Magnesium in PDB 9g0f: Cryoem Structure of Pmctnsc-Dsdna-Amppnp

The binding sites of Magnesium atom in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp (pdb code 9g0f). 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 Pmctnsc-Dsdna-Amppnp, PDB code: 9g0f:
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 Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:39.5 occ:1.00 O1B A:ANP401 1.9 40.6 1.0 N3B A:ANP401 2.0 40.6 1.0 O2G A:ANP401 2.2 40.6 1.0 PG A:ANP401 2.3 40.6 1.0 PB A:ANP401 2.4 40.6 1.0 OG1 A:THR64 2.5 192.2 1.0 O1G A:ANP401 2.7 40.6 1.0 O2A A:ANP401 3.1 40.6 1.0 OE1 A:GLU172 3.2 194.5 1.0 O2B A:ANP401 3.3 40.6 1.0 O3A A:ANP401 3.6 40.6 1.0 CB A:THR64 3.7 192.2 1.0 O3G A:ANP401 3.8 40.6 1.0 PA A:ANP401 3.9 40.6 1.0 N A:THR64 4.0 192.2 1.0 CE A:LYS63 4.1 191.0 1.0 NZ A:LYS63 4.2 191.0 1.0 CD A:GLU172 4.4 194.5 1.0 O1A A:ANP401 4.4 40.6 1.0 CA A:THR64 4.4 192.2 1.0 NH2 B:ARG224 4.5 159.4 1.0 CB A:LYS63 4.6 191.0 1.0 CD A:LYS63 4.8 191.0 1.0 CG2 A:THR64 4.8 192.2 1.0

Magnesium binding site 2 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:39.5 occ:1.00 O1B B:ANP401 1.9 40.6 1.0 N3B B:ANP401 2.0 40.6 1.0 O2G B:ANP401 2.2 40.6 1.0 PG B:ANP401 2.3 40.6 1.0 PB B:ANP401 2.4 40.6 1.0 OG1 B:THR64 2.5 123.4 1.0 O1G B:ANP401 2.7 40.6 1.0 O2A B:ANP401 3.1 40.6 1.0 OE2 B:GLU172 3.1 124.3 1.0 O2B B:ANP401 3.3 40.6 1.0 CB B:THR64 3.6 123.4 1.0 O3A B:ANP401 3.6 40.6 1.0 O3G B:ANP401 3.8 40.6 1.0 PA B:ANP401 3.9 40.6 1.0 N B:THR64 4.2 123.4 1.0 CD B:GLU172 4.2 124.3 1.0 O1A B:ANP401 4.4 40.6 1.0 CA B:THR64 4.5 123.4 1.0 NZ B:LYS63 4.6 120.3 1.0 OE1 B:GLU172 4.6 124.3 1.0 CG2 B:THR64 4.7 123.4 1.0 CE B:LYS63 4.7 120.3 1.0 NE2 C:GLN220 4.9 120.3 1.0

Magnesium binding site 3 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:39.5 occ:1.00 O1B C:ANP401 1.9 40.6 1.0 N3B C:ANP401 2.0 40.6 1.0 O2G C:ANP401 2.2 40.6 1.0 PG C:ANP401 2.3 40.6 1.0 PB C:ANP401 2.4 40.6 1.0 O1G C:ANP401 2.7 40.6 1.0 O2A C:ANP401 3.1 40.6 1.0 OG1 C:THR64 3.1 112.0 1.0 O2B C:ANP401 3.3 40.6 1.0 OE2 C:GLU172 3.6 116.6 1.0 O3A C:ANP401 3.6 40.6 1.0 CB C:LYS63 3.7 109.2 1.0 O3G C:ANP401 3.8 40.6 1.0 N C:THR64 3.8 112.0 1.0 PA C:ANP401 3.9 40.6 1.0 CB C:THR64 4.1 112.0 1.0 NH2 D:ARG224 4.4 110.5 1.0 O1A C:ANP401 4.4 40.6 1.0 CE C:LYS63 4.5 109.2 1.0 CD C:LYS63 4.6 109.2 1.0 CA C:LYS63 4.6 109.2 1.0 CA C:THR64 4.6 112.0 1.0 CD C:GLU172 4.7 116.6 1.0 N C:LYS63 4.7 109.2 1.0 C C:LYS63 4.7 109.2 1.0 CG C:LYS63 4.8 109.2 1.0 OD1 C:ASP171 4.9 120.5 1.0 NZ C:LYS63 4.9 109.2 1.0 OD2 C:ASP171 5.0 120.5 1.0

Magnesium binding site 4 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:39.5 occ:1.00 O1B D:ANP401 1.9 40.6 1.0 N3B D:ANP401 2.0 40.6 1.0 O2G D:ANP401 2.2 40.6 1.0 PG D:ANP401 2.3 40.6 1.0 PB D:ANP401 2.4 40.6 1.0 OG1 D:THR64 2.5 111.3 1.0 O1G D:ANP401 2.7 40.6 1.0 O2A D:ANP401 3.1 40.6 1.0 O2B D:ANP401 3.3 40.6 1.0 CB D:THR64 3.4 111.3 1.0 OE2 D:GLU172 3.5 115.5 1.0 O3A D:ANP401 3.6 40.6 1.0 O3G D:ANP401 3.8 40.6 1.0 PA D:ANP401 3.9 40.6 1.0 N D:THR64 4.0 111.3 1.0 CA D:THR64 4.3 111.3 1.0 O1A D:ANP401 4.4 40.6 1.0 NZ D:LYS63 4.5 108.5 1.0 CG2 D:THR64 4.5 111.3 1.0 CE D:LYS63 4.5 108.5 1.0 CD D:GLU172 4.7 115.5 1.0 NH2 E:ARG224 4.8 116.0 1.0 CB D:LYS63 5.0 108.5 1.0

Magnesium binding site 5 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:39.5 occ:1.00 O1B E:ANP401 1.9 40.6 1.0 N3B E:ANP401 2.0 40.6 1.0 O2G E:ANP401 2.2 40.6 1.0 PG E:ANP401 2.3 40.6 1.0 PB E:ANP401 2.4 40.6 1.0 OG1 E:THR64 2.5 126.4 1.0 O1G E:ANP401 2.7 40.6 1.0 O2A E:ANP401 3.1 40.6 1.0 O2B E:ANP401 3.3 40.6 1.0 CB E:THR64 3.6 126.4 1.0 O3A E:ANP401 3.6 40.6 1.0 N E:THR64 3.8 126.4 1.0 O3G E:ANP401 3.8 40.6 1.0 CD E:LYS63 3.8 125.5 1.0 PA E:ANP401 3.9 40.6 1.0 CG E:LYS63 3.9 125.5 1.0 CA E:THR64 4.3 126.4 1.0 OE2 E:GLU172 4.4 124.9 1.0 O1A E:ANP401 4.4 40.6 1.0 CE E:LYS63 4.5 125.5 1.0 NH2 F:ARG224 4.5 133.0 1.0 CB E:LYS63 4.6 125.5 1.0 C E:LYS63 4.7 125.5 1.0 NZ E:LYS63 4.7 125.5 1.0 CG2 E:THR64 4.8 126.4 1.0 CA E:LYS63 4.9 125.5 1.0 N E:LYS63 4.9 125.5 1.0

Magnesium binding site 6 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:39.5 occ:1.00 O1B F:ANP401 1.9 40.6 1.0 OG1 F:THR64 1.9 144.3 1.0 N3B F:ANP401 2.0 40.6 1.0 O2G F:ANP401 2.2 40.6 1.0 PG F:ANP401 2.3 40.6 1.0 PB F:ANP401 2.4 40.6 1.0 O1G F:ANP401 2.7 40.6 1.0 CG F:LYS63 3.0 145.8 1.0 N F:THR64 3.1 144.3 1.0 O2A F:ANP401 3.1 40.6 1.0 CB F:THR64 3.2 144.3 1.0 O2B F:ANP401 3.3 40.6 1.0 OE2 F:GLU172 3.6 154.9 1.0 CA F:THR64 3.6 144.3 1.0 O3A F:ANP401 3.6 40.6 1.0 CD F:LYS63 3.7 145.8 1.0 O3G F:ANP401 3.8 40.6 1.0 PA F:ANP401 3.9 40.6 1.0 C F:LYS63 4.0 145.8 1.0 CB F:LYS63 4.1 145.8 1.0 NZ F:LYS63 4.2 145.8 1.0 CA F:LYS63 4.3 145.8 1.0 CG2 F:THR64 4.3 144.3 1.0 N F:LYS63 4.4 145.8 1.0 O1A F:ANP401 4.4 40.6 1.0 CE F:LYS63 4.4 145.8 1.0 CD F:GLU172 4.7 154.9 1.0 C F:THR64 5.0 144.3 1.0

Magnesium binding site 7 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp


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 Pmctnsc-Dsdna-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:39.5 occ:1.00 O1B G:ANP401 1.9 40.6 1.0 N3B G:ANP401 2.0 40.6 1.0 O2G G:ANP401 2.2 40.6 1.0 PG G:ANP401 2.3 40.6 1.0 PB G:ANP401 2.4 40.6 1.0 OG1 G:THR64 2.6 251.4 1.0 O1G G:ANP401 2.7 40.6 1.0 OE2 G:GLU172 2.8 246.7 1.0 O2A G:ANP401 3.1 40.6 1.0 O2B G:ANP401 3.3 40.6 1.0 O3A G:ANP401 3.6 40.6 1.0 CD G:GLU172 3.7 246.7 1.0 O3G G:ANP401 3.8 40.6 1.0 CB G:THR64 3.9 251.4 1.0 CE G:LYS63 3.9 251.7 1.0 PA G:ANP401 3.9 40.6 1.0 NZ G:LYS63 3.9 251.7 1.0 N G:THR64 4.0 251.4 1.0 OE1 G:GLU172 4.1 246.7 1.0 CB G:LYS63 4.4 251.7 1.0 O1A G:ANP401 4.4 40.6 1.0 CA G:THR64 4.5 251.4 1.0 CD G:LYS63 4.5 251.7 1.0 C G:LYS63 4.9 251.7 1.0 CG G:GLU172 5.0 246.7 1.0 CG2 G:THR64 5.0 251.4 1.0

G.Finocchio, I.Querques, C.Chanez, K.J.Speichert, M.Jinek. Structural Basis of Tnsc Oligomerization and Transposase Recruitment in Type I-B Crispr-Associated Transposons. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40103227
DOI: 10.1093/NAR/GKAF149