Magnesium in PDB 7ljm: Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp

The structure of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp, PDB code: 7ljm was solved by A.Govande, B.Lowey, J.B.Eaglesham, A.W.Whiteley, P.J.Kranzsuch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.49 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.473, 69.781, 88.697, 90, 110.35, 90
R / Rfree (%)	22.9 / 26.5

The binding sites of Magnesium atom in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp (pdb code 7ljm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp, PDB code: 7ljm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:33.8 occ:1.00 OD1 A:ASP71 2.3 36.7 1.0 O1A A:GTP404 2.3 38.8 1.0 OD2 A:ASP69 2.4 38.5 1.0 OD2 A:ASP121 2.7 49.1 1.0 OD2 A:ASP71 2.9 37.6 1.0 CG A:ASP71 3.0 33.0 1.0 CG A:ASP69 3.0 33.7 1.0 OD1 A:ASP69 3.0 38.7 1.0 PA A:GTP404 3.5 43.0 1.0 MG A:MG402 3.6 37.8 1.0 CG A:ASP121 3.6 36.6 1.0 O2A A:GTP404 3.7 34.5 1.0 CB A:ASP121 3.9 38.0 1.0 O5' A:GTP404 4.0 39.1 1.0 C5' A:GTP404 4.1 36.5 1.0 O A:HOH530 4.4 45.0 1.0 CB A:ASP71 4.4 29.1 1.0 CB A:ASP69 4.5 27.1 1.0 O A:HOH535 4.7 28.8 1.0 O6 A:GTP405 4.7 52.6 1.0 OD1 A:ASP121 4.7 37.9 1.0 O3B A:GTP404 4.8 51.4 1.0 O3A A:GTP404 4.8 52.9 1.0 CA A:ASP71 5.0 34.1 1.0

Magnesium binding site 2 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:37.8 occ:1.00 OD2 A:ASP71 2.2 37.6 1.0 OD2 A:ASP69 2.2 38.5 1.0 O1A A:GTP404 2.5 38.8 1.0 O2B A:GTP404 2.7 37.8 1.0 O3G A:GTP404 2.8 52.2 1.0 O3B A:GTP404 2.8 51.4 1.0 PG A:GTP404 3.2 39.9 1.0 PB A:GTP404 3.2 40.3 1.0 CG A:ASP69 3.3 33.7 1.0 CG A:ASP71 3.4 33.0 1.0 O A:ASP69 3.5 39.9 1.0 MG A:MG401 3.6 33.8 1.0 O1G A:GTP404 3.6 44.9 1.0 PA A:GTP404 3.8 43.0 1.0 OG A:SER53 3.8 41.9 1.0 CB A:ASP69 3.9 27.1 1.0 O3A A:GTP404 4.0 52.9 1.0 OD1 A:ASP71 4.1 36.7 1.0 C A:ASP69 4.1 34.9 1.0 C5' A:GTP404 4.3 36.5 1.0 OD1 A:ASP69 4.4 38.7 1.0 CB A:ASP71 4.5 29.1 1.0 O1B A:GTP404 4.5 46.2 1.0 N A:ASP71 4.5 34.9 1.0 O5' A:GTP404 4.6 39.1 1.0 N A:SER53 4.6 40.3 1.0 O2G A:GTP404 4.6 52.3 1.0 CA A:ASP69 4.7 30.4 1.0 N A:VAL70 4.9 37.7 1.0 O2A A:GTP404 4.9 34.5 1.0 CB A:SER53 4.9 37.2 1.0

Magnesium binding site 3 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:69.2 occ:1.00 O2B A:GTP405 2.7 74.9 1.0 OD1 A:ASP196 2.7 55.2 1.0 OD2 A:ASP196 2.7 56.0 1.0 O3B A:GTP405 2.8 72.1 1.0 O2G A:GTP405 2.9 85.8 1.0 CG A:ASP196 3.0 55.5 1.0 PG A:GTP405 3.2 123.1 1.0 PB A:GTP405 3.3 77.4 1.0 O3G A:GTP405 3.4 84.9 1.0 NH2 A:ARG307 3.4 64.6 1.0 O1B A:GTP405 4.2 59.8 1.0 CB A:ASP196 4.5 48.0 1.0 O3A A:GTP405 4.6 63.0 1.0 O1G A:GTP405 4.7 64.7 1.0 OD2 A:ASP198 4.7 63.9 1.0 N A:ARG197 4.7 42.6 1.0 CZ A:ARG307 4.7 63.4 1.0 N A:ASP198 4.9 52.0 1.0 OE2 A:GLU199 5.0 60.9 1.0

Magnesium binding site 4 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:45.3 occ:1.00 OD2 B:ASP71 2.1 37.1 1.0 O2B B:GTP404 2.2 51.8 1.0 O1G B:GTP404 2.3 43.7 1.0 O1A B:GTP404 2.9 42.3 1.0 PB B:GTP404 3.2 48.5 1.0 CG B:ASP71 3.3 34.7 1.0 O3A B:GTP404 3.4 47.6 1.0 OD2 B:ASP69 3.4 49.1 1.0 PG B:GTP404 3.4 41.6 1.0 MG B:MG402 3.5 33.7 1.0 PA B:GTP404 3.5 44.8 1.0 O B:HOH512 3.5 38.5 1.0 O B:ASP69 3.5 48.2 1.0 O5' B:GTP404 3.6 48.6 1.0 CG B:ASP69 3.6 30.9 1.0 O3B B:GTP404 3.7 45.0 1.0 O2G B:GTP404 3.8 51.0 1.0 OG B:SER53 4.0 37.2 1.0 CB B:ASP71 4.0 36.5 1.0 CB B:ASP69 4.1 41.0 1.0 OD1 B:ASP69 4.1 45.9 1.0 C B:ASP69 4.1 38.3 1.0 N B:SER53 4.2 32.6 1.0 OD1 B:ASP71 4.3 37.7 1.0 N B:ASP71 4.4 35.0 1.0 CA B:GLY52 4.4 37.4 1.0 O1B B:GTP404 4.5 40.5 1.0 C5' B:GTP404 4.7 39.6 1.0 O3G B:GTP404 4.7 28.7 1.0 CA B:ASP69 4.8 32.0 1.0 CA B:ASP71 4.8 28.5 1.0 N B:VAL70 4.8 41.1 1.0 C B:GLY52 4.9 31.3 1.0 CB B:SER53 4.9 42.3 1.0 O2A B:GTP404 5.0 41.2 1.0 C B:VAL70 5.0 31.2 1.0

Magnesium binding site 5 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.7 occ:1.00 O1A B:GTP404 2.1 42.3 1.0 OD2 B:ASP69 2.2 49.1 1.0 OD2 B:ASP121 2.4 45.6 1.0 OD2 B:ASP71 2.4 37.1 1.0 OD1 B:ASP71 2.5 37.7 1.0 CG B:ASP71 2.8 34.7 1.0 CG B:ASP69 2.9 30.9 1.0 OD1 B:ASP69 2.9 45.9 1.0 CG B:ASP121 3.3 45.5 1.0 MG B:MG401 3.5 45.3 1.0 CB B:ASP121 3.5 34.6 1.0 PA B:GTP404 3.5 44.8 1.0 O B:HOH507 3.9 45.0 1.0 O5' B:GTP404 4.1 48.6 1.0 O2A B:GTP404 4.2 41.2 1.0 CB B:ASP71 4.3 36.5 1.0 CB B:ASP69 4.3 41.0 1.0 O1G B:GTP404 4.3 43.7 1.0 OD1 B:ASP121 4.5 46.0 1.0 O3A B:GTP404 4.6 47.6 1.0 C5' B:GTP404 4.6 39.6 1.0 O6 B:GTP405 4.8 42.7 1.0 CA B:ASP71 4.8 28.5 1.0 O2B B:GTP404 5.0 51.8 1.0

Magnesium binding site 6 out of 6 in the Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Salmonella Enterica Cd-Ntase Cdnd in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:72.5 occ:1.00 O1G B:GTP405 2.2 75.2 1.0 OD1 B:ASP196 2.7 66.4 1.0 NH2 B:ARG307 2.7 66.2 1.0 O3B B:GTP405 2.9 81.1 1.0 OD2 B:ASP196 3.0 65.6 1.0 PG B:GTP405 3.1 104.3 1.0 CG B:ASP196 3.2 62.0 1.0 O2B B:GTP405 3.2 62.1 1.0 PB B:GTP405 3.3 74.7 1.0 O1B B:GTP405 3.3 80.2 1.0 O2G B:GTP405 3.9 83.8 1.0 CZ B:ARG307 4.0 67.8 1.0 O3G B:GTP405 4.3 57.8 1.0 CB B:ASP196 4.7 51.3 1.0 NE B:ARG307 4.7 64.8 1.0 N B:ARG197 4.7 56.1 1.0 O3A B:GTP405 4.8 58.6 1.0 NH1 B:ARG307 4.9 63.0 1.0 CB B:ARG197 5.0 55.2 1.0

A.A.Govande, B.Duncan-Lowey, J.B.Eaglesham, A.T.Whiteley, P.J.Kranzusch. Molecular Basis of Cd-Ntase Nucleotide Selection in Cbass Anti-Phage Defense Cell Rep 2021.
ISSN: ESSN 2211-1247