Magnesium in PDB 2rbk: X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily.

The structure of X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily., PDB code: 2rbk was solved by Z.Lu, D.Dunaway-Mariano, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.533, 56.356, 94.026, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.8

The structure of X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily. also contains other interesting chemical elements:

Vanadium

(V)

1 atom

The binding sites of Magnesium atom in the X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily. (pdb code 2rbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily., PDB code: 2rbk:

Magnesium binding site 1 out of 1 in the X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:9.9 occ:1.00 O2 A:VN4601 2.1 10.4 1.0 OD1 A:ASP8 2.1 10.0 1.0 OD1 A:ASP211 2.1 9.9 1.0 O A:HOH605 2.1 11.5 1.0 O A:ASP10 2.1 10.0 1.0 O A:HOH603 2.1 10.6 1.0 CG A:ASP8 3.0 8.7 1.0 CG A:ASP211 3.1 10.1 1.0 C A:ASP10 3.3 9.4 1.0 OD2 A:ASP8 3.3 10.2 1.0 OD2 A:ASP211 3.4 11.2 1.0 V A:VN4601 3.5 15.2 1.0 OD2 A:ASP215 4.0 10.1 1.0 CA A:ASP10 4.0 10.1 1.0 N A:ASP10 4.1 10.0 1.0 CB A:ASP10 4.2 11.4 1.0 CB A:TRP174 4.2 16.4 1.0 OG1 A:THR12 4.2 9.3 1.0 N A:GLY11 4.3 9.8 1.0 CB A:ASP8 4.3 8.5 1.0 CB A:ASP211 4.4 10.1 1.0 N A:GLY212 4.5 9.9 1.0 CA A:GLY11 4.6 9.7 1.0 O A:TRP174 4.6 19.5 1.0 N A:ASP211 4.6 9.0 1.0 O1 A:VN4601 4.6 18.5 1.0 O3 A:VN4601 4.6 15.0 1.0 C A:ASP211 4.8 9.8 1.0 CA A:ASP211 4.8 9.2 1.0 CA A:GLY212 4.8 10.5 1.0 C A:ILE9 4.8 8.7 1.0 OD1 A:ASN214 4.9 14.7 1.0 C A:GLY11 4.9 9.1 1.0 O A:HOH686 4.9 19.1 1.0 CZ A:PHE16 4.9 17.5 1.0 N A:THR12 4.9 8.9 1.0 CG A:ASP215 4.9 9.5 1.0 CE2 A:PHE16 4.9 19.4 1.0

Z.Lu, D.Dunaway-Mariano, K.N.Allen. The Catalytic Scaffold of the Haloalkanoic Acid Dehalogenase Enzyme Superfamily Acts As A Mold For the Trigonal Bipyramidal Transition State. Proc.Natl.Acad.Sci.Usa V. 105 5687 2008.
ISSN: ISSN 0027-8424
PubMed: 18398008
DOI: 10.1073/PNAS.0710800105