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:
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
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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
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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
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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: Fri Aug 2 02:53:08 2024
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