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Magnesium in PDB 2rbk: 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: 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

Other elements in 2rbk:

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 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 2rbk

Go back to Magnesium Binding Sites List in 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

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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