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Fluorine in PDB 6fws: Structure of Ding in Complex with Ssdna and Adpbef

Protein crystallography data

The structure of Structure of Ding in Complex with Ssdna and Adpbef, PDB code: 6fws was solved by K.Cheng, D.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.37 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.771, 119.751, 126.740, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.6

Other elements in 6fws:

The structure of Structure of Ding in Complex with Ssdna and Adpbef also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Ding in Complex with Ssdna and Adpbef (pdb code 6fws). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Ding in Complex with Ssdna and Adpbef, PDB code: 6fws:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 1 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:26.0
occ:1.00
 F1 A:BEF803 0.0 26.0 1.0
BE A:BEF803 1.5 28.0 1.0
O2B A:ADP802 2.5 25.6 1.0
F2 A:BEF803 2.5 31.2 1.0
F3 A:BEF803 2.6 27.0 1.0
NH1 A:ARG659 2.7 23.4 1.0
NH2 A:ARG656 2.8 19.7 1.0
NH1 A:ARG656 3.0 21.0 1.0
NH2 A:ARG659 3.1 21.5 1.0
CZ A:ARG656 3.3 21.3 1.0
CZ A:ARG659 3.3 28.7 1.0
CB A:THR56 3.6 26.6 1.0
CA A:THR56 3.8 24.5 1.0
N A:GLY57 3.9 22.6 1.0
CG2 A:THR56 3.9 28.4 1.0
PB A:ADP802 4.0 28.1 1.0
C A:THR56 4.3 25.6 1.0
OE1 A:GLN652 4.4 27.1 1.0
N A:GLY597 4.4 27.6 1.0
CA A:GLY597 4.4 25.3 1.0
MG A:MG804 4.5 26.0 1.0
O3B A:ADP802 4.5 25.1 1.0
O A:GLY655 4.5 23.3 1.0
O A:HOH935 4.6 18.1 1.0
NE A:ARG659 4.6 25.8 1.0
O3A A:ADP802 4.6 23.8 1.0
NE A:ARG656 4.6 21.0 1.0
O A:HOH996 4.8 23.3 1.0
OG1 A:THR56 4.8 34.4 1.0
C A:GLY597 4.9 23.2 1.0
CA A:GLY57 4.9 24.9 1.0
O A:HOH956 5.0 24.8 1.0
NZ A:LYS60 5.0 23.8 1.0

Fluorine binding site 2 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 2 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:31.2
occ:1.00
 F2 A:BEF803 0.0 31.2 1.0
BE A:BEF803 1.6 28.0 1.0
MG A:MG804 2.0 26.0 1.0
O2B A:ADP802 2.4 25.6 1.0
F3 A:BEF803 2.5 27.0 1.0
F1 A:BEF803 2.5 26.0 1.0
O A:HOH996 2.6 23.3 1.0
O3B A:ADP802 2.8 25.1 1.0
O A:HOH935 2.9 18.1 1.0
PB A:ADP802 3.1 28.1 1.0
O A:HOH979 3.2 21.8 1.0
OE2 A:GLU249 3.3 21.2 1.0
CA A:GLY597 3.5 25.3 1.0
NH2 A:ARG659 3.9 21.5 1.0
O A:HOH977 4.0 28.3 1.0
N A:GLY597 4.1 27.6 1.0
O A:GLY597 4.2 19.6 1.0
O A:HOH956 4.2 24.8 1.0
C A:GLY597 4.2 23.2 1.0
O1B A:ADP802 4.3 23.6 1.0
O3A A:ADP802 4.3 23.8 1.0
NH1 A:ARG656 4.4 21.0 1.0
O2A A:ADP802 4.5 28.5 1.0
CD A:GLU249 4.5 28.3 1.0
CE A:LYS60 4.6 25.4 1.0
NZ A:LYS60 4.6 23.8 1.0
NH2 A:ARG656 4.7 19.7 1.0
NH1 A:ARG659 4.8 23.4 1.0
CZ A:ARG659 4.8 28.7 1.0
OE1 A:GLN652 5.0 27.1 1.0

Fluorine binding site 3 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 3 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:27.0
occ:1.00
 F3 A:BEF803 0.0 27.0 1.0
BE A:BEF803 1.6 28.0 1.0
O2B A:ADP802 2.4 25.6 1.0
F2 A:BEF803 2.5 31.2 1.0
F1 A:BEF803 2.6 26.0 1.0
NZ A:LYS60 2.8 23.8 1.0
O A:HOH956 2.9 24.8 1.0
O A:HOH996 3.3 23.3 1.0
CE A:LYS60 3.3 25.4 1.0
PB A:ADP802 3.5 28.1 1.0
CA A:THR56 3.5 24.5 1.0
CB A:ALA460 3.7 24.2 1.0
O1B A:ADP802 3.9 23.6 1.0
MG A:MG804 3.9 26.0 1.0
CG2 A:THR56 3.9 28.4 1.0
CB A:THR56 4.0 26.6 1.0
O3B A:ADP802 4.0 25.1 1.0
OE1 A:GLN652 4.2 27.1 1.0
N A:GLY57 4.3 22.6 1.0
N A:THR56 4.3 21.6 1.0
OE2 A:GLU249 4.3 21.2 1.0
O A:PRO55 4.4 21.0 1.0
N A:ALA460 4.4 26.2 1.0
C A:THR56 4.5 25.6 1.0
NH2 A:ARG656 4.6 19.7 1.0
C A:PRO55 4.6 22.3 1.0
CA A:ALA460 4.7 20.5 1.0
O A:ALA54 4.8 26.1 1.0
O3A A:ADP802 4.8 23.8 1.0
CD A:LYS60 4.8 36.8 1.0
NH1 A:ARG659 4.9 23.4 1.0
NH2 A:ARG659 5.0 21.5 1.0

Fluorine binding site 4 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 4 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:29.5
occ:1.00
 F1 B:BEF803 0.0 29.5 1.0
BE B:BEF803 1.5 31.9 1.0
NZ B:LYS60 2.3 32.8 1.0
O3B B:ADP802 2.4 30.8 1.0
F2 B:BEF803 2.5 26.9 1.0
F3 B:BEF803 2.5 26.7 1.0
O B:HOH954 2.8 35.4 1.0
CA B:THR56 3.3 28.0 1.0
CG2 B:THR56 3.5 24.4 1.0
PB B:ADP802 3.5 30.0 1.0
CB B:ALA460 3.6 24.1 1.0
CE B:LYS60 3.7 34.8 1.0
O B:HOH903 3.7 30.2 1.0
O B:HOH963 3.8 25.7 1.0
NE2 B:GLN652 3.8 40.9 1.0
O1B B:ADP802 3.9 34.2 1.0
CB B:THR56 3.9 26.2 1.0
N B:THR56 4.0 24.4 1.0
N B:GLY57 4.0 33.4 1.0
O B:PRO55 4.0 26.7 1.0
O2B B:ADP802 4.2 29.5 1.0
MG B:MG804 4.2 31.7 1.0
C B:THR56 4.2 31.5 1.0
C B:PRO55 4.2 25.1 1.0
N B:ALA460 4.4 27.4 1.0
O B:ALA54 4.5 39.3 1.0
CA B:ALA460 4.5 29.4 1.0
OE2 B:GLU249 4.6 27.7 1.0
CD B:LYS60 4.8 32.9 1.0
O3A B:ADP802 4.9 29.3 1.0

Fluorine binding site 5 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 5 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:26.9
occ:1.00
 F2 B:BEF803 0.0 26.9 1.0
BE B:BEF803 1.6 31.9 1.0
F3 B:BEF803 2.4 26.7 1.0
O3B B:ADP802 2.5 30.8 1.0
F1 B:BEF803 2.5 29.5 1.0
NH1 B:ARG656 2.7 26.0 1.0
NH1 B:ARG659 3.1 28.9 1.0
O B:HOH903 3.1 30.2 1.0
NH2 B:ARG659 3.3 22.4 1.0
O B:GLU596 3.5 46.6 1.0
CG2 B:THR56 3.6 24.4 1.0
CZ B:ARG659 3.6 32.3 1.0
CZ B:ARG656 3.7 25.4 1.0
CB B:THR56 3.8 26.2 1.0
CA B:THR56 3.9 28.0 1.0
PB B:ADP802 3.9 30.0 1.0
NH2 B:ARG656 3.9 23.3 1.0
N B:GLY57 4.0 33.4 1.0
NE2 B:GLN652 4.1 40.9 1.0
MG B:MG804 4.2 31.7 1.0
C B:THR56 4.4 31.5 1.0
O2B B:ADP802 4.4 29.5 1.0
O B:HOH946 4.5 24.1 1.0
O B:HOH954 4.5 35.4 1.0
O B:GLY655 4.6 29.3 1.0
NZ B:LYS60 4.6 32.8 1.0
O3A B:ADP802 4.7 29.3 1.0
C B:GLU596 4.7 30.4 1.0
OE2 B:GLU249 4.8 27.7 1.0
CA B:GLY597 4.8 34.8 1.0
NE B:ARG656 4.9 32.7 1.0
NE B:ARG659 4.9 28.2 1.0
O B:HOH963 4.9 25.7 1.0
CA B:GLY57 4.9 35.7 1.0
O1B B:ADP802 4.9 34.2 1.0
O B:GLY597 5.0 29.0 1.0

Fluorine binding site 6 out of 6 in 6fws

Go back to Fluorine Binding Sites List in 6fws
Fluorine binding site 6 out of 6 in the Structure of Ding in Complex with Ssdna and Adpbef


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Ding in Complex with Ssdna and Adpbef within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:26.7
occ:1.00
 F3 B:BEF803 0.0 26.7 1.0
BE B:BEF803 1.5 31.9 1.0
MG B:MG804 2.0 31.7 1.0
F2 B:BEF803 2.4 26.9 1.0
O3B B:ADP802 2.4 30.8 1.0
F1 B:BEF803 2.5 29.5 1.0
O B:HOH963 2.7 25.7 1.0
O2B B:ADP802 2.8 29.5 1.0
PB B:ADP802 3.1 30.0 1.0
O B:HOH946 3.1 24.1 1.0
O B:HOH903 3.1 30.2 1.0
O B:HOH1004 3.2 28.6 1.0
OE2 B:GLU249 3.3 27.7 1.0
O B:HOH954 3.8 35.4 1.0
NZ B:LYS60 3.8 32.8 1.0
O B:HOH951 4.0 20.6 1.0
O B:GLU596 4.0 46.6 1.0
O1B B:ADP802 4.1 34.2 1.0
NH2 B:ARG659 4.3 22.4 1.0
O3A B:ADP802 4.3 29.3 1.0
CA B:GLY597 4.3 34.8 1.0
NH1 B:ARG656 4.3 26.0 1.0
CD B:GLU249 4.5 32.1 1.0
O B:GLY597 4.6 29.0 1.0
NE2 B:GLN652 4.6 40.9 1.0
O2A B:ADP802 4.8 32.6 1.0
C B:GLY597 4.8 37.9 1.0

Reference:

K.Cheng, D.B.Wigley. Dna Translocation Mechanism of An Xpd Family Helicase. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30520735
DOI: 10.7554/ELIFE.42400
Page generated: Thu Aug 1 20:16:29 2024

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