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Vanadium 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:

Magnesium (Mg) 1 atom

Vanadium Binding Sites:

The binding sites of Vanadium 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 Vanadium atom.
In total only one binding site of Vanadium was determined in the X-Ray Crystallographic Structures Show Conservation of A Trigonal- Bipyramidal Intermediate in A Phosphoryl-Transfer Superfamily., PDB code: 2rbk:

Vanadium binding site 1 out of 1 in 2rbk

Go back to Vanadium Binding Sites List in 2rbk
Vanadium 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 Vanadium with other atoms in the V 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:V601

b:15.2
occ:1.00
V A:VN4601 0.0 15.2 1.0
O1 A:VN4601 1.7 18.5 1.0
O2 A:VN4601 1.8 10.4 1.0
O3 A:VN4601 1.8 15.0 1.0
OD2 A:ASP8 2.0 10.2 1.0
O A:HOH686 2.1 19.1 1.0
CG A:ASP8 3.1 8.7 1.0
OD1 A:ASP8 3.5 10.0 1.0
MG A:MG501 3.5 9.9 1.0
N A:ASP10 3.7 10.0 1.0
NZ A:LYS188 3.7 10.3 1.0
OG1 A:THR43 3.7 9.5 1.0
O A:HOH603 3.9 10.6 1.0
N A:ILE9 3.9 8.4 1.0
OD2 A:ASP10 3.9 13.3 1.0
N A:GLY44 4.1 9.3 1.0
CB A:ASP10 4.2 11.4 1.0
CG A:TRP174 4.2 16.7 1.0
CB A:TRP174 4.2 16.4 1.0
CA A:THR43 4.3 8.4 1.0
CB A:ASP8 4.3 8.5 1.0
CD2 A:TRP174 4.4 16.5 1.0
CB A:THR43 4.4 8.9 1.0
O A:ASP10 4.4 10.0 1.0
CA A:ASP10 4.5 10.1 1.0
C A:ILE9 4.5 8.7 1.0
ND2 A:ASN214 4.5 13.0 1.0
CG A:ASP10 4.5 12.6 1.0
CA A:ILE9 4.6 9.2 1.0
CE3 A:TRP174 4.6 16.7 1.0
CA A:ASP8 4.7 8.2 1.0
CB A:ILE9 4.8 9.8 1.0
CD1 A:TRP174 4.8 16.7 1.0
C A:ASP8 4.8 8.4 1.0
C A:THR43 4.8 8.7 1.0
O A:ALA42 4.8 9.3 1.0
O A:HOH605 4.8 11.5 1.0
CE A:LYS188 4.9 11.0 1.0
C A:ASP10 4.9 9.4 1.0
OD1 A:ASN214 4.9 14.7 1.0
CE2 A:TRP174 5.0 16.7 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: Wed Dec 16 02:30:46 2020

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