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Fluorine in PDB 8v7g: Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+

Enzymatic activity of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7g was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.59 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.36, 98.36, 82.047, 90, 90, 120
R / Rfree (%) 18.4 / 19.8

Other elements in 8v7g:

The structure of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ (pdb code 8v7g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7g:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8v7g

Go back to Fluorine Binding Sites List in 8v7g
Fluorine binding site 1 out of 4 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F8

b:22.2
occ:0.70
 F1 P:U7B8 0.0 22.2 0.7
C2' P:U7B8 1.4 22.5 0.7
F1 P:U7B8 1.7 21.9 0.3
C2' P:U7B8 2.1 22.2 0.3
F2 P:U7B8 2.2 20.9 0.7
O3' P:U7B8 2.3 20.1 0.3
C1' P:U7B8 2.3 20.9 0.3
C3' P:U7B8 2.4 25.2 0.7
C1' P:U7B8 2.4 20.9 0.7
C3' P:U7B8 2.5 24.6 0.3
O3' P:U7B8 2.6 19.8 0.7
O A:HOH765 2.7 20.3 1.0
C4' P:U7B8 3.0 20.4 0.3
O A:HOH787 3.1 22.0 1.0
C4' P:U7B8 3.1 20.1 0.7
O4' P:U7B8 3.2 21.7 0.3
O4' P:U7B8 3.3 21.3 0.7
O2 P:U7B8 3.4 21.8 0.7
O2 P:U7B8 3.4 21.8 0.3
CB A:SER113 3.4 17.9 1.0
F2 P:U7B8 3.4 23.8 0.3
OG A:SER113 3.5 20.7 1.0
N1 P:U7B8 3.5 21.3 0.7
N1 P:U7B8 3.5 21.3 0.3
O4' A:DZ4503 3.8 15.3 1.0
C2 P:U7B8 3.9 21.4 0.7
O5' A:DZ4503 3.9 15.0 1.0
C2 P:U7B8 3.9 21.4 0.3
C5' A:DZ4503 4.1 15.9 1.0
CG2 A:ILE114 4.2 16.0 1.0
N A:ILE114 4.4 14.9 1.0
C5' P:U7B8 4.5 24.9 0.3
C5' P:U7B8 4.5 25.0 0.7
C8 A:DZ4503 4.6 17.4 1.0
C4' A:DZ4503 4.6 14.3 1.0
C6 P:U7B8 4.6 22.4 0.7
MG A:MG502 4.6 15.6 1.0
OD1 A:ASP115 4.7 15.3 1.0
C6 P:U7B8 4.7 22.3 0.3
CA A:SER113 4.7 15.0 1.0
OE2 A:GLU116 4.7 21.9 1.0
N9 A:DZ4503 4.8 14.5 1.0
C1' A:DZ4503 4.9 14.7 1.0
O2A A:DZ4503 4.9 17.2 1.0
PA A:DZ4503 4.9 15.6 1.0
C A:SER113 5.0 14.2 1.0

Fluorine binding site 2 out of 4 in 8v7g

Go back to Fluorine Binding Sites List in 8v7g
Fluorine binding site 2 out of 4 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F8

b:21.9
occ:0.30
 F1 P:U7B8 0.0 21.9 0.3
F2 P:U7B8 0.6 20.9 0.7
C2' P:U7B8 1.3 22.5 0.7
C2' P:U7B8 1.4 22.2 0.3
F1 P:U7B8 1.7 22.2 0.7
F2 P:U7B8 2.2 23.8 0.3
C3' P:U7B8 2.4 25.2 0.7
C1' P:U7B8 2.4 20.9 0.3
C3' P:U7B8 2.5 24.6 0.3
C1' P:U7B8 2.7 20.9 0.7
O3' P:U7B8 2.7 20.1 0.3
O A:HOH765 2.8 20.3 1.0
O5' A:DZ4503 2.8 15.0 1.0
C8 A:DZ4503 2.9 17.4 1.0
O3' P:U7B8 2.9 19.8 0.7
O4' A:DZ4503 3.1 15.3 1.0
N1 P:U7B8 3.2 21.3 0.3
N1 P:U7B8 3.2 21.3 0.7
N9 A:DZ4503 3.4 14.5 1.0
O2 P:U7B8 3.4 21.8 0.3
O2 P:U7B8 3.4 21.8 0.7
N7 A:DZ4503 3.5 16.8 1.0
C5' A:DZ4503 3.5 15.9 1.0
O4' P:U7B8 3.5 21.7 0.3
C4' P:U7B8 3.5 20.4 0.3
O A:HOH761 3.5 28.7 0.7
C2 P:U7B8 3.6 21.4 0.7
C2 P:U7B8 3.6 21.4 0.3
O4' P:U7B8 3.6 21.3 0.7
C4' P:U7B8 3.6 20.1 0.7
O2A A:DZ4503 3.7 17.2 1.0
C1' A:DZ4503 3.8 14.7 1.0
C4' A:DZ4503 3.9 14.3 1.0
PA A:DZ4503 4.0 15.6 1.0
C6 P:U7B8 4.1 22.3 0.3
C6 P:U7B8 4.1 22.4 0.7
C4 A:DZ4503 4.1 15.9 1.0
C5 A:DZ4503 4.2 16.9 1.0
O A:HOH787 4.5 22.0 1.0
N3 P:U7B8 4.6 20.1 0.7
C3' A:DZ4503 4.7 14.0 1.0
O1A A:DZ4503 4.7 16.5 1.0
N3 P:U7B8 4.7 20.2 0.3
C5' P:U7B8 4.7 24.9 0.3
C5' P:U7B8 4.8 25.0 0.7
O5' P:U7B8 4.8 30.4 1.0
MG A:MG502 4.8 15.6 1.0
OG A:SER113 4.9 20.7 1.0
C2' A:DZ4503 5.0 14.1 1.0
CG2 A:ILE114 5.0 16.0 1.0

Fluorine binding site 3 out of 4 in 8v7g

Go back to Fluorine Binding Sites List in 8v7g
Fluorine binding site 3 out of 4 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F8

b:20.9
occ:0.70
 F2 P:U7B8 0.0 20.9 0.7
F1 P:U7B8 0.6 21.9 0.3
C2' P:U7B8 1.1 22.2 0.3
C2' P:U7B8 1.3 22.5 0.7
F2 P:U7B8 1.6 23.8 0.3
F1 P:U7B8 2.2 22.2 0.7
C1' P:U7B8 2.2 20.9 0.3
C3' P:U7B8 2.4 25.2 0.7
C3' P:U7B8 2.4 24.6 0.3
C1' P:U7B8 2.5 20.9 0.7
N1 P:U7B8 2.7 21.3 0.3
C8 A:DZ4503 2.8 17.4 1.0
N1 P:U7B8 2.8 21.3 0.7
O A:HOH761 3.0 28.7 0.7
O3' P:U7B8 3.0 20.1 0.3
N7 A:DZ4503 3.1 16.8 1.0
O5' A:DZ4503 3.1 15.0 1.0
O A:HOH765 3.2 20.3 1.0
O3' P:U7B8 3.2 19.8 0.7
C2 P:U7B8 3.2 21.4 0.7
C2 P:U7B8 3.3 21.4 0.3
O4' P:U7B8 3.3 21.7 0.3
O2 P:U7B8 3.3 21.8 0.3
O2 P:U7B8 3.3 21.8 0.7
O4' P:U7B8 3.4 21.3 0.7
N9 A:DZ4503 3.4 14.5 1.0
C4' P:U7B8 3.5 20.4 0.3
O4' A:DZ4503 3.5 15.3 1.0
C6 P:U7B8 3.5 22.3 0.3
C4' P:U7B8 3.5 20.1 0.7
C6 P:U7B8 3.6 22.4 0.7
O2A A:DZ4503 3.6 17.2 1.0
C5 A:DZ4503 3.9 16.9 1.0
C5' A:DZ4503 4.0 15.9 1.0
C4 A:DZ4503 4.0 15.9 1.0
PA A:DZ4503 4.1 15.6 1.0
C1' A:DZ4503 4.1 14.7 1.0
N3 P:U7B8 4.2 20.1 0.7
N3 P:U7B8 4.3 20.2 0.3
C4' A:DZ4503 4.3 14.3 1.0
C5 P:U7B8 4.5 21.7 0.7
O5' P:U7B8 4.5 30.4 1.0
C5 P:U7B8 4.5 21.8 0.3
C5' P:U7B8 4.6 24.9 0.3
C5' P:U7B8 4.6 25.0 0.7
C4 P:U7B8 4.8 21.6 0.7
C4 P:U7B8 4.9 21.6 0.3
C6 A:DZ4503 4.9 20.2 1.0
O A:HOH787 4.9 22.0 1.0
O1A A:DZ4503 4.9 16.5 1.0

Fluorine binding site 4 out of 4 in 8v7g

Go back to Fluorine Binding Sites List in 8v7g
Fluorine binding site 4 out of 4 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F8

b:23.8
occ:0.30
 F2 P:U7B8 0.0 23.8 0.3
C2' P:U7B8 1.4 22.2 0.3
F2 P:U7B8 1.6 20.9 0.7
O A:HOH761 1.6 28.7 0.7
F1 P:U7B8 2.2 21.9 0.3
C2' P:U7B8 2.2 22.5 0.7
C3' P:U7B8 2.4 24.6 0.3
C1' P:U7B8 2.4 20.9 0.3
C3' P:U7B8 2.5 25.2 0.7
N1 P:U7B8 2.6 21.3 0.3
N1 P:U7B8 2.7 21.3 0.7
C1' P:U7B8 2.7 20.9 0.7
C6 P:U7B8 2.8 22.3 0.3
C6 P:U7B8 2.8 22.4 0.7
O2A A:DZ4503 3.0 17.2 1.0
O4' P:U7B8 3.0 21.3 0.7
O4' P:U7B8 3.1 21.7 0.3
N7 A:DZ4503 3.1 16.8 1.0
C8 A:DZ4503 3.3 17.4 1.0
C4' P:U7B8 3.3 20.4 0.3
C4' P:U7B8 3.4 20.1 0.7
F1 P:U7B8 3.4 22.2 0.7
O5' P:U7B8 3.5 30.4 1.0
O3' P:U7B8 3.5 20.1 0.3
C2 P:U7B8 3.6 21.4 0.7
C2 P:U7B8 3.6 21.4 0.3
O3' P:U7B8 3.6 19.8 0.7
O P:HOH110 3.7 34.0 1.0
O5' A:DZ4503 3.7 15.0 1.0
C5 P:U7B8 3.7 21.7 0.7
C5 P:U7B8 3.8 21.8 0.3
C5' P:U7B8 4.0 24.9 0.3
C5' P:U7B8 4.1 25.0 0.7
PA A:DZ4503 4.1 15.6 1.0
O2 P:U7B8 4.1 21.8 0.3
O2 P:U7B8 4.1 21.8 0.7
C5 A:DZ4503 4.2 16.9 1.0
N9 A:DZ4503 4.3 14.5 1.0
N3 P:U7B8 4.3 20.1 0.7
C4 P:U7B8 4.4 21.6 0.7
N3 P:U7B8 4.4 20.2 0.3
C4 P:U7B8 4.5 21.6 0.3
NH1 A:ARG61 4.5 37.4 1.0
O A:HOH765 4.7 20.3 1.0
OP2 P:U7B8 4.7 32.7 1.0
C4 A:DZ4503 4.8 15.9 1.0
P P:U7B8 4.8 30.2 1.0
O A:HOH773 4.8 24.7 1.0
O4' A:DZ4503 4.8 15.3 1.0
C5' A:DZ4503 4.9 15.9 1.0
CZ A:ARG61 5.0 38.2 1.0

Reference:

C.Chang, Y.Gao. Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MN2+ To Be Published.
Page generated: Wed Jul 16 09:39:55 2025

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