Magnesium in PDB 7ljl: Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp

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

Resolution Low / High (Å)	38.87 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.074, 101.372, 68.364, 90, 117.61, 90
R / Rfree (%)	15.2 / 16.5

The binding sites of Magnesium atom in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp (pdb code 7ljl). 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 the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp, PDB code: 7ljl:
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 the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.3 occ:1.00 OD1 A:ASP71 2.3 16.1 1.0 OD2 A:ASP121 2.4 33.0 1.0 O A:HOH823 2.4 24.7 1.0 O1A A:ATP405 2.4 15.2 1.0 O A:HOH687 2.5 32.8 1.0 OD2 A:ASP69 2.5 16.7 1.0 OD1 A:ASP69 2.9 20.6 1.0 CG A:ASP69 3.0 19.6 1.0 CG A:ASP71 3.3 15.9 1.0 CG A:ASP121 3.4 28.5 1.0 MG A:MG402 3.4 16.2 1.0 HB3 A:ASP121 3.5 23.9 1.0 OD2 A:ASP71 3.6 16.6 1.0 PA A:ATP405 3.6 15.3 1.0 HB2 A:ASP121 3.8 23.9 1.0 CB A:ASP121 3.8 19.9 1.0 H5'1 A:ATP405 3.8 18.3 1.0 H5'2 A:ATP405 3.9 18.3 1.0 O A:HOH666 4.1 25.8 1.0 O5' A:ATP405 4.1 14.5 1.0 O2A A:ATP405 4.2 17.7 1.0 C5' A:ATP405 4.2 15.2 1.0 O A:HOH791 4.4 40.2 1.0 OD1 A:ASP121 4.4 27.6 1.0 O A:HOH533 4.4 40.0 1.0 O A:HOH718 4.4 17.5 1.0 O A:HOH786 4.4 36.5 1.0 O A:HOH846 4.4 43.8 1.0 CB A:ASP69 4.5 22.9 1.0 O1G A:ATP405 4.5 18.4 1.0 CB A:ASP71 4.6 14.7 1.0 HB3 A:ASP69 4.8 27.4 1.0 HB2 A:ASP69 4.8 27.4 1.0 HA A:ASP71 4.8 17.1 1.0 HB3 A:ASP71 4.8 17.6 1.0 O2B A:ATP405 4.9 13.9 1.0 O3A A:ATP405 5.0 15.1 1.0 HN62 A:ATP406 5.0 20.8 1.0

Magnesium binding site 2 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.2 occ:1.00 O2B A:ATP405 2.0 13.9 1.0 OD2 A:ASP69 2.0 16.7 1.0 O1G A:ATP405 2.1 18.4 1.0 O1A A:ATP405 2.1 15.2 1.0 OD2 A:ASP71 2.1 16.6 1.0 O A:HOH588 2.1 16.1 1.0 CG A:ASP71 3.1 15.9 1.0 PB A:ATP405 3.1 15.6 1.0 PA A:ATP405 3.3 15.3 1.0 CG A:ASP69 3.3 19.6 1.0 H5'2 A:ATP405 3.3 18.3 1.0 PG A:ATP405 3.3 18.1 1.0 MG A:MG401 3.4 20.3 1.0 OD1 A:ASP71 3.4 16.1 1.0 O3A A:ATP405 3.5 15.1 1.0 H A:SER53 3.6 17.0 1.0 O3B A:ATP405 3.6 16.9 1.0 HB3 A:ASP69 3.6 27.4 1.0 O A:HOH666 3.9 25.8 1.0 OG A:SER53 4.0 16.0 1.0 CB A:ASP69 4.0 22.9 1.0 O3G A:ATP405 4.0 20.2 1.0 O A:HOH648 4.1 15.8 1.0 HA3 A:GLY52 4.1 18.1 1.0 HG A:SER53 4.2 19.2 1.0 O A:ASP69 4.2 19.1 1.0 C5' A:ATP405 4.2 15.2 1.0 OD1 A:ASP69 4.3 20.6 1.0 O5' A:ATP405 4.3 14.5 1.0 N A:SER53 4.4 14.2 1.0 O2A A:ATP405 4.4 17.7 1.0 CB A:ASP71 4.5 14.7 1.0 H A:ASP71 4.5 18.5 1.0 O1B A:ATP405 4.5 15.0 1.0 HB2 A:ASP71 4.5 17.6 1.0 O2G A:ATP405 4.6 18.7 1.0 O A:HOH823 4.6 24.7 1.0 H5'1 A:ATP405 4.6 18.3 1.0 C A:ASP69 4.6 17.3 1.0 HB3 A:SER53 4.7 19.2 1.0 HB2 A:ASP69 4.7 27.4 1.0 CB A:SER53 4.9 16.0 1.0 CA A:GLY52 4.9 15.1 1.0 N A:ASP71 4.9 15.4 1.0 HA2 A:GLY52 4.9 18.1 1.0 H A:ILE54 5.0 18.1 1.0

Magnesium binding site 3 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:21.1 occ:1.00 O1G A:ATP406 2.0 23.6 1.0 O1B A:ATP406 2.0 19.8 1.0 O A:HOH658 2.0 25.2 1.0 OD1 A:ASP196 2.1 18.3 1.0 O A:HOH549 2.1 24.9 1.0 O A:HOH702 2.1 23.1 1.0 CG A:ASP196 3.1 17.4 1.0 PB A:ATP406 3.2 18.1 1.0 HH21 A:ARG307 3.3 27.7 1.0 PG A:ATP406 3.3 25.4 1.0 OD2 A:ASP196 3.4 18.9 1.0 O3B A:ATP406 3.5 19.5 1.0 O2B A:ATP406 3.9 17.3 1.0 O A:HOH689 3.9 43.5 1.0 NH2 A:ARG307 4.0 23.1 1.0 O A:HOH654 4.0 26.3 1.0 O2G A:ATP406 4.1 40.0 1.0 H A:ARG197 4.2 20.8 1.0 HH22 A:ARG307 4.2 27.7 1.0 O A:HOH629 4.2 24.1 1.0 O A:HOH643 4.2 47.6 1.0 O3G A:ATP406 4.4 29.6 1.0 O A:HOH845 4.4 37.8 1.0 O3A A:ATP406 4.4 16.9 1.0 CB A:ASP196 4.4 17.3 1.0 HB2 A:ASP196 4.5 20.7 1.0 O A:HOH816 4.6 24.9 1.0 HB3 A:ARG197 4.7 23.5 1.0 HE A:ARG307 4.8 25.7 1.0 H A:GLU198 4.8 21.4 1.0 HA A:ASP196 4.8 19.2 1.0 HD2 A:LYS199 4.9 37.7 1.0 N A:ARG197 4.9 17.4 1.0

Magnesium binding site 4 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:19.9 occ:1.00 O A:ASN258 2.3 17.0 1.0 O A:HOH590 2.4 18.3 1.0 O A:HOH808 2.4 24.9 1.0 O A:HOH608 2.5 19.7 1.0 O A:LEU260 2.6 18.0 1.0 HZ1 A:LYS217 3.2 21.8 1.0 HH12 A:ARG281 3.3 23.4 1.0 C A:ASN258 3.4 15.7 1.0 HZ3 A:LYS217 3.5 21.8 1.0 C A:LEU260 3.5 16.8 1.0 HA A:ASP261 3.6 20.6 1.0 HA A:ASN258 3.7 19.5 1.0 HH22 A:ARG281 3.8 25.6 1.0 NZ A:LYS217 3.8 18.1 1.0 O A:GLY257 3.8 17.6 1.0 C A:ALA259 4.1 18.2 1.0 NH1 A:ARG281 4.1 19.5 1.0 CA A:ASN258 4.1 16.3 1.0 N A:LEU260 4.2 17.0 1.0 O A:ALA259 4.2 18.4 1.0 N A:ASP261 4.3 16.7 1.0 N A:ALA259 4.3 16.4 1.0 CA A:ASP261 4.3 17.1 1.0 HZ2 A:LYS217 4.4 21.8 1.0 H A:LEU260 4.4 20.4 1.0 HA A:ALA259 4.5 20.3 1.0 CA A:LEU260 4.5 17.0 1.0 HE2 A:LYS217 4.5 20.6 1.0 NH2 A:ARG281 4.5 21.3 1.0 CA A:ALA259 4.6 16.9 1.0 HH11 A:ARG281 4.6 23.4 1.0 OD1 A:ASP261 4.6 21.5 1.0 C A:GLY257 4.7 17.8 1.0 CE A:LYS217 4.8 17.1 1.0 CZ A:ARG281 4.8 19.9 1.0 N A:ASN258 4.9 17.0 1.0 H A:ASN262 5.0 21.8 1.0 HB3 A:LEU260 5.0 20.7 1.0

Magnesium binding site 5 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:22.1 occ:1.00 OD1 B:ASP71 2.3 18.7 1.0 O B:HOH1119 2.3 26.3 1.0 OD2 B:ASP121 2.4 33.5 1.0 O1A B:ATP405 2.4 17.2 1.0 O B:HOH1103 2.5 33.8 1.0 OD2 B:ASP69 2.5 19.2 1.0 OD1 B:ASP69 3.0 22.3 1.0 CG B:ASP69 3.1 21.7 1.0 CG B:ASP71 3.3 17.0 1.0 MG B:MG402 3.4 18.4 1.0 CG B:ASP121 3.4 28.1 1.0 OD2 B:ASP71 3.5 18.4 1.0 PA B:ATP405 3.6 17.9 1.0 HB3 B:ASP121 3.7 26.6 1.0 H5'2 B:ATP405 3.8 21.4 1.0 H5'1 B:ATP405 3.9 21.4 1.0 CB B:ASP121 4.0 22.1 1.0 HB2 B:ASP121 4.0 26.6 1.0 O B:HOH977 4.0 27.7 1.0 O5' B:ATP405 4.1 17.6 1.0 O2A B:ATP405 4.1 19.6 1.0 C5' B:ATP405 4.1 17.8 1.0 O B:HOH1102 4.2 35.1 1.0 O B:HOH1142 4.3 43.9 1.0 O B:HOH1107 4.3 43.9 1.0 OD1 B:ASP121 4.4 30.9 1.0 O B:HOH1025 4.4 18.9 1.0 CB B:ASP69 4.5 23.1 1.0 O1G B:ATP405 4.5 20.0 1.0 CB B:ASP71 4.6 16.5 1.0 HB3 B:ASP69 4.8 27.8 1.0 HB2 B:ASP69 4.8 27.8 1.0 HA B:ASP71 4.8 20.2 1.0 HN62 B:ATP406 4.8 21.7 1.0 HB3 B:ASP71 4.8 19.8 1.0 O3A B:ATP405 4.9 19.1 1.0 O2B B:ATP405 4.9 16.6 1.0 HN61 B:ATP406 5.0 21.7 1.0

Magnesium binding site 6 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


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 Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:18.4 occ:1.00 O1G B:ATP405 2.0 20.0 1.0 OD2 B:ASP69 2.0 19.2 1.0 O2B B:ATP405 2.1 16.6 1.0 O1A B:ATP405 2.1 17.2 1.0 O B:HOH890 2.1 17.2 1.0 OD2 B:ASP71 2.1 18.4 1.0 PB B:ATP405 3.1 17.5 1.0 CG B:ASP71 3.2 17.0 1.0 PG B:ATP405 3.3 20.7 1.0 CG B:ASP69 3.3 21.7 1.0 PA B:ATP405 3.3 17.9 1.0 H5'1 B:ATP405 3.3 21.4 1.0 MG B:MG401 3.4 22.1 1.0 O3A B:ATP405 3.5 19.1 1.0 HB3 B:ASP69 3.5 27.8 1.0 OD1 B:ASP71 3.5 18.7 1.0 O3B B:ATP405 3.6 19.1 1.0 H B:SER53 3.6 19.7 1.0 O B:HOH977 3.8 27.7 1.0 CB B:ASP69 3.9 23.1 1.0 O3G B:ATP405 4.0 23.1 1.0 OG B:SER53 4.0 18.1 1.0 HG B:SER53 4.1 21.8 1.0 O B:HOH906 4.1 16.2 1.0 HA3 B:GLY52 4.2 21.1 1.0 O B:ASP69 4.2 22.8 1.0 C5' B:ATP405 4.2 17.8 1.0 OD1 B:ASP69 4.3 22.3 1.0 O5' B:ATP405 4.3 17.6 1.0 O2A B:ATP405 4.4 19.6 1.0 N B:SER53 4.4 16.4 1.0 CB B:ASP71 4.5 16.5 1.0 O1B B:ATP405 4.5 17.1 1.0 O2G B:ATP405 4.5 20.3 1.0 H B:ASP71 4.5 19.4 1.0 O B:HOH1119 4.5 26.3 1.0 HB2 B:ASP71 4.6 19.8 1.0 HB2 B:ASP69 4.6 27.8 1.0 HB3 B:SER53 4.6 22.1 1.0 C B:ASP69 4.7 20.6 1.0 H5'2 B:ATP405 4.7 21.4 1.0 CB B:SER53 4.8 18.4 1.0 N B:ASP71 4.9 16.1 1.0 CA B:GLY52 5.0 17.6 1.0 HA2 B:GLY52 5.0 21.1 1.0 H B:ILE54 5.0 21.7 1.0 CA B:ASP69 5.0 23.1 1.0

Magnesium binding site 7 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:23.2 occ:1.00 O1G B:ATP406 1.9 27.0 1.0 O1B B:ATP406 2.0 21.2 1.0 OD1 B:ASP196 2.1 21.4 1.0 O B:HOH832 2.1 29.2 1.0 O B:HOH996 2.1 32.2 1.0 O B:HOH997 2.2 26.5 1.0 CG B:ASP196 3.1 20.7 1.0 PB B:ATP406 3.2 19.6 1.0 HH21 B:ARG307 3.2 28.7 1.0 PG B:ATP406 3.2 31.0 1.0 OD2 B:ASP196 3.4 21.5 1.0 O3B B:ATP406 3.5 22.0 1.0 O2B B:ATP406 3.9 19.9 1.0 NH2 B:ARG307 3.9 23.9 1.0 O B:HOH937 4.0 26.3 1.0 O B:HOH1077 4.0 51.2 1.0 O2G B:ATP406 4.1 45.5 1.0 HH22 B:ARG307 4.1 28.7 1.0 H B:ARG197 4.1 21.4 1.0 O B:HOH901 4.3 26.0 1.0 O B:HOH1137 4.3 42.1 1.0 O3G B:ATP406 4.3 37.4 1.0 O3A B:ATP406 4.4 17.2 1.0 CB B:ASP196 4.4 20.3 1.0 O B:HOH1153 4.5 45.2 1.0 HB2 B:ASP196 4.5 24.3 1.0 H B:GLU198 4.7 24.4 1.0 HB3 B:ARG197 4.7 25.8 1.0 O B:HOH1099 4.7 26.9 1.0 HE B:ARG307 4.7 27.5 1.0 HA B:ASP196 4.8 21.9 1.0 N B:ARG197 4.8 17.9 1.0 HD2 B:LYS199 4.9 39.6 1.0

Magnesium binding site 8 out of 8 in the Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Enterobacter Cloacae Cd-Ntase Cdnd in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:21.4 occ:1.00 O B:ASN258 2.3 17.3 1.0 O B:HOH1109 2.4 24.4 1.0 O B:HOH868 2.5 18.1 1.0 O B:HOH892 2.5 18.9 1.0 O B:LEU260 2.6 17.7 1.0 HZ1 B:LYS217 3.1 22.7 1.0 HH12 B:ARG281 3.3 23.5 1.0 HZ3 B:LYS217 3.4 22.7 1.0 C B:ASN258 3.4 17.2 1.0 HA B:ASP261 3.6 21.3 1.0 C B:LEU260 3.6 20.8 1.0 NZ B:LYS217 3.7 18.9 1.0 HA B:ASN258 3.7 21.8 1.0 HH22 B:ARG281 3.8 25.4 1.0 O B:GLY257 3.8 18.8 1.0 NH1 B:ARG281 4.1 19.6 1.0 C B:ALA259 4.1 17.4 1.0 CA B:ASN258 4.2 18.1 1.0 N B:LEU260 4.2 18.4 1.0 O B:ALA259 4.2 19.0 1.0 HZ2 B:LYS217 4.3 22.7 1.0 N B:ASP261 4.3 18.9 1.0 CA B:ASP261 4.4 17.8 1.0 N B:ALA259 4.4 17.9 1.0 H B:LEU260 4.5 22.1 1.0 NH2 B:ARG281 4.5 21.1 1.0 HE2 B:LYS217 4.5 21.4 1.0 CA B:LEU260 4.5 19.1 1.0 HA B:ALA259 4.6 22.0 1.0 OD1 B:ASP261 4.6 23.6 1.0 CA B:ALA259 4.6 18.3 1.0 HH11 B:ARG281 4.7 23.5 1.0 CE B:LYS217 4.7 17.8 1.0 CZ B:ARG281 4.8 19.7 1.0 C B:GLY257 4.8 18.2 1.0 H B:ASN262 5.0 22.4 1.0 N B:ASN258 5.0 16.9 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