Magnesium in PDB 5ihp: Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium

The structure of Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium, PDB code: 5ihp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.63 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.750, 88.750, 120.310, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium (pdb code 5ihp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium, PDB code: 5ihp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:18.2 occ:1.00 O3B A:ADP1001 2.0 15.8 1.0 O A:HOH1157 2.1 17.9 1.0 O A:HOH1142 2.1 16.0 1.0 OG1 A:THR25 2.2 12.5 1.0 O A:HOH1111 2.2 15.3 1.0 O A:HOH1113 2.3 14.0 1.0 CB A:THR25 3.2 16.9 1.0 PB A:ADP1001 3.2 15.2 1.0 O2B A:ADP1001 3.4 16.0 1.0 N A:THR25 3.8 14.7 1.0 O2A A:ADP1001 4.1 16.4 1.0 OD2 A:ASP132 4.1 15.9 1.0 CA A:THR25 4.1 12.9 1.0 OD1 A:ASP132 4.2 14.8 1.0 O A:HOH1217 4.2 48.9 1.0 OD2 A:ASP48 4.2 17.4 1.0 O1B A:ADP1001 4.3 16.5 1.0 O3A A:ADP1001 4.3 13.5 1.0 O A:HOH1133 4.3 14.5 1.0 CG2 A:THR25 4.4 16.5 1.0 CB A:CYS52 4.4 18.3 1.0 PA A:ADP1001 4.5 18.4 1.0 SG A:CYS52 4.5 19.4 1.0 CG A:ASP132 4.6 15.1 1.0 CB A:LYS24 4.6 15.2 1.0 O A:HOH1104 4.7 19.6 1.0 O A:HOH1107 4.9 27.9 1.0 C A:LYS24 4.9 13.9 1.0 O1A A:ADP1001 4.9 17.6 1.0 O A:HOH1159 4.9 19.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Adp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:24.4 occ:1.00 O2B B:ADP1001 1.9 21.5 1.0 OG1 B:THR25 2.1 21.2 1.0 O B:HOH1101 2.1 26.9 1.0 O B:HOH1107 2.1 25.1 1.0 O B:HOH1131 2.2 20.7 1.0 O B:HOH1111 2.3 24.6 1.0 PB B:ADP1001 3.2 24.0 1.0 CB B:THR25 3.2 22.5 1.0 O3B B:ADP1001 3.4 22.1 1.0 N B:THR25 3.7 21.1 1.0 O2A B:ADP1001 3.8 27.9 1.0 CA B:THR25 4.0 22.8 1.0 OD2 B:ASP132 4.0 23.7 1.0 OD1 B:ASP132 4.1 18.2 1.0 O3A B:ADP1001 4.2 18.2 1.0 O1B B:ADP1001 4.2 21.8 1.0 OD2 B:ASP48 4.2 25.3 1.0 O B:HOH1112 4.2 19.6 1.0 CG2 B:THR25 4.3 25.2 1.0 PA B:ADP1001 4.3 36.9 1.0 CB B:CYS52 4.4 24.6 1.0 CB B:LYS24 4.5 20.7 1.0 CG B:ASP132 4.5 21.7 1.0 CE B:LYS24 4.5 27.4 1.0 SG B:CYS52 4.6 28.8 1.0 O1A B:ADP1001 4.7 31.3 1.0 C B:LYS24 4.8 20.0 1.0 O B:HOH1103 4.8 43.0 1.0 NZ B:LYS24 5.0 22.9 1.0

D.R.Davies, P.S.Horanyi, J.A.Abendroth, Ssgcid. Crystal Structure of Cobyrinic Acid A,C-Diamide Synthase From Mycobacterium Smegmatis with Bound Atp Analog and Magnesium To Be Published.