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Vanadium in PDB 1m5o: Transition State Stabilization By A Catalytic Rna

Protein crystallography data

The structure of Transition State Stabilization By A Catalytic Rna, PDB code: 1m5o was solved by P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 259.380, 44.220, 102.500, 90.00, 106.30, 90.00
R / Rfree (%) 22.9 / 26.4

Other elements in 1m5o:

The structure of Transition State Stabilization By A Catalytic Rna also contains other interesting chemical elements:

Calcium (Ca) 37 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Transition State Stabilization By A Catalytic Rna (pdb code 1m5o). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Transition State Stabilization By A Catalytic Rna, PDB code: 1m5o:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 1m5o

Go back to Vanadium Binding Sites List in 1m5o
Vanadium binding site 1 out of 2 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V12

b:95.6
occ:1.00
V A:AVC12 0.0 95.6 1.0
O2V A:AVC12 1.6 91.3 1.0
O1V A:AVC12 1.6 91.0 1.0
O3' A:AVC12 2.0 85.2 1.0
O2' A:AVC12 2.0 92.4 1.0
O5' A:G13 2.0 91.9 1.0
C5' A:G13 2.7 63.3 1.0
C3' A:AVC12 2.9 81.6 1.0
C2' A:AVC12 2.9 82.7 1.0
C4' A:AVC12 3.8 78.1 1.0
C1' A:AVC12 3.8 81.1 1.0
N6 B:A9 4.0 62.1 1.0
N6 B:A57 4.0 74.7 1.0
N2 B:G8 4.0 80.7 1.0
C4' A:G13 4.1 66.8 1.0
N1 B:A57 4.1 76.9 1.0
O4' A:AVC12 4.4 84.1 1.0
C6 B:A57 4.6 78.5 1.0
N1 B:G8 4.7 78.9 1.0
O4' A:G13 4.7 62.4 1.0
C5 A:U14 4.8 81.9 1.0
C2 B:G8 4.9 82.0 1.0
C6 B:A9 4.9 61.6 1.0

Vanadium binding site 2 out of 2 in 1m5o

Go back to Vanadium Binding Sites List in 1m5o
Vanadium binding site 2 out of 2 in the Transition State Stabilization By A Catalytic Rna


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Transition State Stabilization By A Catalytic Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V12

b:0.1
occ:1.00
V D:AVC12 0.0 0.1 1.0
O1V D:AVC12 1.6 83.3 1.0
O2V D:AVC12 1.6 0.6 1.0
O2' D:AVC12 2.0 81.4 1.0
O3' D:AVC12 2.0 87.2 1.0
O5' D:G13 2.0 77.5 1.0
C5' D:G13 2.4 53.9 1.0
C2' D:AVC12 2.9 74.1 1.0
C3' D:AVC12 2.9 69.2 1.0
CA D:CA36 3.6 0.2 1.0
N6 E:A57 3.6 69.0 1.0
N1 E:A57 3.7 72.1 1.0
C1' D:AVC12 3.7 73.7 1.0
C4' D:AVC12 3.8 76.4 1.0
C4' D:G13 3.9 53.2 1.0
C6 E:A57 4.1 70.0 1.0
N2 E:G8 4.2 87.9 1.0
N6 E:A9 4.3 66.3 1.0
O4' D:AVC12 4.4 78.3 1.0
O4' D:G13 4.6 54.2 1.0
C2 E:A57 4.8 70.0 1.0
C5 D:U14 4.8 64.9 1.0
C3' D:G13 4.8 48.4 1.0
N1 E:G8 4.9 90.5 1.0
N9 D:AVC12 5.0 77.5 1.0

Reference:

P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare. Transition State Stabilization By A Catalytic Rna Science V. 298 1421 2002.
ISSN: ISSN 0036-8075
PubMed: 12376595
DOI: 10.1126/SCIENCE.1076093
Page generated: Wed Dec 16 02:30:09 2020

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