Samarium in PDB 5um9: Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Protein crystallography data
The structure of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+, PDB code: 5um9
was solved by
S.E.Tsutakawa,
A.S.Arvai,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.67 /
2.81
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.846,
105.846,
100.709,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.8 /
26.6
|
Other elements in 5um9:
The structure of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ also contains other interesting chemical elements:
Samarium Binding Sites:
The binding sites of Samarium atom in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
(pdb code 5um9). This binding sites where shown within
5.0 Angstroms radius around Samarium atom.
In total 5 binding sites of Samarium where determined in the
Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+, PDB code: 5um9:
Jump to Samarium binding site number:
1;
2;
3;
4;
5;
Samarium binding site 1 out
of 5 in 5um9
Go back to
Samarium Binding Sites List in 5um9
Samarium binding site 1 out
of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 1 of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm402
b:86.8
occ:1.00
|
O
|
A:HOH502
|
2.2
|
88.3
|
1.0
|
OP1
|
E:DT7
|
2.2
|
96.7
|
1.0
|
OD2
|
A:ASP181
|
2.3
|
88.6
|
1.0
|
OD2
|
A:ASP179
|
2.3
|
0.5
|
1.0
|
O
|
A:HOH506
|
2.3
|
0.6
|
1.0
|
OD1
|
A:ASP179
|
2.6
|
91.5
|
1.0
|
CG
|
A:ASP179
|
2.7
|
95.4
|
1.0
|
OD1
|
A:ASP181
|
2.9
|
97.7
|
1.0
|
CG
|
A:ASP181
|
2.9
|
79.3
|
1.0
|
OE1
|
A:GLU160
|
3.1
|
92.1
|
1.0
|
P
|
E:DT7
|
3.4
|
97.8
|
1.0
|
CD
|
A:GLU160
|
3.5
|
0.6
|
1.0
|
HA2
|
A:GLY2
|
3.6
|
0.3
|
1.0
|
HG2
|
A:GLU160
|
3.7
|
0.9
|
1.0
|
O5'
|
E:DT7
|
3.8
|
0.4
|
1.0
|
OE2
|
A:GLU160
|
3.9
|
0.5
|
1.0
|
HH
|
A:TYR234
|
3.9
|
0.6
|
1.0
|
H5'
|
E:DT7
|
4.1
|
0.3
|
1.0
|
OP2
|
E:DT7
|
4.1
|
0.8
|
1.0
|
CG
|
A:GLU160
|
4.1
|
0.6
|
1.0
|
CB
|
A:ASP179
|
4.2
|
0.8
|
1.0
|
HZ2
|
A:LYS93
|
4.3
|
0.8
|
1.0
|
CA
|
A:GLY2
|
4.4
|
92.7
|
1.0
|
HE2
|
A:PHE185
|
4.4
|
0.5
|
1.0
|
HB3
|
A:ASP179
|
4.4
|
0.7
|
1.0
|
CB
|
A:ASP181
|
4.4
|
88.8
|
1.0
|
HZ1
|
A:LYS93
|
4.4
|
0.8
|
1.0
|
OH
|
A:TYR234
|
4.4
|
0.8
|
1.0
|
N
|
A:GLY2
|
4.5
|
98.8
|
1.0
|
C5'
|
E:DT7
|
4.5
|
0.3
|
1.0
|
O3'
|
E:DT6
|
4.6
|
0.8
|
1.0
|
HB3
|
A:ASP181
|
4.6
|
0.6
|
1.0
|
HB2
|
A:ASP179
|
4.6
|
0.7
|
1.0
|
HB2
|
A:GLU160
|
4.6
|
0.1
|
1.0
|
OE1
|
A:GLU158
|
4.7
|
0.8
|
1.0
|
H
|
A:ASP181
|
4.7
|
0.1
|
1.0
|
HA3
|
A:GLY2
|
4.7
|
0.3
|
1.0
|
NZ
|
A:LYS93
|
4.8
|
0.0
|
1.0
|
HB2
|
A:ASP181
|
4.8
|
0.6
|
1.0
|
HG3
|
A:GLU160
|
4.9
|
0.9
|
1.0
|
HE3
|
A:LYS93
|
4.9
|
0.4
|
1.0
|
CB
|
A:GLU160
|
5.0
|
83.4
|
1.0
|
HA
|
A:ASP179
|
5.0
|
0.0
|
1.0
|
|
Samarium binding site 2 out
of 5 in 5um9
Go back to
Samarium Binding Sites List in 5um9
Samarium binding site 2 out
of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 2 of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm403
b:0.9
occ:1.00
|
OE2
|
A:GLU57
|
1.9
|
0.1
|
1.0
|
OE1
|
A:GLU313
|
2.3
|
0.6
|
1.0
|
CD
|
A:GLU57
|
2.8
|
0.8
|
1.0
|
CD
|
A:GLU313
|
3.2
|
0.1
|
1.0
|
OE2
|
A:GLU313
|
3.3
|
97.3
|
1.0
|
OE1
|
A:GLU57
|
3.4
|
0.2
|
1.0
|
HG3
|
A:GLU57
|
3.8
|
0.8
|
1.0
|
HA
|
A:GLU313
|
3.9
|
0.1
|
1.0
|
CG
|
A:GLU57
|
4.0
|
0.0
|
1.0
|
SM
|
A:SM404
|
4.2
|
96.2
|
1.0
|
HG2
|
A:GLU57
|
4.4
|
0.8
|
1.0
|
O
|
A:GLU313
|
4.5
|
96.5
|
1.0
|
CG
|
A:GLU313
|
4.6
|
76.9
|
1.0
|
CA
|
A:GLU313
|
4.7
|
95.1
|
1.0
|
HB2
|
A:GLU313
|
4.8
|
0.1
|
1.0
|
HD22
|
A:ASN55
|
4.8
|
0.7
|
1.0
|
CB
|
A:GLU313
|
5.0
|
84.2
|
1.0
|
|
Samarium binding site 3 out
of 5 in 5um9
Go back to
Samarium Binding Sites List in 5um9
Samarium binding site 3 out
of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 3 of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm404
b:96.2
occ:1.00
|
OE2
|
A:GLU313
|
2.3
|
97.3
|
1.0
|
OE2
|
A:GLU59
|
2.3
|
99.1
|
1.0
|
OE1
|
A:GLU57
|
2.5
|
0.2
|
1.0
|
OE1
|
A:GLU59
|
2.8
|
0.7
|
1.0
|
CD
|
A:GLU59
|
2.9
|
91.2
|
1.0
|
CD
|
A:GLU313
|
3.3
|
0.1
|
1.0
|
CD
|
A:GLU57
|
3.6
|
0.8
|
1.0
|
OE1
|
A:GLU313
|
3.9
|
0.6
|
1.0
|
OE2
|
A:GLU57
|
4.0
|
0.1
|
1.0
|
HZ2
|
A:LYS314
|
4.0
|
0.6
|
1.0
|
HD21
|
A:ASN55
|
4.1
|
0.7
|
1.0
|
SM
|
A:SM403
|
4.2
|
0.9
|
1.0
|
HB2
|
A:GLU57
|
4.2
|
0.4
|
1.0
|
CG
|
A:GLU59
|
4.4
|
0.9
|
1.0
|
HG2
|
A:GLU313
|
4.4
|
92.2
|
1.0
|
CG
|
A:GLU313
|
4.4
|
76.9
|
1.0
|
HG3
|
A:GLU313
|
4.5
|
92.2
|
1.0
|
HB3
|
A:GLU57
|
4.7
|
0.4
|
1.0
|
HG3
|
A:GLU59
|
4.7
|
0.5
|
1.0
|
HG2
|
A:GLU59
|
4.7
|
0.5
|
1.0
|
CG
|
A:GLU57
|
4.7
|
0.0
|
1.0
|
CB
|
A:GLU57
|
4.8
|
0.4
|
1.0
|
ND2
|
A:ASN55
|
4.8
|
96.5
|
1.0
|
HZ3
|
A:LYS314
|
4.8
|
0.6
|
1.0
|
NZ
|
A:LYS314
|
4.8
|
1.0
|
1.0
|
HD22
|
A:ASN55
|
4.9
|
0.7
|
1.0
|
|
Samarium binding site 4 out
of 5 in 5um9
Go back to
Samarium Binding Sites List in 5um9
Samarium binding site 4 out
of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 4 of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm405
b:0.6
occ:0.81
|
O
|
D:HOH107
|
2.3
|
0.4
|
1.0
|
O
|
A:HOH517
|
2.3
|
0.3
|
1.0
|
OE2
|
A:GLU106
|
3.7
|
0.3
|
1.0
|
OE1
|
A:GLU106
|
4.0
|
0.7
|
1.0
|
OP1
|
D:DC8
|
4.1
|
0.2
|
1.0
|
CD
|
A:GLU106
|
4.3
|
0.5
|
1.0
|
OP2
|
D:DC8
|
4.8
|
0.2
|
1.0
|
P
|
D:DC8
|
4.9
|
0.5
|
1.0
|
|
Samarium binding site 5 out
of 5 in 5um9
Go back to
Samarium Binding Sites List in 5um9
Samarium binding site 5 out
of 5 in the Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+
Mono view
Stereo pair view
|
A full contact list of Samarium with other atoms in the Sm binding
site number 5 of Flap Endonuclease 1 (FEN1) D86N with 5'-Flap Substrate Dna and SM3+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Sm406
b:0.4
occ:0.36
|
OE2
|
A:GLU338
|
2.3
|
0.6
|
1.0
|
O
|
A:HOH518
|
2.3
|
0.4
|
1.0
|
O
|
A:HOH507
|
2.3
|
0.3
|
1.0
|
CD
|
A:GLU338
|
2.7
|
0.3
|
1.0
|
OE1
|
A:GLU338
|
3.0
|
0.9
|
1.0
|
HG2
|
A:GLU338
|
3.6
|
0.8
|
1.0
|
HH22
|
A:ARG332
|
3.7
|
0.8
|
1.0
|
CG
|
A:GLU338
|
3.8
|
0.8
|
1.0
|
NH2
|
A:ARG332
|
4.3
|
0.9
|
1.0
|
HH21
|
A:ARG332
|
4.4
|
0.8
|
1.0
|
HB3
|
A:GLU338
|
4.4
|
0.2
|
1.0
|
HG3
|
A:GLU338
|
4.5
|
0.8
|
1.0
|
CB
|
A:GLU338
|
4.7
|
0.3
|
1.0
|
HB2
|
A:GLU300
|
4.8
|
0.9
|
1.0
|
|
Reference:
S.E.Tsutakawa,
M.J.Thompson,
A.S.Arvai,
A.J.Neil,
S.J.Shaw,
S.I.Algasaier,
J.C.Kim,
L.D.Finger,
E.Jardine,
V.J.B.Gotham,
A.H.Sarker,
M.Z.Her,
F.Rashid,
S.M.Hamdan,
S.M.Mirkin,
J.A.Grasby,
J.A.Tainer.
Phosphate Steering By Flap Endonuclease 1 Promotes 5'-Flap Specificity and Incision to Prevent Genome Instability. Nat Commun V. 8 15855 2017.
ISSN: ESSN 2041-1723
PubMed: 28653660
DOI: 10.1038/NCOMMS15855
Page generated: Thu Oct 10 13:57:02 2024
|