxp From Neisseria Meningitidis - Conformation A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:50.0 occ:1.00 O1B D:ATP501 2.1 45.0 1.0 HG1 D:THR126 2.1 44.8 1.0 O1G D:ATP501 2.6 45.0 1.0 OG1 D:THR126 2.6 44.8 1.0 O3G D:ATP501 2.8 45.0 1.0 PB D:ATP501 2.9 45.0 1.0 O2B D:ATP501 3.1 45.0 1.0 PG D:ATP501 3.1 45.0 1.0 HH22 E:ARG306 3.1 41.9 1.0 OD2 D:ASP184 3.3 42.8 1.0 HB D:THR126 3.5 44.8 1.0 O3B D:ATP501 3.5 45.0 1.0 CB D:THR126 3.6 44.8 1.0 OD1 D:ASP184 3.9 42.8 1.0 NH2 E:ARG306 3.9 41.9 1.0 HE21 D:GLN185 3.9 43.0 1.0 CG D:ASP184 4.0 42.8 1.0 H D:THR126 4.1 36.3 1.0 HG21 D:THR126 4.1 44.8 1.0 HH21 E:ARG306 4.2 41.9 1.0 HE22 D:GLN185 4.2 43.0 1.0 HH D:TYR182 4.3 40.5 1.0 O3A D:ATP501 4.4 45.0 1.0 NE2 D:GLN185 4.4 43.0 1.0 O1A D:ATP501 4.4 45.0 1.0 HD3 E:LYS213 4.4 45.3 1.0 HH12 E:ARG306 4.5 41.9 1.0 CG2 D:THR126 4.5 44.8 1.0 HZ3 E:LYS213 4.5 45.3 1.0 O2G D:ATP501 4.6 45.0 1.0 HE2 D:LYS125 4.7 42.0 1.0 HH21 D:ARG369 4.7 42.7 1.0 N D:THR126 4.7 36.3 1.0 CA D:THR126 4.8 36.3 1.0 HB2 D:LYS125 4.8 42.0 1.0 HZ2 E:LYS213 4.9 45.3 1.0 CZ E:ARG306 4.9 41.9 1.0 PA D:ATP501 5.0 45.0 1.0

Z.A.Ripstein, S.Vahidi, W.A.Houry, J.L.Rubinstein, L.E.Kay. A Processive Rotary Mechanism Couples Substrate Unfolding and Proteolysis in the Clpxp Degradation Machinery. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 31916936
DOI: 10.7554/ELIFE.52158