Magnesium in PDB 7ljn: Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp

The structure of Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp, PDB code: 7ljn was solved by A.Govande, B.Lowey, J.B.Eaglesham, A.T.Whiteley, P.J.Kranzusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.94 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.996, 68.687, 112.432, 90, 108.41, 90
R / Rfree (%)	19.7 / 21.8

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

Magnesium binding site 1 out of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng 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 Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.0 occ:1.00 O A:HOH737 2.0 14.0 1.0 O A:HOH685 2.1 12.3 1.0 O1A A:GTP501 2.1 11.2 1.0 O3G A:GTP501 2.1 13.8 1.0 O2B A:GTP501 2.1 11.4 1.0 OD2 A:ASP91 2.1 13.6 1.0 CG A:ASP91 3.1 13.9 1.0 PB A:GTP501 3.1 12.4 1.0 PG A:GTP501 3.3 12.1 1.0 PA A:GTP501 3.3 13.7 1.0 OD1 A:ASP91 3.4 16.3 1.0 O3B A:GTP501 3.4 11.9 1.0 O3A A:GTP501 3.5 11.6 1.0 O A:HOH761 3.8 19.5 1.0 O1G A:GTP501 4.0 12.5 1.0 O A:HOH673 4.0 13.6 1.0 O A:HOH699 4.2 13.4 1.0 OG A:SER72 4.2 12.9 1.0 O5' A:GTP501 4.2 12.6 1.0 O A:ASP89 4.2 19.9 1.0 C5' A:GTP501 4.3 14.0 1.0 O2A A:GTP501 4.4 14.5 1.0 O2G A:GTP501 4.4 13.2 1.0 N A:SER72 4.5 13.1 1.0 CB A:ASP91 4.5 12.0 1.0 O1B A:GTP501 4.5 13.6 1.0 O A:HOH862 4.5 29.2 1.0 O A:HOH668 4.6 14.9 1.0 CB A:SER72 4.7 9.7 1.0 O A:HOH983 4.8 27.9 1.0 N A:ASP91 5.0 13.5 1.0

Magnesium binding site 2 out of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng 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 Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:12.6 occ:1.00 O1A B:GTP501 2.0 11.8 1.0 O3G B:GTP501 2.1 11.2 1.0 O B:HOH744 2.1 12.3 1.0 O1B B:GTP501 2.1 11.3 1.0 O B:HOH643 2.1 14.2 1.0 OD2 B:ASP91 2.2 14.7 1.0 PB B:GTP501 3.1 11.7 1.0 CG B:ASP91 3.1 16.2 1.0 PG B:GTP501 3.2 11.0 1.0 PA B:GTP501 3.3 12.3 1.0 O3B B:GTP501 3.4 9.9 1.0 OD1 B:ASP91 3.5 19.4 1.0 O3A B:GTP501 3.5 11.4 1.0 O1G B:GTP501 4.0 12.8 1.0 O B:ASP89 4.0 23.3 1.0 O B:HOH910 4.0 22.2 1.0 O B:HOH688 4.1 14.3 1.0 OG B:SER72 4.2 12.7 1.0 O B:HOH693 4.2 11.7 1.0 O5' B:GTP501 4.2 13.2 1.0 C5' B:GTP501 4.3 12.7 1.0 O B:HOH894 4.3 36.9 1.0 O2G B:GTP501 4.4 12.7 1.0 O2A B:GTP501 4.4 14.6 1.0 N B:SER72 4.4 10.5 1.0 O2B B:GTP501 4.5 11.8 1.0 CB B:ASP91 4.5 11.0 1.0 O B:HOH685 4.6 12.4 1.0 CB B:SER72 4.7 13.1 1.0 O B:HOH1040 4.9 22.7 1.0 C B:ASP89 5.0 18.7 1.0

Magnesium binding site 3 out of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng 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 Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:11.4 occ:1.00 O2G C:GTP501 2.0 10.8 1.0 O1A C:GTP501 2.1 13.9 1.0 O C:HOH727 2.1 14.4 1.0 O C:HOH679 2.1 13.0 1.0 O2B C:GTP501 2.1 12.7 1.0 OD2 C:ASP91 2.1 13.9 1.0 CG C:ASP91 3.1 12.7 1.0 PB C:GTP501 3.1 12.4 1.0 PG C:GTP501 3.2 12.2 1.0 PA C:GTP501 3.3 11.0 1.0 OD1 C:ASP91 3.4 17.2 1.0 O3B C:GTP501 3.5 11.5 1.0 O3A C:GTP501 3.6 12.8 1.0 O C:HOH830 3.9 23.7 1.0 O3G C:GTP501 4.0 15.4 1.0 O C:HOH785 4.1 15.9 1.0 O C:ASP89 4.1 23.6 1.0 O C:HOH713 4.2 12.2 1.0 OG C:SER72 4.2 10.2 1.0 O5' C:GTP501 4.2 13.1 1.0 C5' C:GTP501 4.3 14.4 1.0 O1G C:GTP501 4.4 13.9 1.0 N C:SER72 4.5 13.5 1.0 CB C:ASP91 4.5 10.8 1.0 O2A C:GTP501 4.5 14.6 1.0 O1B C:GTP501 4.5 11.3 1.0 O C:HOH654 4.5 13.8 1.0 CB C:SER72 4.7 13.3 1.0 O C:HOH931 4.7 25.9 1.0

Magnesium binding site 4 out of 4 in the Structure of the Bradyrhizobium Diazoefficiens Cd-Ntase Cdng 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 Bradyrhizobium Diazoefficiens Cd-Ntase Cdng in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:12.8 occ:1.00 O1A D:GTP501 2.0 13.3 1.0 O2B D:GTP501 2.1 11.6 1.0 O D:HOH743 2.1 13.4 1.0 O D:HOH665 2.1 13.5 1.0 O1G D:GTP501 2.1 11.2 1.0 OD2 D:ASP91 2.1 16.2 1.0 PB D:GTP501 3.1 12.5 1.0 CG D:ASP91 3.1 17.4 1.0 PG D:GTP501 3.2 12.7 1.0 PA D:GTP501 3.3 13.1 1.0 O3B D:GTP501 3.4 9.6 1.0 OD1 D:ASP91 3.5 16.4 1.0 O3A D:GTP501 3.5 11.1 1.0 O D:HOH809 3.8 20.4 1.0 O D:HOH772 3.8 46.9 1.0 O2G D:GTP501 4.0 12.4 1.0 O D:HOH711 4.1 16.6 1.0 O D:ASP89 4.2 24.0 1.0 O D:HOH732 4.2 13.2 1.0 O5' D:GTP501 4.2 13.9 1.0 C5' D:GTP501 4.2 14.2 1.0 OG D:SER72 4.3 14.3 1.0 O2A D:GTP501 4.3 16.8 1.0 O3G D:GTP501 4.4 21.4 1.0 O1B D:GTP501 4.5 13.2 1.0 CB D:ASP91 4.5 14.1 1.0 N D:SER72 4.5 13.4 1.0 O D:HOH708 4.7 13.6 1.0 CB D:SER72 4.7 14.3 1.0 O D:HOH972 4.9 30.3 1.0 CA D:GLY71 5.0 12.0 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