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Magnesium 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:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pistol Ribozyme Transition-State Analog Vanadate (pdb code 6uey). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uey:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6uey

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Magnesium binding site 1 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:88.2
occ:1.00
N7 A:G33 2.6 0.6 1.0
O2V B:Q6110 3.3 0.1 1.0
C8 A:G33 3.5 0.6 1.0
O1V B:Q6110 3.6 0.3 1.0
C5 A:G33 3.6 0.3 1.0
O6 A:G33 3.8 0.4 1.0
O5' B:U11 4.0 0.9 1.0
V B:Q6110 4.1 0.0 1.0
C5' B:U11 4.1 0.4 1.0
C6 A:G33 4.1 1.0 1.0
OP2 A:G33 4.2 0.1 1.0
O4 A:U6 4.3 0.8 1.0
N9 A:G33 4.7 0.9 1.0
OP2 A:U35 4.7 0.2 1.0
O2' A:G32 4.8 0.5 1.0
C4 A:G33 4.8 0.8 1.0

Magnesium binding site 2 out of 9 in 6uey

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Magnesium binding site 2 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:0.1
occ:1.00
N7 A:A38 3.2 0.6 1.0
OP2 A:A37 3.4 0.9 1.0
OP2 A:A38 3.8 0.6 1.0
C8 A:A38 3.8 0.4 1.0
C5 A:A38 4.4 0.1 1.0
P A:A37 4.5 0.3 1.0
O5' A:A37 4.6 0.5 1.0
N7 A:A37 4.7 0.3 1.0
N6 A:A38 4.8 0.6 1.0
C8 A:A37 4.8 0.9 1.0
O1V B:Q6110 4.8 0.3 1.0

Magnesium binding site 3 out of 9 in 6uey

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Magnesium binding site 3 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:80.5
occ:1.00
N6 A:A10 3.7 0.6 1.0
O6 A:G5 4.0 96.4 1.0
O6 A:G11 4.1 93.6 1.0
N7 A:G11 4.4 96.6 1.0
N7 A:A10 4.6 0.9 1.0
N4 A:C12 4.6 0.4 1.0
C6 A:A10 4.7 0.2 1.0
C6 A:G5 4.9 92.6 1.0
C6 A:G11 5.0 95.4 1.0
C5 A:A10 5.0 1.0 1.0

Magnesium binding site 4 out of 9 in 6uey

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Magnesium binding site 4 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:70.3
occ:1.00
OP1 A:U7 2.0 0.7 1.0
P A:U7 3.4 0.8 1.0
C5' A:U7 3.8 0.7 1.0
O3' A:U6 4.0 0.9 1.0
O5' A:U7 4.0 0.9 1.0
OP1 A:C4 4.0 0.3 1.0
OP2 A:G5 4.3 92.4 1.0
OP2 A:U8 4.4 0.6 1.0
OP2 A:U7 4.6 0.7 1.0

Magnesium binding site 5 out of 9 in 6uey

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Magnesium binding site 5 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:79.6
occ:1.00
N7 C:G33 2.7 88.0 1.0
C8 C:G33 3.2 82.1 1.0
O2V D:Q6110 3.7 0.1 0.9
C5 C:G33 4.0 82.4 1.0
O1V D:Q6110 4.0 0.8 1.0
OP2 C:G33 4.1 0.6 1.0
O4 C:U6 4.2 83.2 1.0
C5' D:U11 4.4 0.9 1.0
OP2 C:U35 4.4 83.6 1.0
O5' D:U11 4.5 0.3 1.0
N9 C:G33 4.5 81.6 1.0
O2' C:G32 4.6 97.9 1.0
V D:Q6110 4.6 0.5 1.0
O6 C:G33 4.6 84.1 1.0
C6 C:G33 4.7 83.2 1.0
C4 C:G33 4.9 81.7 1.0

Magnesium binding site 6 out of 9 in 6uey

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Magnesium binding site 6 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:0.2
occ:1.00
N7 C:A38 2.9 92.0 1.0
C8 C:A38 3.6 94.2 1.0
OP2 C:A37 3.8 98.2 1.0
OP2 C:A38 4.0 0.5 1.0
N7 C:A37 4.1 98.9 1.0
C5 C:A38 4.1 91.3 1.0
C8 C:A37 4.4 98.5 1.0
N6 C:A38 4.5 87.8 1.0
C6 C:A38 4.8 89.4 1.0
N7 C:A39 4.8 96.7 1.0
O1V D:Q6110 4.8 0.8 1.0
N9 C:A38 4.9 95.0 1.0
C5 C:A37 4.9 97.9 1.0
O5' C:A37 4.9 99.4 1.0

Magnesium binding site 7 out of 9 in 6uey

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Magnesium binding site 7 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:0.2
occ:1.00
OP2 C:G42 2.3 94.6 1.0
OP2 C:C41 3.1 0.7 1.0
P C:G42 3.6 93.9 1.0
OP1 C:G42 4.1 96.1 1.0
N7 C:G43 4.1 92.7 1.0
O5' C:G42 4.3 91.6 1.0
P C:C41 4.4 0.1 1.0
O5' C:C41 4.4 0.1 1.0
O6 C:G43 4.5 96.3 1.0
O3' C:C41 4.8 99.0 1.0

Magnesium binding site 8 out of 9 in 6uey

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Magnesium binding site 8 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:81.0
occ:1.00
OP1 C:U7 2.1 0.9 1.0
P C:U7 3.6 0.1 1.0
OP2 C:G5 4.1 94.5 1.0
C5' C:U7 4.2 0.2 1.0
O5' C:U7 4.2 0.9 1.0
OP2 C:U8 4.3 0.8 1.0
O3' C:U6 4.4 0.0 1.0
OP2 C:U7 4.5 0.2 1.0
OP1 C:C4 4.6 99.9 1.0
OP1 C:U8 4.8 0.6 1.0
P C:U8 4.9 1.0 1.0

Magnesium binding site 9 out of 9 in 6uey

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Magnesium binding site 9 out of 9 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg105

b:80.5
occ:1.00
O6 C:G11 4.2 85.5 1.0
N6 C:A10 4.3 92.5 1.0
O6 C:G5 4.3 90.2 1.0
N7 C:A10 4.3 97.6 1.0
N7 C:G11 4.4 89.5 1.0
N4 C:C12 4.6 90.8 1.0
C5 C:A10 5.0 96.4 1.0
C6 C:G11 5.0 86.6 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: Tue Dec 15 01:01:37 2020

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