Magnesium in PDB 9p8v: Structure of Cloa in Complex with Dgtp and Dttp

The binding sites of Magnesium atom in the Structure of Cloa in Complex with Dgtp and Dttp (pdb code 9p8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Cloa in Complex with Dgtp and Dttp, PDB code: 9p8v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:103.6 occ:1.00 OD1 A:ASP242 2.1 115.7 1.0 NE2 A:HIS117 2.1 106.6 1.0 NE2 A:HIS69 2.2 107.4 1.0 OD2 A:ASP118 2.2 117.7 1.0 CG A:ASP242 2.7 112.7 1.0 OD2 A:ASP242 2.7 117.7 1.0 CD2 A:HIS117 3.0 107.1 1.0 CE1 A:HIS69 3.1 109.4 1.0 CD2 A:HIS69 3.1 105.7 1.0 CG A:ASP118 3.2 121.3 1.0 CE1 A:HIS117 3.2 108.1 1.0 OD1 A:ASP118 3.8 125.0 1.0 O2A A:DGT502 4.0 141.0 1.0 CB A:ASP242 4.1 103.1 1.0 CG A:HIS117 4.2 105.1 1.0 ND1 A:HIS69 4.2 107.0 1.0 OE1 A:GLN53 4.2 120.6 1.0 CG A:HIS69 4.2 104.2 1.0 ND1 A:HIS117 4.2 109.5 1.0 CB A:ASP118 4.3 113.5 1.0 CD2 A:TYR246 4.7 116.6 1.0 CA A:ASP242 4.7 104.2 1.0 CG2 A:VAL73 4.8 102.4 1.0 O A:ASP242 5.0 111.4 1.0

Magnesium binding site 2 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:110.5 occ:1.00 NE2 B:HIS117 2.1 108.3 1.0 OD2 B:ASP118 2.1 116.1 1.0 OD1 B:ASP242 2.1 113.4 1.0 NE2 B:HIS69 2.2 109.9 1.0 CD2 B:HIS69 2.9 106.8 1.0 CG B:ASP242 2.9 112.6 1.0 CD2 B:HIS117 3.1 108.9 1.0 CE1 B:HIS117 3.1 107.1 1.0 OD2 B:ASP242 3.2 121.7 1.0 CG B:ASP118 3.2 117.7 1.0 CE1 B:HIS69 3.3 109.5 1.0 OD1 B:ASP118 3.8 121.6 1.0 CG B:HIS69 4.1 105.5 1.0 ND1 B:HIS117 4.2 107.7 1.0 CG B:HIS117 4.2 107.2 1.0 CB B:ASP118 4.3 109.6 1.0 ND1 B:HIS69 4.3 106.3 1.0 CB B:ASP242 4.3 106.4 1.0 NH1 B:ARG66 4.4 118.7 1.0 NE2 B:GLN53 4.6 123.0 1.0 CD2 B:TYR246 4.8 114.6 1.0 O5' B:DGT501 4.8 134.4 1.0 OE1 B:GLN53 4.8 119.3 1.0

Magnesium binding site 3 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:103.9 occ:1.00 OD1 C:ASP242 2.1 115.8 1.0 NE2 C:HIS117 2.1 106.8 1.0 NE2 C:HIS69 2.2 107.3 1.0 OD2 C:ASP118 2.2 117.8 1.0 CG C:ASP242 2.7 112.8 1.0 OD2 C:ASP242 2.7 117.7 1.0 CD2 C:HIS117 3.0 106.9 1.0 CE1 C:HIS69 3.1 109.3 1.0 CD2 C:HIS69 3.1 105.5 1.0 CG C:ASP118 3.2 121.3 1.0 CE1 C:HIS117 3.2 107.9 1.0 OD1 C:ASP118 3.8 124.8 1.0 O2A C:DGT502 4.0 141.1 1.0 CB C:ASP242 4.1 103.3 1.0 CG C:HIS117 4.2 105.0 1.0 ND1 C:HIS69 4.2 107.0 1.0 OE1 C:GLN53 4.2 120.5 1.0 CG C:HIS69 4.2 104.1 1.0 ND1 C:HIS117 4.2 109.2 1.0 CB C:ASP118 4.3 113.6 1.0 CD2 C:TYR246 4.7 116.6 1.0 CA C:ASP242 4.7 104.4 1.0 CG2 C:VAL73 4.8 102.5 1.0 O C:ASP242 5.0 111.3 1.0

Magnesium binding site 4 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:110.7 occ:1.00 NE2 D:HIS117 2.1 108.1 1.0 OD2 D:ASP118 2.1 115.7 1.0 OD1 D:ASP242 2.1 113.2 1.0 NE2 D:HIS69 2.2 109.9 1.0 CD2 D:HIS69 2.9 106.5 1.0 CG D:ASP242 2.9 112.5 1.0 CD2 D:HIS117 3.1 108.7 1.0 CE1 D:HIS117 3.1 106.8 1.0 OD2 D:ASP242 3.2 121.9 1.0 CG D:ASP118 3.2 117.2 1.0 CE1 D:HIS69 3.3 109.5 1.0 OD1 D:ASP118 3.8 120.8 1.0 CG D:HIS69 4.1 105.3 1.0 ND1 D:HIS117 4.2 107.5 1.0 CG D:HIS117 4.2 107.1 1.0 CB D:ASP118 4.3 109.5 1.0 ND1 D:HIS69 4.3 106.0 1.0 CB D:ASP242 4.3 106.3 1.0 NH1 D:ARG66 4.4 118.9 1.0 NE2 D:GLN53 4.6 123.2 1.0 CD2 D:TYR246 4.8 115.0 1.0 O5' D:DGT501 4.8 134.2 1.0 OE1 D:GLN53 4.8 119.6 1.0

Magnesium binding site 5 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg503 b:102.8 occ:1.00 OD1 F:ASP242 2.1 115.8 1.0 NE2 F:HIS117 2.1 106.3 1.0 NE2 F:HIS69 2.2 107.3 1.0 OD2 F:ASP118 2.2 117.6 1.0 CG F:ASP242 2.7 112.9 1.0 OD2 F:ASP242 2.7 117.8 1.0 CD2 F:HIS117 3.0 106.9 1.0 CE1 F:HIS69 3.1 109.0 1.0 CD2 F:HIS69 3.1 105.5 1.0 CG F:ASP118 3.2 121.2 1.0 CE1 F:HIS117 3.2 107.5 1.0 OD1 F:ASP118 3.8 124.5 1.0 O2A F:DGT502 4.0 140.9 1.0 CB F:ASP242 4.1 103.2 1.0 CG F:HIS117 4.2 105.0 1.0 ND1 F:HIS69 4.2 106.4 1.0 OE1 F:GLN53 4.2 120.2 1.0 CG F:HIS69 4.2 104.0 1.0 ND1 F:HIS117 4.2 109.3 1.0 CB F:ASP118 4.3 113.6 1.0 CD2 F:TYR246 4.7 116.6 1.0 CA F:ASP242 4.7 104.1 1.0 CG2 F:VAL73 4.8 102.6 1.0 O F:ASP242 5.0 111.4 1.0

Magnesium binding site 6 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg503 b:110.2 occ:1.00 NE2 G:HIS117 2.1 107.9 1.0 OD2 G:ASP118 2.1 115.7 1.0 OD1 G:ASP242 2.1 113.3 1.0 NE2 G:HIS69 2.2 109.5 1.0 CD2 G:HIS69 2.9 106.2 1.0 CG G:ASP242 2.9 112.5 1.0 CD2 G:HIS117 3.1 108.4 1.0 CE1 G:HIS117 3.1 106.7 1.0 OD2 G:ASP242 3.2 121.7 1.0 CG G:ASP118 3.2 117.0 1.0 CE1 G:HIS69 3.3 109.3 1.0 OD1 G:ASP118 3.8 120.6 1.0 CG G:HIS69 4.1 105.0 1.0 ND1 G:HIS117 4.2 107.5 1.0 CG G:HIS117 4.2 106.8 1.0 CB G:ASP118 4.3 109.0 1.0 ND1 G:HIS69 4.3 105.8 1.0 CB G:ASP242 4.3 106.3 1.0 NH1 G:ARG66 4.4 119.0 1.0 NE2 G:GLN53 4.6 123.2 1.0 CD2 G:TYR246 4.8 114.4 1.0 O5' G:DGT501 4.8 133.7 1.0 OE1 G:GLN53 4.8 119.6 1.0

Magnesium binding site 7 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg503 b:102.2 occ:1.00 OD1 J:ASP242 2.1 115.0 1.0 NE2 J:HIS117 2.1 106.8 1.0 OD2 J:ASP118 2.2 117.7 1.0 NE2 J:HIS69 2.2 107.5 1.0 CG J:ASP242 2.7 112.3 1.0 OD2 J:ASP242 2.7 117.3 1.0 CD2 J:HIS117 3.0 107.6 1.0 CE1 J:HIS69 3.1 109.1 1.0 CD2 J:HIS69 3.1 106.1 1.0 CG J:ASP118 3.2 121.3 1.0 CE1 J:HIS117 3.2 108.0 1.0 OD1 J:ASP118 3.8 124.6 1.0 O2A J:DGT502 4.0 140.4 1.0 CB J:ASP242 4.1 102.9 1.0 CG J:HIS117 4.2 105.6 1.0 ND1 J:HIS69 4.2 106.3 1.0 OE1 J:GLN53 4.2 120.8 1.0 CG J:HIS69 4.2 104.4 1.0 ND1 J:HIS117 4.3 109.5 1.0 CB J:ASP118 4.3 113.8 1.0 CD2 J:TYR246 4.7 116.1 1.0 CA J:ASP242 4.7 104.0 1.0 CG2 J:VAL73 4.8 102.4 1.0 O J:ASP242 5.0 111.2 1.0

Magnesium binding site 8 out of 8 in the Structure of Cloa in Complex with Dgtp and Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Cloa in Complex with Dgtp and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg503 b:110.5 occ:1.00 NE2 K:HIS117 2.1 107.9 1.0 OD2 K:ASP118 2.1 116.0 1.0 OD1 K:ASP242 2.1 113.3 1.0 NE2 K:HIS69 2.2 109.6 1.0 CD2 K:HIS69 2.9 106.6 1.0 CG K:ASP242 2.9 112.4 1.0 CD2 K:HIS117 3.1 108.3 1.0 CE1 K:HIS117 3.1 106.9 1.0 OD2 K:ASP242 3.2 121.5 1.0 CG K:ASP118 3.2 117.7 1.0 CE1 K:HIS69 3.3 109.2 1.0 OD1 K:ASP118 3.8 121.5 1.0 CG K:HIS69 4.1 105.1 1.0 ND1 K:HIS117 4.2 107.5 1.0 CG K:HIS117 4.2 106.7 1.0 CB K:ASP118 4.2 109.6 1.0 ND1 K:HIS69 4.3 105.9 1.0 CB K:ASP242 4.3 106.2 1.0 NH1 K:ARG66 4.4 119.0 1.0 NE2 K:GLN53 4.6 123.1 1.0 CD2 K:TYR246 4.8 114.2 1.0 O5' K:DGT501 4.8 134.3 1.0 OE1 K:GLN53 4.8 119.2 1.0

S.Yamaguchi, S.G.Fernandez, D.R.Wassarman, M.Luders, F.Schwede, P.J.Kranzusch. Activating and Inhibiting Nucleotide Signals Coordinate Bacterial Anti-Phage Defense. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 40672243
DOI: 10.1101/2025.07.09.663793