Vanadium in PDB 2p7e: Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization

The structure of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization, PDB code: 2p7e was solved by A.T.Torelli, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.93 / 2.05
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.100, 94.100, 132.400, 90.00, 90.00, 120.00
R / Rfree (%)	25.8 / 27.1

The structure of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Vanadium atom in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization (pdb code 2p7e). 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 Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization, PDB code: 2p7e:

Vanadium binding site 1 out of 1 in the Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Vanadate at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization within 5.0Å range: probe atom residue distance (Å) B Occ A:V5 b:60.1 occ:0.50 V A:AVC5 0.0 60.1 0.5 O1V A:AVC5 1.6 54.2 0.5 O2V A:AVC5 1.6 49.6 0.5 O3' A:AVC5 1.9 61.1 1.0 O5' P:G6 2.0 56.4 1.0 O2' A:AVC5 2.0 57.3 1.0 C2' A:AVC5 2.9 55.1 1.0 C5' P:G6 2.9 53.8 1.0 C3' A:AVC5 2.9 55.6 1.0 C1' A:AVC5 3.4 54.4 1.0 C4' A:AVC5 3.7 55.3 1.0 N2 B:G8 3.8 64.4 0.8 N1 D:A38 3.8 43.1 1.0 O4' A:AVC5 3.9 53.0 1.0 N6 D:A38 4.0 39.8 1.0 O A:HOH106 4.1 62.2 1.0 C4' P:G6 4.2 51.7 1.0 N6 B:A9 4.3 62.5 1.0 C6 D:A38 4.4 43.9 1.0 O P:HOH5 4.4 47.5 1.0 N9 A:AVC5 4.6 54.3 1.0 N1 B:G8 4.7 69.8 0.8 C2 B:G8 4.7 68.9 0.8 C2 D:A38 4.8 46.1 1.0 O4' P:G6 4.9 54.7 1.0 C5 P:U7 5.0 70.5 1.0

A.T.Torelli, J.Krucinska, J.E.Wedekind. A Comparison of Vanadate to A 2'-5' Linkage at the Active Site of A Small Ribozyme Suggests A Role For Water in Transition-State Stabilization Rna V. 13 1052 2007.
ISSN: ISSN 1355-8382
PubMed: 17488874
DOI: 10.1261/RNA.510807