Magnesium in PDB 8v9r: Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx

Enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx

All present enzymatic activity of Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx:
3.4.21.92;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx (pdb code 8v9r). 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 Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx, PDB code: 8v9r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8v9r

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Magnesium binding site 1 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx


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 Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:87.2
occ:1.00
 HG1 A:THR126 1.9 90.8 1.0
O2B A:ATP500 2.0 84.9 1.0
O2G A:ATP500 2.1 84.9 1.0
OG1 A:THR126 2.3 90.8 1.0
OD2 A:ASP184 3.1 97.4 1.0
PB A:ATP500 3.3 84.9 1.0
PG A:ATP500 3.4 84.9 1.0
HB A:THR126 3.4 90.8 1.0
CB A:THR126 3.5 90.8 1.0
O1A A:ATP500 3.5 84.9 1.0
O3B A:ATP500 3.6 84.9 1.0
H A:THR126 3.8 90.8 1.0
CG A:ASP184 4.0 97.4 1.0
HG21 A:THR126 4.0 90.8 1.0
OD1 A:ASP184 4.1 97.4 1.0
HH22 B:ARG307 4.1 79.0 1.0
HE2 A:LYS125 4.2 88.7 1.0
HH A:TYR182 4.2 98.0 1.0
O3A A:ATP500 4.3 84.9 1.0
OE2 A:GLU185 4.3 96.5 1.0
HB2 A:LYS125 4.3 88.7 1.0
HH21 B:ARG307 4.3 79.0 1.0
O1G A:ATP500 4.3 84.9 1.0
CG2 A:THR126 4.4 90.8 1.0
OE2 B:GLU216 4.4 85.3 1.0
N A:THR126 4.4 90.8 1.0
O1B A:ATP500 4.4 84.9 1.0
PA A:ATP500 4.4 84.9 1.0
NH2 B:ARG307 4.4 79.0 1.0
O3G A:ATP500 4.5 84.9 1.0
HH21 A:ARG370 4.5 80.7 1.0
CA A:THR126 4.5 90.8 1.0
OE1 B:GLU216 4.6 85.3 1.0
HH22 A:ARG370 4.7 80.7 1.0
HA A:THR126 4.8 90.8 1.0
HG23 A:THR126 4.9 90.8 1.0
CD B:GLU216 4.9 85.3 1.0
NH2 A:ARG370 5.0 80.7 1.0
OH A:TYR182 5.0 98.0 1.0
HG22 A:THR126 5.0 90.8 1.0

Magnesium binding site 2 out of 4 in 8v9r

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Magnesium binding site 2 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx


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 Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:70.8
occ:1.00
 OG1 B:THR126 2.0 71.2 1.0
O3B B:ATP500 2.1 72.2 1.0
O3A B:ATP500 2.5 72.2 1.0
PB B:ATP500 2.9 72.2 1.0
CB B:THR126 3.3 71.2 1.0
HB B:THR126 3.4 71.2 1.0
H B:THR126 3.5 71.2 1.0
PG B:ATP500 3.5 72.2 1.0
O3G B:ATP500 3.6 72.2 1.0
O2B B:ATP500 3.7 72.2 1.0
OD2 B:ASP184 3.7 72.9 1.0
PA B:ATP500 3.8 72.2 1.0
HG21 B:THR126 4.0 71.2 1.0
O1A B:ATP500 4.0 72.2 1.0
O1G B:ATP500 4.0 72.2 1.0
HB2 B:LYS125 4.0 70.3 1.0
HH22 B:ARG370 4.1 70.8 1.0
O1B B:ATP500 4.1 72.2 1.0
N B:THR126 4.1 71.2 1.0
HH21 B:ARG370 4.1 70.8 1.0
HE2 B:LYS125 4.1 70.3 1.0
HH22 C:ARG307 4.1 68.5 1.0
CG2 B:THR126 4.2 71.2 1.0
HH21 C:ARG307 4.2 68.5 1.0
CA B:THR126 4.3 71.2 1.0
OD1 B:ASP184 4.3 72.9 1.0
NH2 C:ARG307 4.4 68.5 1.0
OE1 C:GLU216 4.4 72.8 1.0
CG B:ASP184 4.4 72.9 1.0
NH2 B:ARG370 4.4 70.8 1.0
OE2 B:GLU185 4.5 72.8 1.0
HG23 B:THR126 4.5 71.2 1.0
O2G B:ATP500 4.5 72.2 1.0
O5' B:ATP500 4.7 72.2 1.0
HA B:THR126 4.7 71.2 1.0
HH B:TYR182 4.7 72.5 1.0
HZ3 C:LYS213 4.8 72.0 1.0
O2A B:ATP500 4.8 72.2 1.0
CB B:LYS125 4.9 70.3 1.0
HB3 B:LYS125 5.0 70.3 1.0

Magnesium binding site 3 out of 4 in 8v9r

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Magnesium binding site 3 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx


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 Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:71.9
occ:1.00
 O2B C:ATP500 2.0 70.7 1.0
OG1 C:THR126 2.0 68.1 1.0
O2G C:ATP500 2.2 70.7 1.0
OD2 C:ASP184 3.0 70.5 1.0
PB C:ATP500 3.4 70.7 1.0
CB C:THR126 3.4 68.1 1.0
OD1 C:ASP184 3.5 70.5 1.0
PG C:ATP500 3.5 70.7 1.0
CG C:ASP184 3.6 70.5 1.0
O3B C:ATP500 3.7 70.7 1.0
HG21 C:THR126 3.7 68.1 1.0
HB C:THR126 3.7 68.1 1.0
H C:THR126 3.9 68.1 1.0
OE2 C:GLU185 4.0 70.8 1.0
CG2 C:THR126 4.0 68.1 1.0
O1A C:ATP500 4.1 70.7 1.0
HG23 C:THR126 4.2 68.1 1.0
O1G C:ATP500 4.2 70.7 1.0
HH21 D:ARG307 4.2 72.5 1.0
HE2 C:LYS125 4.3 69.0 1.0
O3A C:ATP500 4.4 70.7 1.0
HH22 D:ARG307 4.4 72.5 1.0
N C:THR126 4.4 68.1 1.0
HH C:TYR182 4.4 68.1 1.0
O1B C:ATP500 4.4 70.7 1.0
HZ3 D:LYS213 4.4 74.0 1.0
CA C:THR126 4.4 68.1 1.0
HB2 C:LYS125 4.4 69.0 1.0
HZ2 D:LYS213 4.5 74.0 1.0
NH2 D:ARG307 4.6 72.5 1.0
HH21 C:ARG370 4.6 72.2 1.0
HH22 C:ARG370 4.6 72.2 1.0
HA C:THR126 4.6 68.1 1.0
OE1 D:GLU216 4.6 74.9 1.0
O3G C:ATP500 4.7 70.7 1.0
PA C:ATP500 4.9 70.7 1.0
NZ D:LYS213 4.9 74.0 1.0
HG22 C:THR126 4.9 68.1 1.0
CD C:GLU185 4.9 70.8 1.0
NH2 C:ARG370 4.9 72.2 1.0
HG2 C:GLU185 5.0 70.8 1.0
HG2 D:LYS213 5.0 74.0 1.0

Magnesium binding site 4 out of 4 in 8v9r

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Magnesium binding site 4 out of 4 in the Cryo-Em Structure of A Proteolytic Clpxp Aaa+ Machine Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx


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 Poised to Unfold A Branched-Degron Dhfr-Ssra Substrate Bound with Mtx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:72.7
occ:1.00
 O2B D:ADP500 2.0 80.0 1.0
HG22 D:THR126 2.1 76.3 1.0
HG21 D:THR126 2.6 76.3 1.0
HB D:THR126 2.7 76.3 1.0
CG2 D:THR126 2.7 76.3 1.0
CB D:THR126 3.2 76.3 1.0
PB D:ADP500 3.4 80.0 1.0
O2A D:ADP500 3.5 80.0 1.0
H D:THR126 3.5 76.3 1.0
HG23 D:THR126 3.6 76.3 1.0
OD2 D:ASP184 3.7 80.4 1.0
O1B D:ADP500 3.8 80.0 1.0
N D:THR126 4.1 76.3 1.0
OG1 D:THR126 4.2 76.3 1.0
HB2 D:LYS125 4.2 75.3 1.0
OD1 D:ASP184 4.2 80.4 1.0
PA D:ADP500 4.2 80.0 1.0
O3A D:ADP500 4.2 80.0 1.0
CA D:THR126 4.3 76.3 1.0
HE2 D:LYS125 4.3 75.3 1.0
CG D:ASP184 4.3 80.4 1.0
O3B D:ADP500 4.5 80.0 1.0
HH22 E:ARG307 4.5 111.1 1.0
O1A D:ADP500 4.5 80.0 1.0
HH21 D:ARG370 4.6 97.9 1.0
OE2 D:GLU185 4.7 85.2 1.0
HG1 D:THR126 4.7 76.3 1.0
HZ3 E:LYS213 4.7 113.9 1.0
HA D:THR126 4.8 76.3 1.0
HH D:TYR182 4.9 72.6 1.0
HZ3 D:LYS125 5.0 75.3 1.0

Reference:

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.
Page generated: Thu Oct 31 22:15:23 2024

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