Magnesium in PDB 9gmz: Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook

The binding sites of Magnesium atom in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook (pdb code 9gmz). 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 in Complex with Pmctnsab Hook, PDB code: 9gmz:
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 in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:155.2 occ:1.00 O1B A:ANP401 2.0 157.2 1.0 N3B A:ANP401 2.1 156.6 1.0 O2G A:ANP401 2.2 161.7 1.0 OG1 A:THR64 2.2 146.9 1.0 PG A:ANP401 2.4 159.5 1.0 PB A:ANP401 2.5 158.7 1.0 O1G A:ANP401 2.7 153.4 1.0 O2A A:ANP401 3.2 145.7 1.0 O3A A:ANP401 3.4 150.2 1.0 CB A:THR64 3.5 151.0 1.0 PA A:ANP401 3.7 148.5 1.0 OE1 A:GLU172 3.8 164.6 1.0 O2B A:ANP401 3.8 156.5 1.0 O3G A:ANP401 3.9 153.1 1.0 NH2 B:ARG224 3.9 154.0 1.0 N A:THR64 4.0 150.1 1.0 O1A A:ANP401 4.3 155.3 1.0 CA A:THR64 4.4 152.8 1.0 CG2 A:THR64 4.5 152.1 1.0 NZ A:LYS63 5.0 152.6 1.0

Magnesium binding site 2 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:120.8 occ:1.00 O1B B:ANP401 2.0 119.7 1.0 N3B B:ANP401 2.1 128.8 1.0 O1G B:ANP401 2.3 132.3 1.0 PG B:ANP401 2.3 131.7 1.0 PB B:ANP401 2.4 132.0 1.0 O2A B:ANP401 2.4 121.3 1.0 O2G B:ANP401 2.4 117.3 1.0 OG1 B:THR64 2.9 101.3 1.0 PA B:ANP401 2.9 117.0 1.0 O3A B:ANP401 3.0 119.4 1.0 O1A B:ANP401 3.5 113.6 1.0 CB B:THR64 3.8 106.3 1.0 O3G B:ANP401 3.8 129.6 1.0 O2B B:ANP401 3.8 131.4 1.0 N B:THR64 3.9 107.8 1.0 CA B:THR64 4.5 105.0 1.0 O5' B:ANP401 4.5 110.0 1.0 N B:LYS63 4.7 109.8 1.0 CB B:LYS63 4.9 101.9 1.0 C B:LYS63 4.9 107.4 1.0 CE B:LYS63 4.9 112.5 1.0 NZ B:LYS63 5.0 119.7 1.0

Magnesium binding site 3 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:125.7 occ:1.00 O1B C:ANP401 1.9 119.4 1.0 O2G C:ANP401 2.1 130.7 1.0 N3B C:ANP401 2.1 130.7 1.0 PG C:ANP401 2.3 147.5 1.0 PB C:ANP401 2.4 125.3 1.0 O1G C:ANP401 2.5 135.9 1.0 OG1 C:THR64 3.1 114.8 1.0 OE2 C:GLU172 3.3 135.7 1.0 O2B C:ANP401 3.6 124.0 1.0 O2A C:ANP401 3.7 116.0 1.0 O3A C:ANP401 3.7 121.2 1.0 O3G C:ANP401 3.8 139.5 1.0 NZ C:LYS63 3.8 115.6 1.0 PA C:ANP401 4.1 118.2 1.0 CE C:LYS63 4.1 108.5 1.0 NH2 D:ARG224 4.3 132.3 1.0 CD C:GLU172 4.3 131.7 1.0 CB C:THR64 4.4 117.6 1.0 N C:THR64 4.6 108.6 1.0 OE1 C:GLU172 4.6 134.8 1.0 O1A C:ANP401 4.6 115.1 1.0 CD C:LYS63 4.8 97.5 1.0 OE1 D:GLN220 4.9 129.2 1.0 NE2 D:GLN220 4.9 123.2 1.0

Magnesium binding site 4 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:114.3 occ:1.00 O1B D:ANP401 2.0 112.2 1.0 O2G D:ANP401 2.0 110.6 1.0 N3B D:ANP401 2.1 123.9 1.0 PG D:ANP401 2.3 135.8 1.0 PB D:ANP401 2.4 115.6 1.0 O1G D:ANP401 2.7 129.8 1.0 OG1 D:THR64 2.7 100.1 1.0 O2B D:ANP401 3.5 112.3 1.0 O3A D:ANP401 3.7 105.6 1.0 O2A D:ANP401 3.8 106.2 1.0 O3G D:ANP401 3.8 123.2 1.0 CB D:THR64 4.0 102.3 1.0 NZ D:LYS63 4.2 110.8 1.0 PA D:ANP401 4.2 106.0 1.0 CE D:LYS63 4.3 102.9 1.0 N D:THR64 4.3 98.7 1.0 CA D:THR64 4.8 98.4 1.0 OD1 D:ASP171 4.8 115.1 1.0 CB D:LYS63 4.9 85.8 1.0 O1A D:ANP401 4.9 105.8 1.0

Magnesium binding site 5 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:121.2 occ:1.00 N3B E:ANP401 2.0 126.8 1.0 O1B E:ANP401 2.1 117.6 1.0 PG E:ANP401 2.4 132.6 1.0 PB E:ANP401 2.4 129.2 1.0 O1G E:ANP401 2.4 128.2 1.0 O2G E:ANP401 2.4 123.0 1.0 O2A E:ANP401 2.6 115.4 1.0 OG1 E:THR64 2.6 104.3 1.0 PA E:ANP401 2.9 108.6 1.0 O3A E:ANP401 3.0 121.8 1.0 O1A E:ANP401 3.3 111.5 1.0 CB E:THR64 3.5 107.0 1.0 CG E:LYS63 3.8 106.7 1.0 N E:THR64 3.8 110.7 1.0 O2B E:ANP401 3.8 123.3 1.0 O3G E:ANP401 3.8 119.7 1.0 NH2 F:ARG224 4.1 130.1 1.0 CA E:THR64 4.3 107.6 1.0 O5' E:ANP401 4.5 106.5 1.0 N E:LYS63 4.5 110.5 1.0 CD E:LYS63 4.6 108.8 1.0 CG2 E:THR64 4.7 101.9 1.0 C E:LYS63 4.8 108.8 1.0 NZ E:LYS63 4.8 112.3 1.0 CB E:LYS63 4.9 99.2 1.0 OE2 E:GLU172 4.9 135.2 1.0 CA E:LYS63 4.9 104.9 1.0

Magnesium binding site 6 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:136.3 occ:1.00 O1B F:ANP401 1.9 127.0 1.0 O1G F:ANP401 2.0 139.7 1.0 N3B F:ANP401 2.2 128.7 1.0 OG1 F:THR64 2.3 116.0 1.0 PG F:ANP401 2.3 133.6 1.0 PB F:ANP401 2.5 127.1 1.0 O2G F:ANP401 2.7 123.2 1.0 O2A F:ANP401 2.9 115.5 1.0 CB F:THR64 3.2 115.0 1.0 O3A F:ANP401 3.4 122.4 1.0 PA F:ANP401 3.5 119.4 1.0 OE2 F:GLU172 3.8 139.7 1.0 O3G F:ANP401 3.8 134.1 1.0 O2B F:ANP401 3.8 125.7 1.0 N F:THR64 3.8 117.7 1.0 NZ F:LYS63 4.1 125.3 1.0 CA F:THR64 4.1 112.4 1.0 O1A F:ANP401 4.2 120.9 1.0 NH2 G:ARG224 4.3 129.0 1.0 CG2 F:THR64 4.3 115.0 1.0 CD F:GLU172 4.9 143.0 1.0 CE F:LYS63 4.9 116.0 1.0 N F:LYS63 5.0 110.2 1.0 C F:LYS63 5.0 115.1 1.0

Magnesium binding site 7 out of 7 in the Cryoem Structure of Pmctnsc-Dsdna-Amppnp in Complex with Pmctnsab Hook


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 in Complex with Pmctnsab Hook within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:175.1 occ:1.00 O1B G:ANP401 2.0 176.1 1.0 N3B G:ANP401 2.3 177.8 1.0 O2G G:ANP401 2.3 170.5 1.0 O1G G:ANP401 2.3 169.9 1.0 PG G:ANP401 2.3 174.1 1.0 O2A G:ANP401 2.5 176.1 1.0 PB G:ANP401 2.5 183.7 1.0 OG1 G:THR64 2.7 164.6 1.0 OE2 G:GLU172 2.9 171.3 1.0 O3A G:ANP401 3.3 181.6 1.0 PA G:ANP401 3.3 181.2 1.0 CB G:THR64 3.8 164.8 1.0 O3G G:ANP401 3.9 179.5 1.0 O2B G:ANP401 4.0 179.1 1.0 CD G:GLU172 4.0 175.3 1.0 O1A G:ANP401 4.0 172.9 1.0 N G:THR64 4.1 171.5 1.0 OE1 G:GLU172 4.4 182.8 1.0 CA G:THR64 4.6 169.1 1.0 CE G:LYS63 4.7 170.4 1.0 NZ G:LYS63 4.7 173.2 1.0 O5' G:ANP401 4.8 176.9 1.0 CB G:LYS63 4.9 162.9 1.0 CG2 G:THR64 4.9 161.6 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