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Fluorine in PDB 6mu4: Bst Dna Polymerase I Fana/Dna Binary Complex

Enzymatic activity of Bst Dna Polymerase I Fana/Dna Binary Complex

All present enzymatic activity of Bst Dna Polymerase I Fana/Dna Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of Bst Dna Polymerase I Fana/Dna Binary Complex, PDB code: 6mu4 was solved by L.N.Jackson, N.Chim, J.C.Chaput, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.09 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.835, 93.898, 105.809, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.1

Other elements in 6mu4:

The structure of Bst Dna Polymerase I Fana/Dna Binary Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Fluorine atom in the Bst Dna Polymerase I Fana/Dna Binary Complex (pdb code 6mu4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 13 binding sites of Fluorine where determined in the Bst Dna Polymerase I Fana/Dna Binary Complex, PDB code: 6mu4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 13 in 6mu4

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Fluorine binding site 1 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F4

b:0.6
occ:1.00
 F T:GFL4 0.0 0.6 1.0
C2' T:GFL4 1.4 0.5 1.0
C3' T:GFL4 2.2 0.4 1.0
C1' T:GFL4 2.6 0.5 1.0
H53 A:MPD901 2.7 65.0 1.0
N9 T:GFL4 2.8 86.0 1.0
C4 T:GFL4 2.9 82.5 1.0
NH2 A:ARG789 2.9 43.7 1.0
O3' T:GFL4 3.0 0.4 1.0
N3 T:GFL4 3.0 81.9 1.0
O A:HOH1311 3.2 41.3 1.0
O5' T:UF25 3.4 0.6 1.0
C4' T:GFL4 3.5 0.2 1.0
H51 A:MPD901 3.5 65.0 1.0
C5 A:MPD901 3.5 54.1 1.0
O4' T:GFL4 3.5 0.2 1.0
C5' T:UF25 3.7 0.2 1.0
C8 T:GFL4 3.8 83.2 1.0
P T:UF25 3.8 0.2 1.0
C5 T:GFL4 3.9 83.0 1.0
H52 A:MPD901 4.0 65.0 1.0
C2 T:GFL4 4.1 82.7 1.0
CZ A:ARG789 4.2 43.4 1.0
N7 T:GFL4 4.3 77.1 1.0
C5' T:GFL4 4.5 0.3 1.0
CD1 A:PHE786 4.5 41.4 1.0
O2P T:UF25 4.5 0.6 1.0
CB A:PHE786 4.6 32.6 1.0
NH1 A:ARG789 4.6 48.4 1.0
O4' T:UF25 4.7 0.1 1.0
C4' T:UF25 4.7 0.3 1.0
C4 A:MPD901 4.8 54.7 1.0
C6 T:GFL4 4.8 82.7 1.0
O4 A:MPD901 4.8 53.5 1.0
N1 T:GFL4 4.9 84.2 1.0
N2 T:GFL4 4.9 84.9 1.0
CG A:PHE786 4.9 37.5 1.0

Fluorine binding site 2 out of 13 in 6mu4

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Fluorine binding site 2 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F5

b:0.7
occ:1.00
 F2' T:UF25 0.0 0.7 1.0
C2' T:UF25 1.1 0.6 1.0
C3' T:UF25 1.9 0.9 1.0
C1' T:UF25 2.3 0.4 1.0
N1 T:UF25 2.7 97.8 1.0
C4' T:UF25 2.8 0.3 1.0
O4' T:UF25 2.8 0.1 1.0
O5' T:UF25 2.9 0.6 1.0
C6 T:UF25 2.9 93.8 1.0
O3' T:UF25 3.2 0.4 1.0
C5' T:UF25 3.2 0.2 1.0
C8 T:A5L6 3.4 85.2 1.0
P T:UF25 3.6 0.2 1.0
O1P T:UF25 3.6 1.0 1.0
N7 T:A5L6 3.7 84.9 1.0
O2P T:UF25 3.9 0.6 1.0
OP2 T:A5L6 4.0 0.4 1.0
C2 T:UF25 4.0 98.3 1.0
C5 T:UF25 4.2 93.1 1.0
P T:A5L6 4.2 0.1 1.0
N9 T:A5L6 4.4 86.6 1.0
O4' T:A5L6 4.4 98.4 1.0
O2 T:UF25 4.5 96.3 1.0
H51 A:MPD901 4.5 65.0 1.0
C5' T:A5L6 4.7 1.0 1.0
C5 T:A5L6 4.8 84.9 1.0
N3 T:UF25 5.0 97.8 1.0

Fluorine binding site 3 out of 13 in 6mu4

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Fluorine binding site 3 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F6

b:98.3
occ:1.00
 F T:A5L6 0.0 98.3 1.0
C2' T:A5L6 1.4 99.2 1.0
C1' T:A5L6 2.3 94.7 1.0
C3' T:A5L6 2.5 0.7 1.0
N9 T:A5L6 2.6 86.6 1.0
C8 T:A5L6 2.7 85.2 1.0
O4' T:A5L6 3.1 98.4 1.0
C4' T:A5L6 3.1 0.6 1.0
C5' T:A5L6 3.3 1.0 1.0
C6 T:CFL7 3.4 76.0 1.0
C5 T:CFL7 3.5 74.0 1.0
O3' T:A5L6 3.7 99.4 1.0
C4 T:A5L6 3.7 84.8 1.0
N7 T:A5L6 3.9 84.9 1.0
O1P T:CFL7 4.1 92.3 1.0
P T:CFL7 4.3 94.4 1.0
C5 T:A5L6 4.4 84.9 1.0
O5' T:CFL7 4.4 90.5 1.0
N3 T:A5L6 4.6 83.1 1.0
N1 T:CFL7 4.6 76.3 1.0
O4' T:CFL7 4.7 85.5 1.0
O5' T:A5L6 4.7 1.0 1.0
C4 T:CFL7 4.8 72.2 1.0

Fluorine binding site 4 out of 13 in 6mu4

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Fluorine binding site 4 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F7

b:56.5
occ:1.00
 F T:CFL7 0.0 56.5 1.0
C2' T:CFL7 1.3 72.9 1.0
C3' T:CFL7 2.4 78.8 1.0
C1' T:CFL7 2.4 79.7 1.0
N1 T:CFL7 2.8 76.3 1.0
C6 T:CFL7 2.9 76.0 1.0
O4' T:CFL7 3.0 85.5 1.0
C4' T:CFL7 3.1 84.5 1.0
C8 T:GFL8 3.2 56.6 1.0
O5' T:CFL7 3.5 90.5 1.0
O3' T:CFL7 3.6 71.4 1.0
N7 T:GFL8 3.7 56.0 1.0
C5' T:GFL8 3.8 62.0 1.0
O2P T:GFL8 3.8 44.8 1.0
C5' T:CFL7 3.9 87.6 1.0
C2 T:CFL7 4.0 69.8 1.0
C5 T:CFL7 4.1 74.0 1.0
P T:GFL8 4.2 57.0 1.0
N9 T:GFL8 4.2 57.8 1.0
O5' T:GFL8 4.4 60.2 1.0
O2 T:CFL7 4.5 62.0 1.0
O4' T:GFL8 4.6 54.5 1.0
F T:GFL8 4.7 41.9 1.0
C4' T:GFL8 4.8 58.0 1.0
C5 T:GFL8 4.8 58.0 1.0
C2' T:A5L6 4.9 99.2 1.0
N3 T:CFL7 5.0 69.4 1.0
P T:CFL7 5.0 94.4 1.0
C1' T:GFL8 5.0 55.5 1.0

Fluorine binding site 5 out of 13 in 6mu4

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Fluorine binding site 5 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F8

b:41.9
occ:1.00
 F T:GFL8 0.0 41.9 1.0
C2' T:GFL8 1.4 51.3 1.0
C3' T:GFL8 2.2 45.4 1.0
C1' T:GFL8 2.5 55.5 1.0
N9 T:GFL8 2.7 57.8 1.0
C8 T:GFL8 2.8 56.6 1.0
C4' T:GFL8 3.0 58.0 1.0
C5' T:GFL8 3.0 62.0 1.0
O4' T:GFL8 3.2 54.5 1.0
C6 T:UF29 3.3 52.4 1.0
O3' T:GFL8 3.5 38.1 1.0
C5 T:UF29 3.6 53.7 1.0
C4 T:GFL8 3.9 53.6 1.0
O1P T:UF29 3.9 36.3 1.0
O T:HOH118 4.0 52.2 1.0
N7 T:GFL8 4.0 56.0 1.0
P T:UF29 4.1 37.7 1.0
O5' T:UF29 4.1 33.9 1.0
O4' T:UF29 4.2 42.3 1.0
O5' T:GFL8 4.3 60.2 1.0
N1 T:UF29 4.5 44.3 1.0
C5 T:GFL8 4.5 58.0 1.0
F T:CFL7 4.7 56.5 1.0
N3 T:GFL8 4.9 51.1 1.0
C5' T:UF29 4.9 36.8 1.0
C1' T:UF29 4.9 50.3 1.0
C2' T:CFL7 4.9 72.9 1.0
F2' T:UF29 4.9 55.5 1.0
C4 T:UF29 5.0 54.4 1.0
O2P T:GFL8 5.0 44.8 1.0

Fluorine binding site 6 out of 13 in 6mu4

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Fluorine binding site 6 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F9

b:55.5
occ:1.00
 F2' T:UF29 0.0 55.5 1.0
C2' T:UF29 1.1 59.0 1.0
C3' T:UF29 2.0 47.7 1.0
C1' T:UF29 2.3 50.3 1.0
N1 T:UF29 2.7 44.3 1.0
C6 T:UF29 2.9 52.4 1.0
O4' T:UF29 2.9 42.3 1.0
C4' T:UF29 3.1 44.4 1.0
C8 T:GFL10 3.1 59.6 1.0
O3' T:UF29 3.1 40.7 1.0
O2P T:GFL10 3.3 49.3 1.0
O T:HOH118 3.4 52.2 1.0
O T:HOH112 3.5 45.2 1.0
N7 T:GFL10 3.6 56.2 1.0
O5' T:UF29 3.6 33.9 1.0
P T:GFL10 3.7 43.5 1.0
C2 T:UF29 3.9 43.9 1.0
C5' T:UF29 3.9 36.8 1.0
O5' T:GFL10 4.1 48.0 1.0
C5 T:UF29 4.1 53.7 1.0
O T:HOH108 4.1 61.4 1.0
N9 T:GFL10 4.2 54.3 1.0
O2 T:UF29 4.4 33.0 1.0
O4' T:GFL10 4.5 44.9 1.0
C5 T:GFL10 4.8 56.6 1.0
C2' T:GFL8 4.8 51.3 1.0
N3 T:UF29 4.9 45.4 1.0
C1' T:GFL10 4.9 51.4 1.0
F T:GFL10 4.9 58.0 1.0
F T:GFL8 4.9 41.9 1.0
C5' T:GFL10 5.0 56.2 1.0
C4 T:UF29 5.0 54.4 1.0

Fluorine binding site 7 out of 13 in 6mu4

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Fluorine binding site 7 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F10

b:58.0
occ:1.00
 F T:GFL10 0.0 58.0 1.0
C2' T:GFL10 1.4 53.6 1.0
C3' T:GFL10 2.2 49.0 1.0
C1' T:GFL10 2.5 51.4 1.0
N9 T:GFL10 2.7 54.3 1.0
C8 T:GFL10 2.9 59.6 1.0
O5' T:GFL10 3.0 48.0 1.0
O T:HOH112 3.1 45.2 1.0
O T:HOH124 3.1 61.2 1.0
O4' T:GFL10 3.1 44.9 1.0
C4' T:GFL10 3.2 53.5 1.0
O3' T:GFL10 3.4 44.2 1.0
OP2 T:A5L11 3.7 37.5 1.0
C5' T:GFL10 3.7 56.2 1.0
C4 T:GFL10 3.8 57.3 1.0
C8 T:A5L11 3.9 45.5 1.0
O T:HOH119 4.0 64.8 1.0
P T:A5L11 4.0 39.0 1.0
N7 T:GFL10 4.1 56.2 1.0
O5' T:A5L11 4.3 33.6 1.0
O2P T:GFL10 4.3 49.3 1.0
N7 T:A5L11 4.3 42.7 1.0
P T:GFL10 4.3 43.5 1.0
C5 T:GFL10 4.5 56.6 1.0
O4' T:A5L11 4.7 37.9 1.0
N3 T:GFL10 4.7 50.9 1.0
C2' T:UF29 4.9 59.0 1.0
F2' T:UF29 4.9 55.5 1.0
N9 T:A5L11 5.0 46.5 1.0

Fluorine binding site 8 out of 13 in 6mu4

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Fluorine binding site 8 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F11

b:47.4
occ:1.00
 F T:A5L11 0.0 47.4 1.0
C2' T:A5L11 1.4 42.0 1.0
C1' T:A5L11 2.3 46.4 1.0
C3' T:A5L11 2.5 43.5 1.0
N9 T:A5L11 2.6 46.5 1.0
C8 T:A5L11 2.8 45.5 1.0
C6 T:UF212 3.0 54.4 1.0
O4' T:A5L11 3.1 37.9 1.0
C5 T:UF212 3.3 54.7 1.0
C4' T:A5L11 3.4 41.6 1.0
O1P T:UF212 3.4 46.0 1.0
O3' T:A5L11 3.5 40.4 1.0
C4 T:A5L11 3.6 46.5 1.0
O5' T:UF212 3.7 40.8 1.0
P T:UF212 3.8 41.8 1.0
N7 T:A5L11 3.9 42.7 1.0
O4' T:UF212 4.0 50.4 1.0
O5' T:A5L11 4.0 33.6 1.0
N1 T:UF212 4.2 53.2 1.0
C5 T:A5L11 4.3 45.1 1.0
C5' T:A5L11 4.3 38.4 1.0
C5' T:UF212 4.4 45.8 1.0
N3 T:A5L11 4.5 48.6 1.0
C1' T:UF212 4.7 55.7 1.0
C4 T:UF212 4.7 60.7 1.0
C4' T:UF212 4.8 46.9 1.0
F2' T:UF212 4.9 53.8 1.0

Fluorine binding site 9 out of 13 in 6mu4

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Fluorine binding site 9 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F12

b:53.8
occ:1.00
 F2' T:UF212 0.0 53.8 1.0
C2' T:UF212 1.1 55.6 1.0
C3' T:UF212 2.0 50.9 1.0
C1' T:UF212 2.3 55.7 1.0
N1 T:UF212 2.7 53.2 1.0
O4' T:UF212 2.9 50.4 1.0
C6 T:UF212 3.0 54.4 1.0
C4' T:UF212 3.0 46.9 1.0
C6 T:CFL13 3.1 64.5 1.0
O3' T:UF212 3.2 46.3 1.0
C5 T:CFL13 3.4 62.4 1.0
O5' T:UF212 3.5 40.8 1.0
C5' T:UF212 3.8 45.8 1.0
C2 T:UF212 3.8 55.6 1.0
P T:CFL13 3.9 48.0 1.0
O4' T:CFL13 3.9 70.4 1.0
O5' T:CFL13 3.9 57.6 1.0
O2P T:CFL13 3.9 49.6 1.0
N1 T:CFL13 4.2 67.1 1.0
C5 T:UF212 4.2 54.7 1.0
O2 T:UF212 4.3 56.6 1.0
C1' T:CFL13 4.6 70.1 1.0
C5' T:CFL13 4.7 64.7 1.0
C4 T:CFL13 4.8 64.3 1.0
N3 T:UF212 4.9 57.4 1.0
F T:A5L11 4.9 47.4 1.0
P T:UF212 4.9 41.8 1.0
C4' T:CFL13 4.9 69.2 1.0

Fluorine binding site 10 out of 13 in 6mu4

Go back to Fluorine Binding Sites List in 6mu4
Fluorine binding site 10 out of 13 in the Bst Dna Polymerase I Fana/Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Bst Dna Polymerase I Fana/Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F13

b:65.5
occ:1.00
 F T:CFL13 0.0 65.5 1.0
C2' T:CFL13 1.3 68.6 1.0
C3' T:CFL13 2.4 73.3 1.0
C1' T:CFL13 2.4 70.1 1.0
N1 T:CFL13 2.7 67.1 1.0
C6 T:CFL13 2.9 64.5 1.0
O4' T:CFL13 3.0 70.4 1.0
C8 T:GFL14 3.1 0.4 1.0
C4' T:CFL13 3.2 69.2 1.0
O1P T:GFL14 3.3 77.3 1.0
O3' T:CFL13 3.5 81.9 1.0
N7 T:GFL14 3.5 0.1 1.0
C2 T:CFL13 3.8 67.0 1.0
P T:GFL14 3.8 82.1 1.0
O5' T:CFL13 3.9 57.6 1.0
N9 T:GFL14 4.0 0.3 1.0
O5' T:GFL14 4.1 91.5 1.0
C5 T:CFL13 4.1 62.4 1.0
C5' T:CFL13 4.2 64.7 1.0
O2 T:CFL13 4.3 62.1 1.0
O4' T:GFL14 4.3 0.5 1.0
C5' T:GFL14 4.3 98.1 1.0
C5 T:GFL14 4.5 1.0 1.0
C1' T:GFL14 4.7 0.1 1.0
C4 T:GFL14 4.7 0.4 1.0
N3 T:CFL13 4.8 66.9 1.0
C4 T:CFL13 4.9 64.3 1.0
C4' T:GFL14 5.0 0.8 1.0

Reference:

L.N.Jackson, N.Chim, C.Shi, J.C.Chaput. Crystal Structures of A Natural Dna Polymerase That Functions As An Xna Reverse Transcriptase. Nucleic Acids Res. V. 47 6973 2019.
ISSN: ESSN 1362-4962
PubMed: 31170294
DOI: 10.1093/NAR/GKZ513
Page generated: Thu Aug 1 22:19:37 2024

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