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Fluorine in PDB 6v3w: Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397

Protein crystallography data

The structure of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397, PDB code: 6v3w was solved by K.K.Swinger, J.M.Gozgit, M.M.Vasbinder, T.J.Wigle, K.W.Kuntz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.78 / 2.04
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.466, 80.466, 142.648, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 25.5

Other elements in 6v3w:

The structure of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 (pdb code 6v3w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397, PDB code: 6v3w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 1 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:77.3
occ:1.00
F22 A:QO4701 0.0 77.3 1.0
C21 A:QO4701 1.4 67.1 1.0
F24 A:QO4701 2.2 77.4 1.0
F23 A:QO4701 2.3 74.1 1.0
C18 A:QO4701 2.4 68.0 1.0
C19 A:QO4701 2.8 65.2 1.0
C17 A:QO4701 3.6 63.8 1.0
CB A:VAL570 3.8 68.5 1.0
CG1 A:VAL570 4.0 73.9 1.0
CA A:GLY573 4.1 65.5 1.0
N20 A:QO4701 4.1 69.2 1.0
O A:VAL570 4.2 63.0 1.0
C A:GLY573 4.3 66.0 1.0
CA A:VAL570 4.4 68.3 1.0
N A:ILE574 4.4 62.3 1.0
CG1 A:ILE574 4.7 62.2 1.0
N16 A:QO4701 4.7 62.0 1.0
C A:VAL570 4.8 62.4 1.0
O A:GLY573 4.9 64.5 1.0
C15 A:QO4701 4.9 66.7 1.0
CG2 A:VAL570 5.0 65.3 1.0

Fluorine binding site 2 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 2 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:74.1
occ:1.00
F23 A:QO4701 0.0 74.1 1.0
C21 A:QO4701 1.4 67.1 1.0
F24 A:QO4701 2.2 77.4 1.0
F22 A:QO4701 2.3 77.3 1.0
C18 A:QO4701 2.3 68.0 1.0
C17 A:QO4701 3.0 63.8 1.0
C19 A:QO4701 3.3 65.2 1.0
CG2 A:VAL583 3.8 0.5 1.0
N16 A:QO4701 4.2 62.0 1.0
N20 A:QO4701 4.4 69.2 1.0
C15 A:QO4701 4.8 66.7 1.0
C A:GLY573 4.9 66.0 1.0
CB A:VAL583 4.9 0.4 1.0
O A:ASN578 4.9 62.1 1.0
O A:GLY573 5.0 64.5 1.0
CB A:HIS577 5.0 77.1 1.0
CG1 A:VAL583 5.0 0.2 1.0

Fluorine binding site 3 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 3 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:77.4
occ:1.00
F24 A:QO4701 0.0 77.4 1.0
C21 A:QO4701 1.4 67.1 1.0
F23 A:QO4701 2.2 74.1 1.0
F22 A:QO4701 2.2 77.3 1.0
C18 A:QO4701 2.4 68.0 1.0
C A:GLY573 2.9 66.0 1.0
C17 A:QO4701 2.9 63.8 1.0
O A:GLY573 3.1 64.5 1.0
N A:ILE574 3.1 62.3 1.0
CA A:GLY573 3.4 65.5 1.0
C19 A:QO4701 3.7 65.2 1.0
CA A:ILE574 3.7 60.6 1.0
CG1 A:ILE574 3.7 62.2 1.0
O A:ASN578 3.9 62.1 1.0
N16 A:QO4701 4.2 62.0 1.0
CB A:HIS577 4.3 77.1 1.0
CB A:ILE574 4.3 60.9 1.0
O A:VAL570 4.4 63.0 1.0
N A:GLY573 4.6 65.0 1.0
N20 A:QO4701 4.7 69.2 1.0
CD2 A:HIS577 4.8 85.7 1.0
CD1 A:ILE574 4.9 63.0 1.0
CG A:HIS577 4.9 81.7 1.0
C A:ILE574 4.9 62.2 1.0
C15 A:QO4701 5.0 66.7 1.0
C A:ASN578 5.0 57.0 1.0

Fluorine binding site 4 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 4 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:70.9
occ:1.00
F34 A:QO4701 0.0 70.9 1.0
C33 A:QO4701 1.4 58.4 1.0
F35 A:QO4701 2.2 62.5 1.0
F36 A:QO4701 2.3 63.8 1.0
C27 A:QO4701 2.4 57.4 1.0
N25 A:QO4701 2.4 61.4 1.0
C26 A:QO4701 2.7 59.2 1.0
CB A:TYR596 3.3 60.0 1.0
C28 A:QO4701 3.6 56.1 1.0
CE2 A:TYR603 3.7 66.4 1.0
C2 A:QO4701 3.7 65.9 1.0
C1 A:QO4701 4.0 63.3 1.0
CD2 A:TYR596 4.0 66.9 1.0
O29 A:QO4701 4.1 58.2 1.0
CG A:TYR596 4.1 64.5 1.0
CE1 A:PHE607 4.1 63.4 1.0
C32 A:QO4701 4.1 56.9 1.0
CD2 A:TYR603 4.2 64.7 1.0
C A:TYR596 4.4 53.3 1.0
O A:TYR596 4.5 56.9 1.0
CA A:TYR596 4.5 55.1 1.0
CZ A:PHE607 4.5 68.4 1.0
CG2 A:ILE660 4.5 63.8 1.0
CD1 A:PHE607 4.6 63.4 1.0
N A:PHE597 4.6 51.0 1.0
C3 A:QO4701 4.7 62.5 1.0
N30 A:QO4701 4.7 57.3 1.0
CZ A:TYR603 4.7 73.4 1.0
OH A:TYR603 4.8 78.8 1.0
C A:PHE597 4.9 54.5 1.0
CB A:ALA598 4.9 52.3 1.0
N31 A:QO4701 4.9 63.2 1.0
O A:PHE597 5.0 53.8 1.0

Fluorine binding site 5 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 5 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:62.5
occ:1.00
F35 A:QO4701 0.0 62.5 1.0
C33 A:QO4701 1.4 58.4 1.0
F34 A:QO4701 2.2 70.9 1.0
F36 A:QO4701 2.2 63.8 1.0
C27 A:QO4701 2.4 57.4 1.0
O29 A:QO4701 2.7 58.2 1.0
C28 A:QO4701 2.9 56.1 1.0
O A:TYR596 3.3 56.9 1.0
C A:PHE597 3.4 54.5 1.0
N A:ALA598 3.4 54.1 1.0
CA A:PHE597 3.4 48.6 1.0
C A:TYR596 3.5 53.3 1.0
N A:PHE597 3.5 51.0 1.0
C26 A:QO4701 3.5 59.2 1.0
CB A:ALA598 3.7 52.3 1.0
OG A:SER604 3.8 53.1 1.0
CB A:TYR596 3.8 60.0 1.0
O A:PHE563 3.9 51.9 1.0
N25 A:QO4701 3.9 61.4 1.0
O A:PHE597 4.0 53.8 1.0
CA A:ALA598 4.1 50.9 1.0
N30 A:QO4701 4.2 57.3 1.0
CA A:TYR596 4.3 55.1 1.0
ND1 A:HIS564 4.4 57.3 1.0
C32 A:QO4701 4.6 56.9 1.0
CA A:HIS564 4.8 50.7 1.0
CD2 A:TYR603 4.8 64.7 1.0
CB A:SER604 4.9 57.0 1.0
N31 A:QO4701 4.9 63.2 1.0
CE2 A:TYR603 4.9 66.4 1.0
CB A:PHE597 4.9 49.8 1.0
C A:PHE563 4.9 49.1 1.0
CE1 A:HIS564 5.0 57.5 1.0

Fluorine binding site 6 out of 6 in 6v3w

Go back to Fluorine Binding Sites List in 6v3w
Fluorine binding site 6 out of 6 in the Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Poly(Adp-Ribose) Polymerase 12, Catalytic Fragment with Four Point Mutations in Complex with Rbn-2397 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:63.8
occ:1.00
F36 A:QO4701 0.0 63.8 1.0
C33 A:QO4701 1.4 58.4 1.0
F35 A:QO4701 2.2 62.5 1.0
F34 A:QO4701 2.3 70.9 1.0
C27 A:QO4701 2.4 57.4 1.0
O29 A:QO4701 2.8 58.2 1.0
C28 A:QO4701 2.9 56.1 1.0
CD2 A:TYR603 3.2 64.7 1.0
CE2 A:TYR603 3.3 66.4 1.0
CE1 A:PHE607 3.4 63.4 1.0
C26 A:QO4701 3.5 59.2 1.0
CD1 A:PHE607 3.5 63.4 1.0
OG A:SER604 3.5 53.1 1.0
CA A:SER604 3.6 57.1 1.0
CB A:ALA598 3.8 52.3 1.0
N25 A:QO4701 3.9 61.4 1.0
N A:SER604 4.0 52.6 1.0
O A:TYR603 4.0 56.7 1.0
CB A:SER604 4.1 57.0 1.0
C A:TYR603 4.2 56.4 1.0
N30 A:QO4701 4.2 57.3 1.0
CG A:TYR603 4.3 60.0 1.0
CZ A:PHE607 4.4 68.4 1.0
CZ A:TYR603 4.5 73.4 1.0
CG A:PHE607 4.6 65.5 1.0
C32 A:QO4701 4.6 56.9 1.0
N A:ALA598 4.8 54.1 1.0
C A:SER604 4.8 56.4 1.0
CB A:TYR603 4.9 58.3 1.0
CA A:ALA598 4.9 50.9 1.0
N31 A:QO4701 4.9 63.2 1.0
O A:SER604 5.0 54.1 1.0

Reference:

J.M.Gozgit, M.M.Vasbinder, R.Abo, K.Kunii, K.Kuplast-Barr, B.Gui, A.Lu, K.K.Swinger, T.J.Wigle, D.Blackwell, C.R.Majer, Y.Ren, M.Niepel, Z.Varsamis, S.Nayak, E.Bamberg, J.Mo, W.D.Church, J.Song, L.Utley, K.W.Kuntz, V.Richon, H.Keilhack. PARP7 Negatively Regulates the Type I Interferon Response in Cancer Cells, and Its Inhibition Triggers Antitumor Immunity To Be Published.
Page generated: Tue Jul 15 16:31:23 2025

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