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Manganese 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:

Vanadium (V) 2 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Manganese atom in the Pistol Ribozyme Transition-State Analog Vanadate (pdb code 6uf1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 17 binding sites of Manganese where determined in the Pistol Ribozyme Transition-State Analog Vanadate, PDB code: 6uf1:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 17 in 6uf1

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Manganese binding site 1 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:0.6
occ:1.00
N7 A:G33 2.3 0.6 1.0
C8 A:G33 3.2 0.1 1.0
C5 A:G33 3.4 0.8 1.0
O6 A:G33 3.6 0.9 1.0
O2V B:Q6110 3.6 0.6 1.0
C6 A:G33 3.9 0.7 1.0
OP2 A:G33 3.9 0.2 1.0
C5' B:U11 4.1 0.3 1.0
O4 A:U6 4.3 0.4 1.0
N9 A:G33 4.4 0.2 1.0
C4 A:G33 4.5 0.1 1.0
OP2 A:U35 4.6 0.6 1.0
O5' B:U11 4.7 0.3 1.0
O1V B:Q6110 4.8 1.0 1.0
V B:Q6110 4.8 0.4 0.5
O2' A:G32 4.8 0.1 1.0
P A:G33 5.0 0.7 1.0

Manganese binding site 2 out of 17 in 6uf1

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Manganese binding site 2 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn102

b:0.2
occ:1.00
N7 A:A38 2.4 1.0 1.0
N6 A:A38 2.8 0.2 1.0
C5 A:A38 3.1 0.8 1.0
C6 A:A38 3.4 0.8 1.0
C8 A:A38 3.5 0.3 1.0
O1V B:Q6110 3.9 1.0 1.0
OP2 A:A37 4.0 0.7 1.0
OP2 A:A38 4.0 0.4 1.0
C4 A:A38 4.4 0.7 1.0
N7 A:A37 4.5 0.9 1.0
C8 A:A37 4.6 0.8 1.0
N9 A:A38 4.6 0.7 1.0
N1 A:A38 4.7 0.8 1.0
N7 A:A39 4.8 0.1 1.0
O5' A:A37 5.0 0.4 1.0

Manganese binding site 3 out of 17 in 6uf1

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Manganese binding site 3 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:0.7
occ:1.00
O6 A:G11 3.6 0.6 1.0
O6 A:G5 4.0 0.9 1.0
N7 A:G11 4.0 0.9 1.0
N6 A:A10 4.4 0.6 1.0
N7 A:A10 4.4 0.9 1.0
C6 A:G11 4.5 1.0 1.0
N4 A:C12 4.5 0.7 1.0
C5 A:G11 4.7 0.8 1.0
C6 A:G5 4.9 0.9 1.0

Manganese binding site 4 out of 17 in 6uf1

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Manganese binding site 4 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn104

b:0.4
occ:1.00
OP2 C:G15 3.8 0.4 1.0
N7 C:G15 4.2 0.8 1.0
OP2 A:A14 4.2 0.9 1.0
N7 A:G15 4.5 0.5 1.0
N7 A:A14 4.5 0.4 1.0
C8 C:G15 4.7 0.1 1.0
C8 A:A14 4.9 0.5 1.0

Manganese binding site 5 out of 17 in 6uf1

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Manganese binding site 5 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn105

b:0.7
occ:1.00
N7 A:G24 2.9 0.9 1.0
OP2 A:A23 3.1 0.0 1.0
OP1 A:A23 3.4 0.9 1.0
C8 A:G24 3.5 0.4 1.0
OP2 A:G24 3.6 0.1 1.0
P A:A23 3.6 0.9 1.0
O5' A:A23 4.2 0.7 1.0
C5 A:G24 4.2 0.1 1.0
OP2 A:U26 4.3 0.1 1.0
MN A:MN106 4.4 1.0 1.0
O6 A:G24 4.6 0.8 1.0
OP1 A:U26 4.7 0.4 1.0
C6 A:G24 4.8 0.5 1.0
N9 A:G24 4.9 0.6 1.0
P A:G24 5.0 0.6 1.0

Manganese binding site 6 out of 17 in 6uf1

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Manganese binding site 6 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn106

b:1.0
occ:1.00
OP1 A:U26 2.2 0.4 1.0
OP2 A:G24 2.3 0.1 1.0
OP1 A:A23 3.1 0.9 1.0
P A:G24 3.2 0.6 1.0
OP1 A:G24 3.2 0.1 1.0
P A:U26 3.2 0.9 1.0
O3' A:U25 3.4 0.0 1.0
OP2 A:U26 4.0 0.1 1.0
O3' A:A23 4.2 0.5 1.0
O5' A:G24 4.3 0.1 1.0
P A:A23 4.4 0.9 1.0
MN A:MN105 4.4 0.7 1.0
C5' A:A23 4.5 0.1 1.0
O5' A:U26 4.5 0.3 1.0
C5' A:U26 4.7 0.6 1.0
C3' A:U25 4.7 0.0 1.0
O5' A:A23 4.7 0.7 1.0
C3' A:A23 4.8 0.1 1.0

Manganese binding site 7 out of 17 in 6uf1

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Manganese binding site 7 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn107

b:0.7
occ:1.00
O6 A:G28 3.3 0.6 1.0
N7 A:G27 3.7 0.2 1.0
N7 A:G28 3.8 0.3 1.0
C6 A:G28 4.1 0.9 1.0
O6 A:G27 4.1 0.4 1.0
C5 A:G28 4.3 0.5 1.0
C5 A:G27 4.6 0.7 1.0
O4 A:U26 4.6 0.1 1.0
C6 A:G27 4.7 0.8 1.0
C8 A:G27 4.7 0.7 1.0
C4 A:U26 4.8 0.6 1.0
C5 A:U26 4.9 0.0 1.0
O4 A:U29 5.0 0.8 1.0

Manganese binding site 8 out of 17 in 6uf1

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Manganese binding site 8 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn108

b:0.9
occ:1.00
OP2 A:G42 2.2 0.1 1.0
OP2 A:C41 3.0 0.9 1.0
P A:G42 3.3 0.3 1.0
O5' A:G42 3.3 0.3 1.0
O5' A:C41 3.8 0.4 1.0
P A:C41 4.1 0.7 1.0
N7 A:G43 4.1 0.9 1.0
OP1 A:G42 4.2 0.6 1.0
C8 A:G42 4.2 0.2 1.0
OP2 A:G43 4.3 0.8 1.0
O3' A:C41 4.4 0.2 1.0
N7 A:G42 4.5 0.2 1.0
C3' A:C41 4.6 0.6 1.0
C5' A:G42 4.7 0.1 1.0
C8 A:G43 4.7 0.1 1.0
O3' A:G40 4.8 0.7 1.0

Manganese binding site 9 out of 17 in 6uf1

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Manganese binding site 9 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn109

b:0.3
occ:1.00
OP1 A:U7 1.8 0.2 1.0
OP2 A:G5 2.9 0.3 1.0
P A:U7 3.0 0.2 1.0
O3' A:U6 3.2 0.4 1.0
P A:G5 3.9 0.7 1.0
O5' A:U7 4.0 0.7 1.0
OP2 A:U7 4.1 0.4 1.0
C5' A:U7 4.1 0.4 1.0
OP1 A:G5 4.1 0.6 1.0
OP1 A:C4 4.5 0.3 1.0
O3' A:C4 4.5 1.0 1.0
C3' A:U6 4.6 0.2 1.0
OP2 A:C4 4.6 0.9 1.0
O5' A:C4 4.8 0.1 1.0
P A:C4 4.8 0.9 1.0

Manganese binding site 10 out of 17 in 6uf1

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Manganese binding site 10 out of 17 in the Pistol Ribozyme Transition-State Analog Vanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Pistol Ribozyme Transition-State Analog Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn101

b:0.8
occ:1.00
N7 C:G33 2.5 96.1 1.0
C5 C:G33 3.5 93.9 1.0
C8 C:G33 3.5 92.6 1.0
O6 C:G33 3.6 97.3 1.0
OP2 C:G33 3.8 86.9 1.0
O2V D:Q6110 3.8 0.0 0.6
C6 C:G33 3.9 95.1 1.0
C5' D:U11 4.1 97.4 1.0
O1V D:Q6110 4.3 0.6 0.9
O4 C:U6 4.4 88.7 1.0
O2' C:G32 4.4 94.5 1.0
O5' D:U11 4.5 0.9 1.0
N9 C:G33 4.6 87.3 1.0
V D:Q6110 4.6 0.6 0.6
C4 C:G33 4.6 89.6 1.0
OP2 C:U35 4.7 93.7 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: Tue Dec 15 05:02:31 2020

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