Magnesium in PDB 3vkd: Crystal Structure of MOEO5 Soaked with 3-Phosphoglycerate

The structure of Crystal Structure of MOEO5 Soaked with 3-Phosphoglycerate, PDB code: 3vkd was solved by F.Ren, T.-P.Ko, C.-H.Huang, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.66
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.778, 58.729, 59.242, 97.83, 112.62, 108.16
R / Rfree (%)	15.8 / 18.7

The binding sites of Magnesium atom in the Crystal Structure of MOEO5 Soaked with 3-Phosphoglycerate (pdb code 3vkd). 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 MOEO5 Soaked with 3-Phosphoglycerate, PDB code: 3vkd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of MOEO5 Soaked with 3-Phosphoglycerate


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 MOEO5 Soaked with 3-Phosphoglycerate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:11.6 occ:1.00 O A:PHE140 2.4 12.5 1.0 O B:PHE140 2.4 11.4 1.0 O A:ALA138 2.5 12.4 1.0 O B:ALA138 2.5 12.7 1.0 O B:LEU137 2.6 9.4 1.0 O A:LEU137 2.6 10.8 1.0 C A:ALA138 3.1 11.6 1.0 C B:ALA138 3.2 10.6 1.0 C A:PHE140 3.5 14.3 1.0 C B:PHE140 3.5 12.4 1.0 CA A:ALA138 3.5 10.5 1.0 CA B:ALA138 3.5 10.6 1.0 C B:LEU137 3.7 9.8 1.0 C A:LEU137 3.7 9.3 1.0 O A:HOH318 3.7 32.7 1.0 N A:PHE140 3.8 13.1 1.0 N B:PHE140 3.8 10.3 1.0 CA A:PHE140 4.0 12.1 1.0 N A:ALA138 4.1 9.3 1.0 CA B:PHE140 4.1 10.0 1.0 N B:ALA138 4.1 9.3 1.0 N A:ALA139 4.1 11.0 1.0 N B:ALA139 4.2 11.2 1.0 CB A:PHE140 4.2 12.4 1.0 O B:HOH414 4.2 25.0 1.0 C A:ALA139 4.3 12.6 1.0 CB B:PHE140 4.3 9.7 1.0 CD2 A:PHE140 4.3 13.7 1.0 CD2 B:PHE140 4.3 12.6 1.0 C B:ALA139 4.3 12.0 1.0 N A:PRO141 4.6 14.7 1.0 N B:PRO141 4.6 15.0 1.0 CA A:ALA139 4.6 12.5 1.0 CA B:ALA139 4.7 11.6 1.0 CD A:PRO141 4.8 16.6 1.0 CG A:PHE140 4.8 13.1 1.0 CG B:PHE140 4.8 11.1 1.0 CD B:PRO141 4.8 15.7 1.0 O A:ALA139 4.9 14.9 1.0 CB A:ALA138 4.9 11.0 1.0 CA B:LEU137 4.9 9.2 1.0 CB B:ALA138 4.9 12.0 1.0 O B:ALA139 4.9 14.8 1.0 O B:HOH418 4.9 26.4 1.0 CA A:LEU137 5.0 10.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of MOEO5 Soaked with 3-Phosphoglycerate


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 MOEO5 Soaked with 3-Phosphoglycerate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:30.9 occ:1.00 O B:HOH355 2.0 21.0 1.0 OG B:SER69 2.1 18.0 1.0 OD1 B:ASP71 2.2 24.9 1.0 O B:HOH484 2.4 33.3 1.0 OD2 B:ASP41 2.4 16.9 1.0 O2 B:PO4802 2.7 46.2 1.0 O3 B:PO4802 2.8 47.1 1.0 CG B:ASP71 3.0 23.4 1.0 CG B:ASP41 3.2 12.7 1.0 OD2 B:ASP71 3.3 26.1 1.0 P B:PO4802 3.3 46.0 1.0 CB B:SER69 3.3 12.2 1.0 OD1 B:ASP41 3.4 9.7 1.0 CA B:SER69 3.9 10.1 1.0 N B:THR70 4.0 12.3 1.0 O B:HOH485 4.1 32.5 1.0 N B:ASP71 4.1 14.8 1.0 O4 B:PO4802 4.1 46.5 1.0 O B:ASP71 4.3 16.4 1.0 CB B:ASP71 4.4 18.1 1.0 C B:SER69 4.4 9.8 1.0 NZ B:LYS44 4.6 31.6 1.0 O1 B:PO4802 4.6 43.2 1.0 CB B:ASP41 4.6 10.3 1.0 CA B:ASP71 4.7 15.3 1.0 CE B:LYS44 4.9 27.2 1.0 C B:ASP71 5.0 14.1 1.0 CA B:THR70 5.0 12.2 1.0

F.Ren, T.-P.Ko, X.Feng, C.-H.Huang, H.-C.Chan, Y.Hu, K.Wang, Y.Ma, P.-H.Liang, A.H.-J.Wang, E.Oldfield, R.-T.Guo. Insights Into the Mechanism of the Antibiotic-Synthesizing Enzyme MOEO5 From Crystal Structures of Different Complexes Angew.Chem.Int.Ed.Engl. V. 51 4157 2012.
ISSN: ISSN 1433-7851
PubMed: 22431288
DOI: 10.1002/ANIE.201108002