Magnesium in PDB 9c88: Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate

All present enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate:
3.4.21.92;

The binding sites of Magnesium atom in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate (pdb code 9c88). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate, PDB code: 9c88:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate


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 A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:150.3 occ:1.00 OG1 A:THR126 2.2 160.3 1.0 O2B A:ATP500 2.2 154.5 1.0 O2G A:ATP500 2.3 155.7 1.0 OD2 A:ASP184 2.9 167.1 1.0 PG A:ATP500 3.1 158.6 1.0 O3B A:ATP500 3.2 159.3 1.0 PB A:ATP500 3.3 157.0 1.0 OD1 A:ASP184 3.4 167.2 1.0 O1G A:ATP500 3.4 152.5 1.0 CB A:THR126 3.5 160.0 1.0 HB A:THR126 3.5 159.4 1.0 CG A:ASP184 3.5 167.6 1.0 H A:THR126 3.6 156.2 1.0 OE2 A:GLU185 3.7 160.4 1.0 HH22 B:ARG307 4.0 150.0 1.0 HE2 A:LYS125 4.0 152.7 1.0 HB2 A:LYS125 4.1 151.2 1.0 HZ3 B:LYS213 4.1 160.5 1.0 O3A A:ATP500 4.1 156.3 1.0 HG21 A:THR126 4.2 159.7 1.0 HH A:TYR182 4.2 160.1 1.0 N A:THR126 4.2 156.1 1.0 O1A A:ATP500 4.4 160.1 1.0 CG2 A:THR126 4.4 159.6 1.0 HH21 A:ARG370 4.4 155.1 1.0 CA A:THR126 4.4 159.8 1.0 OE1 B:GLU216 4.5 152.5 1.0 O1B A:ATP500 4.5 151.8 1.0 HD3 B:LYS213 4.5 160.1 1.0 O3G A:ATP500 4.5 149.6 1.0 NH2 B:ARG307 4.5 150.1 1.0 HH21 B:ARG307 4.7 149.6 1.0 HA A:THR126 4.7 159.4 1.0 H A:GLY249 4.7 162.9 1.0 OE2 B:GLU216 4.7 159.5 1.0 HZ2 B:LYS213 4.7 159.6 1.0 HG23 A:THR126 4.7 159.7 1.0 CD A:GLU185 4.7 163.0 1.0 HH22 A:ARG370 4.8 155.6 1.0 NZ B:LYS213 4.9 159.1 1.0 OH A:TYR182 4.9 160.6 1.0 PA A:ATP500 4.9 155.9 1.0 NH2 A:ARG370 4.9 156.8 1.0 HZ3 A:LYS125 4.9 151.5 1.0 H A:GLU185 5.0 164.3 1.0 CE A:LYS125 5.0 153.3 1.0 HD2 B:LYS213 5.0 157.9 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate


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 A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:134.3 occ:1.00 O3G B:ATP500 2.0 140.1 1.0 OG1 B:THR126 2.1 135.2 1.0 OD2 B:ASP184 2.7 139.4 1.0 O3B B:ATP500 2.9 141.9 1.0 HH22 C:ARG307 2.9 132.0 1.0 PG B:ATP500 3.0 140.8 1.0 O2B B:ATP500 3.1 134.8 1.0 OD1 B:ASP184 3.1 136.3 1.0 CG B:ASP184 3.3 136.2 1.0 CB B:THR126 3.4 137.2 1.0 PB B:ATP500 3.4 144.8 1.0 OE2 B:GLU185 3.5 132.5 1.0 O3A B:ATP500 3.6 141.4 1.0 NH2 C:ARG307 3.6 129.7 1.0 HB B:THR126 3.6 137.8 1.0 H B:THR126 3.7 133.9 1.0 HH21 C:ARG307 3.7 131.5 1.0 O2G B:ATP500 3.8 137.9 1.0 HH B:TYR182 4.0 135.8 1.0 OE1 C:GLU216 4.0 138.1 1.0 HE2 B:LYS125 4.1 126.3 1.0 HB2 B:LYS125 4.1 127.6 1.0 HG21 B:THR126 4.1 137.6 1.0 HH21 B:ARG370 4.1 131.7 1.0 O1G B:ATP500 4.2 131.7 1.0 N B:THR126 4.2 134.7 1.0 CG2 B:THR126 4.3 137.7 1.0 CA B:THR126 4.3 134.8 1.0 CD B:GLU185 4.4 130.4 1.0 HH22 B:ARG370 4.5 133.1 1.0 HA B:THR126 4.6 134.7 1.0 HH12 C:ARG307 4.6 129.7 1.0 HG23 B:THR126 4.6 136.7 1.0 O1A B:ATP500 4.6 138.7 1.0 HD3 C:LYS213 4.6 134.8 1.0 NH2 B:ARG370 4.6 133.3 1.0 PA B:ATP500 4.7 135.9 1.0 OH B:TYR182 4.7 135.7 1.0 H B:GLU185 4.7 132.7 1.0 CZ C:ARG307 4.8 128.0 1.0 OE2 C:GLU216 4.8 140.2 1.0 CB B:ASP184 4.8 130.8 1.0 OE1 B:GLU185 4.8 127.3 1.0 CD C:GLU216 4.8 140.0 1.0 O1B B:ATP500 4.9 135.6 1.0 CB B:LYS125 5.0 127.2 1.0 CE B:LYS125 5.0 125.4 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate


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 A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:113.8 occ:1.00 OG1 C:THR126 2.1 117.0 1.0 OD2 C:ASP184 2.4 128.4 1.0 O2B C:ATP500 2.4 131.0 1.0 O3B C:ATP500 2.8 137.4 1.0 O2G C:ATP500 2.8 127.8 1.0 OD1 C:ASP184 3.1 125.9 1.0 CG C:ASP184 3.1 124.4 1.0 PB C:ATP500 3.2 129.7 1.0 PG C:ATP500 3.2 136.5 1.0 CB C:THR126 3.4 121.8 1.0 O1G C:ATP500 3.5 129.7 1.0 HB C:THR126 3.7 122.1 1.0 HH22 C:ARG370 3.7 122.3 1.0 OE2 C:GLU185 3.7 124.3 1.0 H C:THR126 3.8 118.8 1.0 HG21 C:THR126 4.0 120.8 1.0 O3A C:ATP500 4.0 123.8 1.0 HH21 D:ARG307 4.1 122.2 1.0 HD3 D:LYS213 4.1 121.8 1.0 CG2 C:THR126 4.2 121.4 1.0 OE1 D:GLU216 4.2 130.9 1.0 CD C:GLU185 4.2 122.9 1.0 HH22 D:ARG307 4.2 123.1 1.0 OE1 C:GLU185 4.2 123.3 1.0 HH C:TYR182 4.3 118.6 1.0 HG23 C:THR126 4.3 120.9 1.0 HD2 D:LYS213 4.3 121.5 1.0 N C:THR126 4.3 117.4 1.0 HE2 C:LYS125 4.3 117.1 1.0 HB2 C:LYS125 4.4 115.6 1.0 CA C:THR126 4.4 120.9 1.0 NH2 D:ARG307 4.4 122.9 1.0 O1B C:ATP500 4.4 116.2 1.0 NH2 C:ARG370 4.5 122.7 1.0 HA C:THR126 4.6 120.3 1.0 CB C:ASP184 4.6 117.5 1.0 O3G C:ATP500 4.7 123.2 1.0 CD D:LYS213 4.7 121.8 1.0 O1A C:ATP500 4.7 116.6 1.0 HH21 C:ARG370 4.7 120.4 1.0 HE3 D:LYS213 4.7 120.8 1.0 HB2 C:ASP184 4.9 116.6 1.0 H C:GLU185 4.9 119.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Translocating A Portion of A Branched-Degron Dhfr Substrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:136.3 occ:1.00 O3B D:ADP500 1.9 149.9 1.0 OG1 D:THR126 2.1 137.6 1.0 OD2 D:ASP184 3.3 150.3 1.0 PB D:ADP500 3.4 151.2 1.0 CB D:THR126 3.4 136.7 1.0 O2A D:ADP500 3.4 162.8 1.0 HB D:THR126 3.6 136.8 1.0 H D:THR126 3.6 137.0 1.0 OD1 D:ASP184 3.9 143.2 1.0 CG D:ASP184 4.0 146.8 1.0 HZ2 E:LYS213 4.1 152.2 1.0 HG21 D:THR126 4.1 134.5 1.0 HH22 E:ARG307 4.1 156.8 1.0 O3A D:ADP500 4.2 150.2 1.0 N D:THR126 4.2 137.5 1.0 PA D:ADP500 4.2 158.4 1.0 O2B D:ADP500 4.2 148.5 1.0 O1B D:ADP500 4.3 148.2 1.0 CG2 D:THR126 4.3 134.7 1.0 HH D:TYR182 4.3 133.6 1.0 HB2 D:LYS125 4.3 134.4 1.0 CA D:THR126 4.4 138.5 1.0 HG23 D:THR126 4.5 134.9 1.0 OE2 D:GLU185 4.5 151.9 1.0 HE2 D:LYS125 4.5 135.4 1.0 HH21 E:ARG307 4.5 158.3 1.0 HH21 D:ARG370 4.5 164.3 1.0 HZ1 E:LYS213 4.6 150.2 1.0 HA D:THR126 4.6 138.7 1.0 HZ3 E:LYS213 4.6 150.1 1.0 NH2 E:ARG307 4.6 154.8 1.0 NZ E:LYS213 4.6 151.3 1.0 O1A D:ADP500 4.7 144.9 1.0 HH22 D:ARG370 4.7 162.2 1.0 NH2 D:ARG370 5.0 164.2 1.0

A.Ghanbarpour, R.T.Sauer, J.H.Davis. Cryo-Em Structure of A Fully-Engaged Dhfr-Ssra Substrate and the Aaa+ Clpxp Protease To Be Published.