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Vanadium in PDB 6uey: Pistol Ribozyme Transition-State Analog Vanadate

Protein crystallography data

The structure of Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uey was solved by M.Teplova, C.Falschlunger, O.Krasheninina, D.J.Patel, R.Micura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 91.829, 91.829, 123.444, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.2

Other elements in 6uey:

The structure of Pistol Ribozyme Transition-State Analog Vanadate also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Pistol Ribozyme Transition-State Analog Vanadate (pdb code 6uey). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uey:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6uey

Go back to Vanadium Binding Sites List in 6uey
Vanadium binding site 1 out of 2 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V10

b:0.0
occ:1.00
V B:Q6110 0.0 0.0 1.0
O2V B:Q6110 1.6 0.1 1.0
O1V B:Q6110 1.6 0.3 1.0
O5' B:U11 2.0 0.9 1.0
O3' B:Q6110 2.0 0.6 1.0
O2' B:Q6110 2.0 0.8 1.0
C2' B:Q6110 2.9 0.6 1.0
C3' B:Q6110 2.9 0.6 1.0
C5' B:U11 3.1 0.4 1.0
C1' B:Q6110 3.9 0.5 1.0
MG A:MG101 4.1 88.2 1.0
C4' B:U11 4.1 0.1 1.0
C4' B:Q6110 4.1 0.8 1.0
N1 A:G40 4.1 0.8 1.0
N2 A:G40 4.2 0.0 1.0
O4' B:Q6110 4.4 0.7 1.0
O3' B:U11 4.4 0.0 1.0
C2 A:G40 4.7 0.7 1.0
N2 A:G32 4.7 0.6 1.0
C3' B:U11 4.8 0.6 1.0

Vanadium binding site 2 out of 2 in 6uey

Go back to Vanadium Binding Sites List in 6uey
Vanadium binding site 2 out of 2 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V10

b:0.5
occ:1.00
V D:Q6110 0.0 0.5 1.0
O2V D:Q6110 1.6 0.1 0.9
O1V D:Q6110 1.6 0.8 1.0
O3' D:Q6110 2.0 0.7 1.0
O5' D:U11 2.0 0.3 1.0
O2' D:Q6110 2.0 0.7 1.0
C2' D:Q6110 2.9 0.7 1.0
C3' D:Q6110 2.9 0.9 1.0
C5' D:U11 3.2 0.9 1.0
C1' D:Q6110 3.8 0.5 1.0
C4' D:Q6110 4.0 0.0 1.0
N2 C:G40 4.1 90.0 1.0
C4' D:U11 4.3 0.9 1.0
O4' D:Q6110 4.3 0.7 1.0
N1 C:G40 4.3 94.0 1.0
MG C:MG101 4.6 79.6 1.0
O3' D:U11 4.6 0.5 1.0
C2 C:G40 4.7 91.7 1.0
C3' D:U11 4.9 0.0 1.0
OP2 D:C12 4.9 0.2 1.0
N2 C:G32 5.0 0.2 1.0

Reference:

M.Teplova, C.Falschlunger, O.Krasheninina, M.Egger, A.Ren, D.J.Patel, R.Micura. On Crucial Roles of Two Hydrated MG2+ Ions in Reaction Catalysis of the Pistol Ribozyme. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31804735
DOI: 10.1002/ANIE.201912522
Page generated: Thu Oct 29 07:06:20 2020

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