Magnesium in PDB 8vcj: Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp

The structure of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp (pdb code 8vcj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp, PDB code: 8vcj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:63.6 occ:1.00 O3B A:ADP601 2.4 94.5 1.0 OG1 A:THR143 2.5 72.5 1.0 O2B A:ADP601 2.7 94.5 1.0 PB A:ADP601 3.0 94.5 1.0 O2A A:ADP601 3.3 94.5 1.0 CB A:THR143 3.3 72.5 1.0 O3A A:ADP601 4.0 94.5 1.0 PA A:ADP601 4.1 94.5 1.0 CG2 A:THR143 4.1 72.5 1.0 O1B A:ADP601 4.3 94.5 1.0 O1A A:ADP601 4.4 94.5 1.0 CD A:GLU233 4.4 88.0 1.0 CG A:GLU233 4.4 88.0 1.0 OE2 A:GLU233 4.5 88.0 1.0 CA A:THR143 4.6 72.5 1.0 N A:THR143 4.6 72.5 1.0 OE1 A:GLU233 4.8 88.0 1.0

Magnesium binding site 2 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:28.8 occ:1.00 O3B B:ADP601 2.0 29.8 1.0 OG1 B:THR143 3.2 21.7 1.0 PB B:ADP601 3.4 29.8 1.0 CB B:THR143 4.0 21.7 1.0 O2B B:ADP601 4.1 29.8 1.0 O1B B:ADP601 4.3 29.8 1.0 O3A B:ADP601 4.4 29.8 1.0 O1A B:ADP601 4.6 29.8 1.0 O2A B:ADP601 4.6 29.8 1.0 PA B:ADP601 4.7 29.8 1.0 OD2 B:ASP232 4.8 29.0 1.0 OE2 B:GLU233 4.8 35.5 1.0 CG2 B:THR143 4.8 21.7 1.0 OD1 B:ASP232 4.8 29.0 1.0

Magnesium binding site 3 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:24.9 occ:1.00 O2G C:AGS601 2.1 34.7 1.0 OG1 C:THR143 2.1 23.7 1.0 CB C:THR143 3.3 23.7 1.0 OD2 C:ASP232 3.6 28.2 1.0 PG C:AGS601 3.6 34.7 1.0 O3A C:AGS601 3.8 34.7 1.0 O2B C:AGS601 3.9 34.7 1.0 OD1 C:ASP232 4.0 28.2 1.0 CG2 C:THR143 4.1 23.7 1.0 CG C:ASP232 4.2 28.2 1.0 O3G C:AGS601 4.3 34.7 1.0 PB C:AGS601 4.3 34.7 1.0 O3B C:AGS601 4.4 34.7 1.0 CA C:THR143 4.4 23.7 1.0 N C:THR143 4.5 23.7 1.0 S1G C:AGS601 4.7 34.7 1.0 PA C:AGS601 4.9 34.7 1.0 OE2 C:GLU233 5.0 31.1 1.0

Magnesium binding site 4 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:64.8 occ:1.00 OE2 D:GLU233 2.0 68.9 1.0 O1B D:ADP601 2.1 85.1 1.0 OG1 D:THR143 2.5 64.7 1.0 CD D:GLU233 3.1 68.9 1.0 PB D:ADP601 3.2 85.1 1.0 OE1 D:GLU233 3.5 68.9 1.0 CB D:THR143 3.6 64.7 1.0 O3B D:ADP601 3.7 85.1 1.0 O2B D:ADP601 3.8 85.1 1.0 CG D:GLU233 4.4 68.9 1.0 OD2 D:ASP232 4.5 61.0 1.0 N D:THR143 4.5 64.7 1.0 O3A D:ADP601 4.5 85.1 1.0 CG2 D:THR143 4.5 64.7 1.0 OD1 D:ASP232 4.7 61.0 1.0 CA D:THR143 4.7 64.7 1.0 O2A D:ADP601 4.9 85.1 1.0 CG D:ASP232 4.9 61.0 1.0 O1A D:ADP601 5.0 85.1 1.0

Magnesium binding site 5 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:33.8 occ:1.00 O1B E:ADP601 2.1 30.0 1.0 PB E:ADP601 2.9 30.0 1.0 O3B E:ADP601 3.0 30.0 1.0 OG1 E:THR143 3.2 24.8 1.0 OE2 E:GLU233 3.2 33.8 1.0 O2B E:ADP601 3.6 30.0 1.0 CD E:GLU233 4.2 33.8 1.0 O3A E:ADP601 4.3 30.0 1.0 CG E:GLU233 4.3 33.8 1.0 CB E:THR143 4.3 24.8 1.0 O2A E:ADP601 4.4 30.0 1.0 NE2 E:GLN235 4.8 39.3 1.0 PA E:ADP601 4.8 30.0 1.0 OD2 E:ASP232 4.9 27.5 1.0 NZ E:LYS142 4.9 24.4 1.0

Magnesium binding site 6 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg603 b:45.4 occ:1.00 O1B F:ADP601 2.1 23.6 1.0 OG1 F:THR143 2.8 16.2 1.0 NH2 E:ARG284 2.9 52.1 0.0 PB F:ADP601 3.4 23.6 1.0 O2B F:ADP601 3.9 23.6 1.0 CB F:THR143 4.0 16.2 1.0 CZ E:ARG284 4.1 52.1 0.0 O3B F:ADP601 4.2 23.6 1.0 O3A F:ADP601 4.5 23.6 1.0 OD2 F:ASP232 4.5 33.8 1.0 O2A F:ADP601 4.6 23.6 1.0 NE E:ARG284 4.7 52.1 0.0 N F:THR143 4.7 16.2 1.0 OD1 F:ASP232 4.9 33.8 1.0 CG2 F:THR143 4.9 16.2 1.0 OE2 F:GLU233 4.9 28.0 1.0 PA F:ADP601 5.0 23.6 1.0 CA F:THR143 5.0 16.2 1.0

Magnesium binding site 7 out of 7 in the Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of the Tnsc(1-503)-Tnsd(1-318)-Dna Complex in A 7:2:1 Stoichiometry From E. Coli TN7 Bound to Atpgs and Adp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:24.3 occ:1.00 O2B G:AGS601 2.1 24.0 1.0 S1G G:AGS601 2.4 24.0 1.0 OG1 G:THR143 2.7 21.3 1.0 O2A G:AGS601 3.2 24.0 1.0 CB G:THR143 3.4 21.3 1.0 PB G:AGS601 3.6 24.0 1.0 PG G:AGS601 3.8 24.0 1.0 O3B G:AGS601 4.1 24.0 1.0 NH2 F:ARG284 4.1 23.9 1.0 CG2 G:THR143 4.2 21.3 1.0 O2G G:AGS601 4.3 24.0 1.0 PA G:AGS601 4.3 24.0 1.0 O1B G:AGS601 4.4 24.0 1.0 OD2 G:ASP232 4.5 32.0 1.0 O3A G:AGS601 4.5 24.0 1.0 CA G:THR143 4.7 21.3 1.0 N G:THR143 4.7 21.3 1.0 O1A G:AGS601 4.8 24.0 1.0 ND2 F:ASN257 5.0 26.0 1.0

Y.Shen, S.S.Krishnan, M.T.Petassi, M.A.Hancock, J.E.Peters, A.Guarne. Assembly of the TN7 Targeting Complex By A Regulated Stepwise Process. Mol.Cell V. 84 2368 2024.
ISSN: ISSN 1097-2765
PubMed: 38834067
DOI: 10.1016/J.MOLCEL.2024.05.012