Magnesium in PDB 6vfx: Clpxp From Neisseria Meningitidis - Conformation B

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

The binding sites of Magnesium atom in the Clpxp From Neisseria Meningitidis - Conformation B (pdb code 6vfx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Clpxp From Neisseria Meningitidis - Conformation B, PDB code: 6vfx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Clpxp From Neisseria Meningitidis - Conformation B


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 B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:50.0 occ:1.00 OG1 C:THR126 2.2 42.1 1.0 O3G C:ATP501 2.3 48.5 1.0 OD2 C:ASP184 2.4 36.6 1.0 O1B C:ATP501 3.0 48.5 1.0 HE21 C:GLN185 3.0 35.8 1.0 CG C:ASP184 3.2 36.6 1.0 OD1 C:ASP184 3.2 36.6 1.0 HH22 D:ARG306 3.4 34.0 1.0 CB C:THR126 3.5 42.1 1.0 HH21 D:ARG306 3.6 34.0 1.0 NE2 C:GLN185 3.6 35.8 1.0 HE22 C:GLN185 3.6 35.8 1.0 PG C:ATP501 3.7 48.5 1.0 HG21 C:THR126 3.7 42.1 1.0 HD3 D:LYS213 3.8 36.7 1.0 NH2 D:ARG306 3.9 34.0 1.0 HB C:THR126 3.9 42.1 1.0 HG23 C:THR126 4.0 42.1 1.0 CG2 C:THR126 4.0 42.1 1.0 OE1 D:GLU216 4.1 37.2 1.0 H C:THR126 4.1 42.1 1.0 HH C:TYR182 4.2 35.4 1.0 PB C:ATP501 4.2 48.5 1.0 HZ3 D:LYS213 4.2 36.7 1.0 O1G C:ATP501 4.2 48.5 1.0 O3B C:ATP501 4.4 48.5 1.0 HD2 D:LYS213 4.4 36.7 1.0 HE2 C:LYS125 4.5 37.5 1.0 CD D:LYS213 4.5 36.7 1.0 HZ2 D:LYS213 4.6 36.7 1.0 HG2 C:GLN185 4.6 35.8 1.0 CA C:THR126 4.6 42.1 1.0 CB C:ASP184 4.7 36.6 1.0 N C:THR126 4.7 42.1 1.0 HH21 C:ARG369 4.7 34.9 1.0 HB2 C:LYS125 4.7 37.5 1.0 HA C:THR126 4.8 42.1 1.0 O1A C:ATP501 4.8 48.5 1.0 NZ D:LYS213 4.8 36.7 1.0 O2G C:ATP501 4.8 48.5 1.0 CD C:GLN185 4.8 35.8 1.0 H C:GLN185 4.8 35.8 1.0 HE2 C:TYR182 4.9 35.4 1.0 HB3 C:ASP184 4.9 36.6 1.0 HB2 C:ASP184 4.9 36.6 1.0 HG22 C:THR126 5.0 42.1 1.0 CD D:GLU216 5.0 37.2 1.0 OE2 D:GLU216 5.0 37.2 1.0 OH C:TYR182 5.0 35.4 1.0

Magnesium binding site 2 out of 5 in the Clpxp From Neisseria Meningitidis - Conformation B


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 B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:50.0 occ:1.00 OG1 B:THR126 2.2 44.0 1.0 O3G B:ATP501 2.3 48.5 1.0 O1B B:ATP501 2.6 48.5 1.0 OD2 B:ASP184 2.8 41.0 1.0 HH22 C:ARG306 3.2 35.3 1.0 HH21 C:ARG306 3.3 35.3 1.0 CB B:THR126 3.3 44.0 1.0 HB B:THR126 3.4 44.0 1.0 CG B:ASP184 3.6 41.0 1.0 NH2 C:ARG306 3.6 35.3 1.0 OD1 B:ASP184 3.6 41.0 1.0 HE21 B:GLN185 3.7 41.0 1.0 PG B:ATP501 3.7 48.5 1.0 HE22 B:GLN185 3.7 41.0 1.0 HG21 B:THR126 3.8 44.0 1.0 H B:THR126 3.9 44.0 1.0 PB B:ATP501 3.9 48.5 1.0 NE2 B:GLN185 3.9 41.0 1.0 HZ3 C:LYS213 4.0 39.9 1.0 HD3 C:LYS213 4.0 39.9 1.0 OE1 C:GLU216 4.1 39.2 1.0 O3B B:ATP501 4.1 48.5 1.0 CG2 B:THR126 4.2 44.0 1.0 O1A B:ATP501 4.2 48.5 1.0 HH21 B:ARG369 4.2 35.0 1.0 HH B:TYR182 4.2 41.0 1.0 HZ2 C:LYS213 4.4 39.9 1.0 O1G B:ATP501 4.4 48.5 1.0 HD2 C:LYS213 4.4 39.9 1.0 CA B:THR126 4.5 44.0 1.0 N B:THR126 4.5 44.0 1.0 HE2 B:LYS125 4.6 39.7 1.0 NZ C:LYS213 4.6 39.9 1.0 HB2 B:LYS125 4.6 39.7 1.0 CD C:LYS213 4.7 39.9 1.0 HA B:THR126 4.7 44.0 1.0 OE2 C:GLU216 4.7 39.2 1.0 HH22 B:ARG369 4.7 35.0 1.0 HG23 B:THR126 4.8 44.0 1.0 O2G B:ATP501 4.8 48.5 1.0 NH2 B:ARG369 4.8 35.0 1.0 HG22 B:THR126 4.8 44.0 1.0 CD C:GLU216 4.8 39.2 1.0 O2B B:ATP501 4.9 48.5 1.0 CZ C:ARG306 4.9 35.3 1.0 O3A B:ATP501 4.9 48.5 1.0 CD B:GLN185 4.9 41.0 1.0

Magnesium binding site 3 out of 5 in the Clpxp From Neisseria Meningitidis - Conformation B


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 B within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:50.0 occ:1.00 OG1 E:THR126 2.1 41.7 1.0 O3G E:ATP501 2.3 44.5 1.0 O1B E:ATP501 2.5 44.5 1.0 OD2 E:ASP184 3.0 42.8 1.0 CB E:THR126 3.2 41.7 1.0 HB E:THR126 3.3 41.7 1.0 HG21 E:THR126 3.4 41.7 1.0 O1A E:ATP501 3.6 44.5 1.0 HH22 E:ARG369 3.6 55.1 1.0 PG E:ATP501 3.7 44.5 1.0 CG2 E:THR126 3.8 41.7 1.0 PB E:ATP501 3.8 44.5 1.0 O3B E:ATP501 3.9 44.5 1.0 HG23 E:THR126 4.0 41.7 1.0 H E:THR126 4.0 41.7 1.0 CG E:ASP184 4.0 42.8 1.0 NH2 E:ARG369 4.3 55.1 1.0 HH21 E:ARG369 4.3 55.1 1.0 OD1 E:ASP184 4.4 42.8 1.0 CA E:THR126 4.5 41.7 1.0 HE21 E:GLN185 4.5 42.2 1.0 N E:THR126 4.6 41.7 1.0 O3A E:ATP501 4.6 44.5 1.0 O1G E:ATP501 4.6 44.5 1.0 O2G E:ATP501 4.6 44.5 1.0 PA E:ATP501 4.7 44.5 1.0 HG22 E:THR126 4.7 41.7 1.0 HA E:THR126 4.8 41.7 1.0 HH E:TYR182 4.8 38.9 1.0 HG2 F:GLU302 4.8 68.3 1.0 O2B E:ATP501 4.9 44.5 1.0

Magnesium binding site 4 out of 5 in the Clpxp From Neisseria Meningitidis - Conformation B


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 B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:50.0 occ:1.00 OG1 D:THR126 2.2 36.3 1.0 O3G D:ATP501 2.3 43.2 1.0 OD2 D:ASP184 2.5 34.7 1.0 O1B D:ATP501 2.9 43.2 1.0 HE21 D:GLN185 3.1 34.8 1.0 CG D:ASP184 3.2 34.7 1.0 OD1 D:ASP184 3.3 34.7 1.0 HH22 E:ARG306 3.5 35.5 1.0 CB D:THR126 3.5 36.3 1.0 HE22 D:GLN185 3.5 34.8 1.0 NE2 D:GLN185 3.6 34.8 1.0 HH21 E:ARG306 3.7 35.5 1.0 OE2 E:GLU216 3.7 38.1 1.0 PG D:ATP501 3.7 43.2 1.0 HG21 D:THR126 3.8 36.3 1.0 HB D:THR126 3.9 36.3 1.0 HH D:TYR182 3.9 32.9 1.0 NH2 E:ARG306 3.9 35.5 1.0 HZ3 E:LYS213 4.0 37.8 1.0 HG23 D:THR126 4.0 36.3 1.0 CG2 D:THR126 4.0 36.3 1.0 H D:THR126 4.1 36.3 1.0 PB D:ATP501 4.1 43.2 1.0 O1G D:ATP501 4.2 43.2 1.0 O3B D:ATP501 4.3 43.2 1.0 HE2 D:LYS125 4.4 34.1 1.0 HZ2 E:LYS213 4.4 37.8 1.0 CA D:THR126 4.6 36.3 1.0 HH21 D:ARG369 4.6 34.6 1.0 NZ E:LYS213 4.6 37.8 1.0 N D:THR126 4.6 36.3 1.0 HD3 E:LYS213 4.7 37.8 1.0 HB2 D:LYS125 4.7 34.1 1.0 CB D:ASP184 4.7 34.7 1.0 OH D:TYR182 4.7 32.9 1.0 HA D:THR126 4.7 36.3 1.0 CD E:GLU216 4.7 38.1 1.0 O1A D:ATP501 4.7 43.2 1.0 HG2 D:GLN185 4.7 34.8 1.0 CD D:GLN185 4.8 34.8 1.0 HE2 D:TYR182 4.8 32.9 1.0 O2G D:ATP501 4.9 43.2 1.0 H D:GLN185 4.9 34.8 1.0 HB2 D:ASP184 5.0 34.7 1.0 OE1 E:GLU216 5.0 38.1 1.0 O2B D:ATP501 5.0 43.2 1.0 HB3 D:ASP184 5.0 34.7 1.0 HG22 D:THR126 5.0 36.3 1.0

Magnesium binding site 5 out of 5 in the Clpxp From Neisseria Meningitidis - Conformation B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Clpxp From Neisseria Meningitidis - Conformation B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.0 occ:1.00 OG1 A:THR126 2.2 61.6 1.0 O3G A:ATP501 2.3 57.0 1.0 O1B A:ATP501 2.4 57.0 1.0 OD2 A:ASP184 2.6 66.8 1.0 OD1 A:ASP184 3.2 66.8 1.0 CG A:ASP184 3.2 66.8 1.0 PG A:ATP501 3.5 57.0 1.0 CB A:THR126 3.6 61.6 1.0 PB A:ATP501 3.6 57.0 1.0 HG21 A:THR126 3.9 61.6 1.0 HH22 B:ARG306 3.9 47.3 1.0 O1G A:ATP501 3.9 57.0 1.0 HB A:THR126 3.9 61.6 1.0 O3B A:ATP501 4.0 57.0 1.0 H A:THR126 4.0 61.6 1.0 HH A:TYR182 4.0 67.4 1.0 CG2 A:THR126 4.1 61.6 1.0 HG23 A:THR126 4.2 61.6 1.0 HE2 A:LYS125 4.3 61.5 1.0 HH21 B:ARG306 4.3 47.3 1.0 O2B A:ATP501 4.3 57.0 1.0 HB2 A:LYS125 4.4 61.5 1.0 NH2 B:ARG306 4.4 47.3 1.0 O1A A:ATP501 4.5 57.0 1.0 N A:THR126 4.5 61.6 1.0 CA A:THR126 4.5 61.6 1.0 CB A:ASP184 4.6 66.8 1.0 HA A:THR126 4.7 61.6 1.0 OH A:TYR182 4.8 67.4 1.0 HB2 A:ASP184 4.8 66.8 1.0 O2G A:ATP501 4.8 57.0 1.0 HH21 A:ARG369 4.8 50.9 1.0 O3A A:ATP501 4.8 57.0 1.0 HB3 A:ASP184 4.9 66.8 1.0 HG3 A:GLN185 4.9 64.1 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