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Vanadium in PDB 6uf1: Pistol Ribozyme Transition-State Analog Vanadate

Protein crystallography data

The structure of Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uf1 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) 19.98 / 3.10
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.570, 90.570, 122.558, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.5

Other elements in 6uf1:

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

Manganese (Mn) 17 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Pistol Ribozyme Transition-State Analog Vanadate (pdb code 6uf1). 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: 6uf1:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6uf1

Go back to Vanadium Binding Sites List in 6uf1
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:0.4
occ:0.46
V B:Q6110 0.0 0.4 0.5
O1V B:Q6110 1.6 1.0 1.0
O2V B:Q6110 1.6 0.6 1.0
O3' B:Q6110 2.0 0.3 1.0
O5' B:U11 2.0 0.3 1.0
O2' B:Q6110 2.0 0.5 1.0
C3' B:Q6110 2.9 0.2 1.0
C2' B:Q6110 2.9 0.6 1.0
C5' B:U11 3.0 0.3 1.0
C1' B:Q6110 4.0 0.5 1.0
N2 A:G40 4.0 0.8 1.0
C4' B:U11 4.0 0.3 1.0
C4' B:Q6110 4.1 0.7 1.0
N1 A:G40 4.1 0.6 1.0
O3' B:U11 4.5 0.1 1.0
O4' B:Q6110 4.5 0.3 1.0
C2 A:G40 4.6 0.8 1.0
C3' B:U11 4.8 0.2 1.0
MN A:MN101 4.8 0.6 1.0
OP1 B:C12 4.9 0.8 1.0
OP2 B:C12 5.0 0.1 1.0

Vanadium binding site 2 out of 2 in 6uf1

Go back to Vanadium Binding Sites List in 6uf1
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:0.6
occ:0.63
V D:Q6110 0.0 0.6 0.6
O2V D:Q6110 1.6 0.0 0.6
O1V D:Q6110 1.6 0.6 0.9
O3' D:Q6110 2.0 0.2 1.0
O5' D:U11 2.0 0.9 1.0
O2' D:Q6110 2.0 0.6 1.0
C3' D:Q6110 2.9 0.3 1.0
C2' D:Q6110 2.9 0.3 1.0
C5' D:U11 3.1 97.4 1.0
C1' D:Q6110 3.8 1.0 1.0
C4' D:Q6110 4.0 0.8 1.0
C4' D:U11 4.1 92.3 1.0
N2 C:G40 4.1 0.2 1.0
N1 C:G40 4.3 97.5 1.0
O4' D:Q6110 4.4 0.5 1.0
O3' D:U11 4.4 0.8 1.0
MN C:MN101 4.6 0.8 1.0
C3' D:U11 4.8 98.5 1.0
C2 C:G40 4.8 0.9 1.0
N9 D:Q6110 5.0 0.7 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: Wed Dec 16 02:32:09 2020

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