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Magnesium in PDB 2rb5: 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: 2rb5 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 / 1.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.387, 56.467, 94.447, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 13.6

Other elements in 2rb5:

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:

Tungsten (W) 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 2rb5). 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: 2rb5:

Magnesium binding site 1 out of 1 in 2rb5

Go back to Magnesium Binding Sites List in 2rb5
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:Mg701

b:8.0
occ:1.00
OD1 A:ASP211 2.1 8.3 1.0
O A:HOH807 2.1 9.6 1.0
OD1 A:ASP8 2.1 7.7 1.0
O A:ASP10 2.1 8.6 1.0
O2 A:WO6801 2.1 8.4 1.0
O A:HOH805 2.1 8.7 1.0
CG A:ASP8 3.0 7.7 1.0
CG A:ASP211 3.1 8.4 1.0
C A:ASP10 3.2 8.3 1.0
OD2 A:ASP8 3.4 7.9 1.0
OD2 A:ASP211 3.4 9.5 1.0
W A:WO6801 3.6 10.3 1.0
OD2 A:ASP215 4.0 7.8 1.0
CA A:ASP10 4.0 8.6 1.0
N A:ASP10 4.1 7.8 1.0
CB A:ASP10 4.1 10.3 1.0
OG1 A:THR12 4.2 7.9 1.0
CB A:TRP174 4.3 12.6 1.0
N A:GLY11 4.3 8.5 1.0
CB A:ASP8 4.4 7.0 1.0
CB A:ASP211 4.4 8.5 1.0
N A:GLY212 4.5 8.6 1.0
O A:TRP174 4.5 14.8 1.0
CA A:GLY11 4.5 8.6 1.0
O4 A:WO6801 4.6 9.2 1.0
N A:ASP211 4.6 7.5 1.0
O3 A:WO6801 4.6 9.4 1.0
CA A:GLY212 4.8 9.3 1.0
C A:ASP211 4.8 8.1 1.0
C A:ILE9 4.8 7.3 1.0
O1 A:WO6801 4.8 11.4 1.0
CA A:ASP211 4.8 7.9 1.0
OD1 A:ASN214 4.8 10.2 1.0
C A:GLY11 4.9 8.0 1.0
N A:THR12 4.9 7.4 1.0
CZ A:PHE16 4.9 15.2 1.0
CA A:TRP174 4.9 13.4 1.0
CE2 A:PHE16 4.9 14.9 1.0
CG A:ASP215 5.0 7.4 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 07:38:16 2020

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