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Fluorine in PDB 2is6: Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex

Protein crystallography data

The structure of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex, PDB code: 2is6 was solved by W.Yang, J.Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.336, 96.609, 110.930, 90.00, 94.05, 90.00
R / Rfree (%) 21 / 24

Other elements in 2is6:

The structure of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex (pdb code 2is6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex, PDB code: 2is6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2is6

Go back to Fluorine Binding Sites List in 2is6
Fluorine binding site 1 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F699

b:33.6
occ:1.00
F1 A:MGF699 0.0 33.6 1.0
MG A:MGF699 1.6 35.2 1.0
MG A:MG681 2.0 36.9 1.0
O A:HOH702 2.6 32.4 1.0
O3B A:ADP700 2.7 32.2 1.0
O A:HOH837 2.8 33.0 1.0
O A:HOH838 2.9 24.3 1.0
OE2 A:GLU221 2.9 31.7 1.0
O1B A:ADP700 2.9 29.6 1.0
O A:HOH839 2.9 32.4 1.0
F3 A:MGF699 3.2 33.7 1.0
F2 A:MGF699 3.3 35.9 1.0
PB A:ADP700 3.5 33.1 1.0
CA A:GLY564 3.5 33.0 1.0
O A:HOH748 3.5 34.0 1.0
OG1 A:THR36 4.0 31.1 1.0
CD A:GLU221 4.1 33.3 1.0
N A:GLY564 4.1 31.5 1.0
NH2 A:ARG605 4.2 24.6 1.0
O A:GLY564 4.2 37.1 1.0
C A:GLY564 4.2 34.9 1.0
NH2 A:ARG284 4.2 30.3 1.0
O2B A:ADP700 4.5 31.5 1.0
O3A A:ADP700 4.6 33.5 1.0
O2A A:ADP700 4.7 35.8 1.0
OE1 A:GLU221 4.7 34.5 1.0

Fluorine binding site 2 out of 6 in 2is6

Go back to Fluorine Binding Sites List in 2is6
Fluorine binding site 2 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F699

b:35.9
occ:1.00
F2 A:MGF699 0.0 35.9 1.0
MG A:MGF699 2.0 35.2 1.0
O3B A:ADP700 2.6 32.2 1.0
O A:HOH702 2.7 32.4 1.0
NH1 A:ARG284 2.7 32.7 1.0
NH2 A:ARG605 2.8 24.6 1.0
F3 A:MGF699 2.9 33.7 1.0
NH1 A:ARG605 3.1 24.0 1.0
NH2 A:ARG284 3.1 30.3 1.0
F1 A:MGF699 3.3 33.6 1.0
CB A:ALA31 3.3 31.9 1.0
CZ A:ARG605 3.3 29.8 1.0
CZ A:ARG284 3.4 35.3 1.0
N A:GLY32 3.4 36.9 1.0
CA A:ALA31 3.5 34.8 1.0
C A:ALA31 3.9 35.5 1.0
OE1 A:GLN251 3.9 31.4 1.0
NE2 A:GLN251 4.1 30.0 1.0
PB A:ADP700 4.2 33.1 1.0
CA A:GLY32 4.4 38.5 1.0
CD A:GLN251 4.4 31.7 1.0
OG1 A:THR604 4.6 27.2 1.0
NE A:ARG605 4.6 32.5 1.0
NE A:ARG284 4.7 36.5 1.0
N A:GLY564 4.8 31.5 1.0
N A:ALA31 4.9 34.4 1.0
O1B A:ADP700 4.9 29.6 1.0
O3A A:ADP700 4.9 33.5 1.0
CA A:GLY564 4.9 33.0 1.0
O A:THR604 4.9 30.1 1.0
MG A:MG681 5.0 36.9 1.0

Fluorine binding site 3 out of 6 in 2is6

Go back to Fluorine Binding Sites List in 2is6
Fluorine binding site 3 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F699

b:33.7
occ:1.00
F3 A:MGF699 0.0 33.7 1.0
MG A:MGF699 1.8 35.2 1.0
O A:HOH702 2.7 32.4 1.0
O3B A:ADP700 2.7 32.2 1.0
O A:HOH748 2.8 34.0 1.0
NZ A:LYS35 2.8 27.1 1.0
NE2 A:GLN251 2.8 30.0 1.0
F2 A:MGF699 2.9 35.9 1.0
F1 A:MGF699 3.2 33.6 1.0
CE A:LYS35 3.3 29.1 1.0
CA A:ALA31 3.4 34.8 1.0
OE1 A:GLN251 3.6 31.4 1.0
CD A:GLN251 3.6 31.7 1.0
PB A:ADP700 3.7 33.1 1.0
O2B A:ADP700 3.8 31.5 1.0
N A:GLY32 4.0 36.9 1.0
CB A:ALA31 4.1 31.9 1.0
N A:ALA31 4.1 34.4 1.0
O A:HOH839 4.2 32.4 1.0
O1B A:ADP700 4.2 29.6 1.0
O A:GLY30 4.3 32.8 1.0
C A:ALA31 4.3 35.5 1.0
C A:GLY30 4.4 33.7 1.0
MG A:MG681 4.5 36.9 1.0
OE2 A:GLU221 4.5 31.7 1.0
O A:ALA29 4.8 28.8 1.0
CD A:LYS35 4.8 30.3 1.0
CB A:ASP248 4.8 31.9 1.0
CG A:GLN251 5.0 32.6 1.0

Fluorine binding site 4 out of 6 in 2is6

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Fluorine binding site 4 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:36.5
occ:1.00
F1 B:MGF701 0.0 36.5 1.0
MG B:MGF701 1.6 34.5 1.0
MG B:MG681 1.9 33.4 1.0
O3B B:ADP702 2.6 32.0 1.0
O B:HOH703 2.7 29.0 1.0
O B:HOH777 2.8 30.5 1.0
O1B B:ADP702 2.8 30.1 1.0
O B:HOH778 2.8 29.4 1.0
O B:HOH732 3.0 36.8 1.0
OE2 B:GLU221 3.1 30.7 1.0
F2 B:MGF701 3.2 29.6 1.0
F3 B:MGF701 3.2 31.1 1.0
PB B:ADP702 3.3 32.7 1.0
CA B:GLY564 3.5 28.3 1.0
O B:HOH752 3.7 38.1 1.0
OG1 B:THR36 3.9 26.4 1.0
O B:GLY564 4.0 32.8 1.0
NH2 B:ARG284 4.1 35.3 1.0
C B:GLY564 4.1 29.5 1.0
CD B:GLU221 4.2 35.5 1.0
N B:GLY564 4.3 28.0 1.0
O2B B:ADP702 4.4 33.6 1.0
O3A B:ADP702 4.4 30.6 1.0
O2A B:ADP702 4.5 29.8 1.0
NH2 B:ARG605 4.6 28.3 1.0
OE1 B:GLU221 4.9 35.8 1.0
CB B:THR36 5.0 29.5 1.0

Fluorine binding site 5 out of 6 in 2is6

Go back to Fluorine Binding Sites List in 2is6
Fluorine binding site 5 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:29.6
occ:1.00
F2 B:MGF701 0.0 29.6 1.0
MG B:MGF701 1.9 34.5 1.0
O3B B:ADP702 2.5 32.0 1.0
F3 B:MGF701 2.8 31.1 1.0
NH1 B:ARG284 2.8 33.8 1.0
O B:HOH703 2.8 29.0 1.0
NH1 B:ARG605 2.9 28.0 1.0
NH2 B:ARG605 3.1 28.3 1.0
F1 B:MGF701 3.2 36.5 1.0
NH2 B:ARG284 3.2 35.3 1.0
CB B:ALA31 3.2 35.0 1.0
N B:GLY32 3.4 32.1 1.0
CZ B:ARG605 3.4 31.1 1.0
CZ B:ARG284 3.4 34.4 1.0
CA B:ALA31 3.5 32.7 1.0
C B:ALA31 3.9 31.8 1.0
OE1 B:GLN251 3.9 34.0 1.0
NE2 B:GLN251 4.1 30.0 1.0
PB B:ADP702 4.1 32.7 1.0
CA B:GLY32 4.4 32.2 1.0
CD B:GLN251 4.4 34.4 1.0
O1B B:ADP702 4.7 30.1 1.0
NE B:ARG605 4.7 26.0 1.0
NE B:ARG284 4.7 32.6 1.0
N B:GLY564 4.8 28.0 1.0
O3A B:ADP702 4.8 30.6 1.0
CA B:GLY564 4.9 28.3 1.0
N B:ALA31 4.9 33.7 1.0
O2B B:ADP702 4.9 33.6 1.0
OG1 B:THR604 4.9 30.3 1.0
MG B:MG681 5.0 33.4 1.0
O B:THR604 5.0 34.1 1.0

Fluorine binding site 6 out of 6 in 2is6

Go back to Fluorine Binding Sites List in 2is6
Fluorine binding site 6 out of 6 in the Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Uvrd-Dna-ADPMGF3 Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:31.1
occ:1.00
F3 B:MGF701 0.0 31.1 1.0
MG B:MGF701 1.9 34.5 1.0
F2 B:MGF701 2.8 29.6 1.0
O3B B:ADP702 2.8 32.0 1.0
O B:HOH703 2.8 29.0 1.0
NZ B:LYS35 2.8 32.2 1.0
NE2 B:GLN251 2.9 30.0 1.0
O B:HOH752 2.9 38.1 1.0
F1 B:MGF701 3.2 36.5 1.0
CA B:ALA31 3.4 32.7 1.0
CE B:LYS35 3.4 31.5 1.0
OE1 B:GLN251 3.6 34.0 1.0
CD B:GLN251 3.6 34.4 1.0
PB B:ADP702 3.8 32.7 1.0
CB B:ALA31 3.8 35.0 1.0
O2B B:ADP702 3.9 33.6 1.0
N B:GLY32 4.1 32.1 1.0
N B:ALA31 4.1 33.7 1.0
O1B B:ADP702 4.2 30.1 1.0
O B:GLY30 4.2 35.4 1.0
O B:HOH732 4.2 36.8 1.0
C B:ALA31 4.3 31.8 1.0
C B:GLY30 4.4 33.7 1.0
OE2 B:GLU221 4.5 30.7 1.0
MG B:MG681 4.5 33.4 1.0
O B:ALA29 4.8 35.2 1.0
CB B:ASP248 4.9 36.4 1.0
OE1 B:GLU221 4.9 35.8 1.0
NH1 B:ARG605 4.9 28.0 1.0
CD B:LYS35 4.9 34.2 1.0

Reference:

J.Y.Lee, W.Yang. Uvrd Helicase Unwinds Dna One Base Pair at A Time By A Two-Part Power Stroke. Cell(Cambridge,Mass.) V. 127 1349 2006.
ISSN: ISSN 0092-8674
PubMed: 17190599
DOI: 10.1016/J.CELL.2006.10.049
Page generated: Sun Dec 13 11:37:26 2020

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