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

Protein crystallography data

The structure of X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily., PDB code: 2rar 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) 28.24 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.363, 56.476, 94.421, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19

Other elements in 2rar:

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

Magnesium Binding Sites:

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 2rar). 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: 2rar:

Magnesium binding site 1 out of 1 in 2rar

Go back to Magnesium Binding Sites List in 2rar
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:14.3
occ:1.00
O A:HOH610 2.1 13.7 1.0
OD1 A:ASP8 2.1 12.3 1.0
O3 A:VN4601 2.1 13.3 1.0
OD1 A:ASP211 2.1 11.9 1.0
O A:HOH606 2.1 14.4 1.0
O A:ALA10 2.2 14.2 1.0
CG A:ASP8 3.0 11.5 1.0
CG A:ASP211 3.1 12.8 1.0
C A:ALA10 3.3 11.4 1.0
OD2 A:ASP211 3.4 15.6 1.0
V A:VN4601 3.5 15.5 1.0
OD2 A:ASP8 3.5 11.9 1.0
OD2 A:ASP215 3.9 11.4 1.0
CA A:ALA10 4.0 12.6 1.0
CB A:ALA10 4.0 15.3 1.0
N A:ALA10 4.1 11.6 1.0
CB A:TRP174 4.2 16.4 1.0
OG1 A:THR12 4.3 11.3 1.0
N A:GLY11 4.4 12.9 1.0
CB A:ASP8 4.4 11.7 1.0
CB A:ASP211 4.4 13.4 1.0
N A:GLY212 4.4 12.0 1.0
O A:TRP174 4.5 21.4 1.0
O1 A:VN4601 4.6 13.6 1.0
O2 A:VN4601 4.6 12.0 1.0
N A:ASP211 4.6 12.0 1.0
CA A:GLY11 4.7 12.4 1.0
CA A:GLY212 4.7 12.9 1.0
C A:ILE9 4.8 11.6 1.0
C A:ASP211 4.8 12.0 1.0
OD1 A:ASN214 4.9 16.1 1.0
CA A:ASP211 4.9 12.4 1.0
N A:THR12 4.9 11.1 1.0
CG A:ASP215 4.9 10.5 1.0
C A:GLY11 4.9 12.6 1.0
CA A:TRP174 5.0 17.3 1.0
CE2 A:PHE16 5.0 22.1 1.0

Reference:

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
Page generated: Mon Dec 14 07:38:13 2020

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