Iron in PDB 9bs2: Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Enzymatic activity of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
All present enzymatic activity of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution:
3.2.2.31;
Protein crystallography data
The structure of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution, PDB code: 9bs2
was solved by
C.H.Trasvina-Arenas,
N.Tamayo,
W.J.Lin,
M.Demir,
A.J.Fisher,
S.S.David,
M.P.Horvath,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.00 /
1.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.5,
86,
140.64,
90,
90,
90
|
R / Rfree (%)
|
20.6 /
23
|
Other elements in 9bs2:
The structure of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
(pdb code 9bs2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution, PDB code: 9bs2:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 1 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:23.9
occ:0.53
|
FE1
|
A:SF4401
|
0.0
|
23.9
|
0.5
|
S4
|
A:SF4401
|
1.4
|
23.1
|
0.5
|
FE1
|
A:SF4401
|
1.5
|
23.4
|
0.5
|
FE2
|
A:SF4401
|
1.5
|
25.0
|
0.5
|
S3
|
A:SF4401
|
2.2
|
22.6
|
0.5
|
S3
|
A:SF4401
|
2.3
|
23.5
|
0.5
|
S2
|
A:SF4401
|
2.3
|
22.9
|
0.5
|
SG
|
A:CYS208
|
2.3
|
32.8
|
0.5
|
S4
|
A:SF4401
|
2.3
|
23.1
|
0.5
|
FE3
|
A:SF4401
|
2.5
|
22.9
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.3
|
0.5
|
HB2
|
A:CYS208
|
2.7
|
49.2
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
FE2
|
A:SF4401
|
2.7
|
25.9
|
0.5
|
FE4
|
A:SF4401
|
2.9
|
25.2
|
0.5
|
HB2
|
A:CYS208
|
3.0
|
54.4
|
0.5
|
CB
|
A:CYS208
|
3.1
|
45.3
|
0.5
|
HB3
|
A:CYS208
|
3.1
|
49.2
|
0.5
|
CB
|
A:CYS208
|
3.1
|
41.0
|
0.5
|
HA
|
A:CYS205
|
3.2
|
57.1
|
0.5
|
HA
|
A:CYS205
|
3.2
|
57.4
|
0.5
|
SG
|
A:CYS208
|
3.2
|
37.7
|
0.5
|
S2
|
A:SF4401
|
3.2
|
23.2
|
0.5
|
S1
|
A:SF4401
|
3.2
|
23.9
|
0.5
|
HB3
|
A:CYS208
|
3.2
|
54.4
|
0.5
|
SG
|
A:CYS205
|
3.5
|
42.3
|
0.5
|
S1
|
A:SF4401
|
3.8
|
23.9
|
0.5
|
HG12
|
A:VAL197
|
3.9
|
43.1
|
1.0
|
HB2
|
A:CYS198
|
4.0
|
35.6
|
0.5
|
CA
|
A:CYS205
|
4.1
|
47.6
|
0.5
|
HA
|
A:GLN211
|
4.1
|
58.6
|
0.5
|
CA
|
A:CYS205
|
4.1
|
47.8
|
0.5
|
HB3
|
A:CYS205
|
4.3
|
56.5
|
0.5
|
CB
|
A:CYS205
|
4.3
|
47.9
|
0.5
|
HA
|
A:GLN211
|
4.4
|
61.5
|
0.5
|
HB2
|
A:CYS198
|
4.5
|
34.5
|
0.5
|
SG
|
A:CYS198
|
4.5
|
27.2
|
0.5
|
HG23
|
A:VAL210
|
4.5
|
49.9
|
0.5
|
HB2
|
A:CYS214
|
4.5
|
60.1
|
0.5
|
CA
|
A:CYS208
|
4.5
|
48.7
|
0.5
|
CB
|
A:CYS205
|
4.5
|
47.1
|
0.5
|
HB3
|
A:CYS205
|
4.6
|
57.4
|
0.5
|
HA
|
A:CYS198
|
4.6
|
34.5
|
0.5
|
HG23
|
A:VAL210
|
4.6
|
50.1
|
0.5
|
HB2
|
A:GLN211
|
4.6
|
64.6
|
0.5
|
HG11
|
A:VAL197
|
4.6
|
43.1
|
1.0
|
CA
|
A:CYS208
|
4.6
|
48.4
|
0.5
|
HB2
|
A:CYS214
|
4.6
|
60.4
|
0.5
|
HA
|
A:CYS198
|
4.6
|
34.7
|
0.5
|
CG1
|
A:VAL197
|
4.7
|
36.0
|
1.0
|
CB
|
A:CYS198
|
4.7
|
29.7
|
0.5
|
SG
|
A:CYS205
|
4.7
|
34.8
|
0.5
|
SG
|
A:CYS198
|
4.8
|
27.5
|
0.5
|
HA
|
A:CYS208
|
4.8
|
58.4
|
0.5
|
O
|
A:CYS205
|
4.8
|
53.3
|
1.0
|
SG
|
A:CYS214
|
4.8
|
38.0
|
0.5
|
N
|
A:CYS205
|
4.8
|
45.4
|
1.0
|
CA
|
A:GLN211
|
4.9
|
48.8
|
0.5
|
CB
|
A:CYS198
|
4.9
|
28.8
|
0.5
|
HA
|
A:CYS208
|
4.9
|
58.1
|
0.5
|
HB2
|
A:PRO203
|
4.9
|
49.6
|
1.0
|
N
|
A:GLN211
|
4.9
|
47.9
|
0.5
|
H
|
A:CYS208
|
5.0
|
60.0
|
0.5
|
HG22
|
A:VAL210
|
5.0
|
50.1
|
0.5
|
HD21
|
A:LEU193
|
5.0
|
49.3
|
1.0
|
C
|
A:CYS205
|
5.0
|
42.6
|
1.0
|
HB2
|
A:GLN211
|
5.0
|
65.2
|
0.5
|
SG
|
A:CYS214
|
5.0
|
49.5
|
0.5
|
HB2
|
A:PHE217
|
5.0
|
68.6
|
1.0
|
H
|
A:GLN211
|
5.0
|
57.4
|
0.5
|
|
Iron binding site 2 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 2 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:23.4
occ:0.47
|
FE1
|
A:SF4401
|
0.0
|
23.4
|
0.5
|
FE1
|
A:SF4401
|
1.5
|
23.9
|
0.5
|
SG
|
A:CYS208
|
1.9
|
32.8
|
0.5
|
S2
|
A:SF4401
|
2.0
|
22.9
|
0.5
|
SG
|
A:CYS208
|
2.2
|
37.7
|
0.5
|
S2
|
A:SF4401
|
2.2
|
23.2
|
0.5
|
S4
|
A:SF4401
|
2.3
|
23.1
|
0.5
|
S3
|
A:SF4401
|
2.3
|
22.6
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.2
|
0.5
|
FE2
|
A:SF4401
|
2.8
|
25.0
|
0.5
|
HB2
|
A:CYS208
|
3.0
|
49.2
|
0.5
|
HG23
|
A:VAL210
|
3.0
|
49.9
|
0.5
|
CB
|
A:CYS208
|
3.1
|
41.0
|
0.5
|
HG23
|
A:VAL210
|
3.2
|
50.1
|
0.5
|
S3
|
A:SF4401
|
3.2
|
23.5
|
0.5
|
HB3
|
A:CYS208
|
3.2
|
49.2
|
0.5
|
FE4
|
A:SF4401
|
3.3
|
25.3
|
0.5
|
CB
|
A:CYS208
|
3.3
|
45.3
|
0.5
|
HB3
|
A:CYS208
|
3.4
|
54.4
|
0.5
|
FE3
|
A:SF4401
|
3.5
|
22.9
|
0.5
|
S4
|
A:SF4401
|
3.5
|
23.1
|
0.5
|
HG22
|
A:VAL210
|
3.5
|
50.1
|
0.5
|
HB2
|
A:CYS208
|
3.6
|
54.4
|
0.5
|
HA
|
A:GLN211
|
3.7
|
58.6
|
0.5
|
CG2
|
A:VAL210
|
3.8
|
41.8
|
0.5
|
HG22
|
A:VAL210
|
3.8
|
49.9
|
0.5
|
HD21
|
A:LEU193
|
3.8
|
49.3
|
1.0
|
CG2
|
A:VAL210
|
3.8
|
41.6
|
0.5
|
S1
|
A:SF4401
|
3.9
|
23.9
|
0.5
|
H
|
A:VAL210
|
3.9
|
51.6
|
0.5
|
HA
|
A:GLN211
|
4.0
|
61.5
|
0.5
|
H
|
A:VAL210
|
4.1
|
51.5
|
0.5
|
HB2
|
A:CYS198
|
4.1
|
35.6
|
0.5
|
HB2
|
A:CYS214
|
4.1
|
60.1
|
0.5
|
FE2
|
A:SF4401
|
4.1
|
25.9
|
0.5
|
N
|
A:GLN211
|
4.1
|
47.9
|
0.5
|
HB2
|
A:CYS214
|
4.2
|
60.4
|
0.5
|
HD11
|
A:LEU193
|
4.2
|
47.7
|
1.0
|
H
|
A:GLN211
|
4.3
|
57.4
|
0.5
|
HG21
|
A:VAL210
|
4.3
|
50.1
|
0.5
|
C
|
A:VAL210
|
4.3
|
49.0
|
0.5
|
HA
|
A:CYS205
|
4.3
|
57.1
|
0.5
|
HG21
|
A:VAL210
|
4.3
|
49.9
|
0.5
|
HD21
|
A:LEU154
|
4.3
|
54.8
|
1.0
|
HA
|
A:CYS205
|
4.3
|
57.4
|
0.5
|
HG12
|
A:VAL197
|
4.3
|
43.1
|
1.0
|
CA
|
A:GLN211
|
4.4
|
48.8
|
0.5
|
C
|
A:VAL210
|
4.4
|
49.2
|
0.5
|
N
|
A:GLN211
|
4.4
|
48.7
|
0.5
|
HB2
|
A:CYS198
|
4.5
|
34.5
|
0.5
|
CA
|
A:CYS208
|
4.5
|
48.4
|
0.5
|
CA
|
A:CYS208
|
4.6
|
48.7
|
0.5
|
HB2
|
A:GLN211
|
4.6
|
64.6
|
0.5
|
O
|
A:VAL210
|
4.6
|
46.8
|
0.5
|
O
|
A:VAL210
|
4.6
|
46.7
|
0.5
|
N
|
A:VAL210
|
4.6
|
42.9
|
0.5
|
H
|
A:GLN211
|
4.6
|
58.4
|
0.5
|
CA
|
A:GLN211
|
4.7
|
51.3
|
0.5
|
SG
|
A:CYS198
|
4.7
|
27.2
|
0.5
|
N
|
A:VAL210
|
4.7
|
43.1
|
0.5
|
HD2
|
A:PRO209
|
4.7
|
43.3
|
0.5
|
HA
|
A:CYS208
|
4.7
|
58.4
|
0.5
|
HD23
|
A:LEU154
|
4.7
|
54.8
|
1.0
|
HG11
|
A:VAL197
|
4.7
|
43.1
|
1.0
|
CD2
|
A:LEU193
|
4.8
|
41.1
|
1.0
|
HA
|
A:CYS208
|
4.8
|
58.1
|
0.5
|
SG
|
A:CYS205
|
4.8
|
42.3
|
0.5
|
HB2
|
A:GLN211
|
4.8
|
65.2
|
0.5
|
S1
|
A:SF4401
|
4.8
|
23.9
|
0.5
|
CA
|
A:VAL210
|
4.8
|
46.8
|
0.5
|
CB
|
A:CYS214
|
4.9
|
50.1
|
0.5
|
HD2
|
A:PRO209
|
4.9
|
43.6
|
0.5
|
CB
|
A:CYS214
|
4.9
|
50.4
|
0.5
|
C
|
A:CYS208
|
4.9
|
49.5
|
0.5
|
HG
|
A:LEU193
|
4.9
|
42.7
|
1.0
|
CA
|
A:VAL210
|
4.9
|
47.1
|
0.5
|
CB
|
A:VAL210
|
4.9
|
46.1
|
0.5
|
SG
|
A:CYS214
|
4.9
|
49.5
|
0.5
|
CB
|
A:VAL210
|
5.0
|
46.2
|
0.5
|
SG
|
A:CYS214
|
5.0
|
38.0
|
0.5
|
CB
|
A:CYS198
|
5.0
|
29.7
|
0.5
|
CD2
|
A:LEU154
|
5.0
|
45.6
|
1.0
|
|
Iron binding site 3 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 3 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:25.9
occ:0.53
|
FE2
|
A:SF4401
|
0.0
|
25.9
|
0.5
|
SG
|
A:CYS205
|
1.2
|
42.3
|
0.5
|
FE2
|
A:SF4401
|
1.5
|
25.0
|
0.5
|
SG
|
A:CYS205
|
2.2
|
34.8
|
0.5
|
S4
|
A:SF4401
|
2.2
|
23.1
|
0.5
|
S1
|
A:SF4401
|
2.3
|
23.9
|
0.5
|
S3
|
A:SF4401
|
2.3
|
23.5
|
0.5
|
FE1
|
A:SF4401
|
2.7
|
23.9
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.3
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
S1
|
A:SF4401
|
2.8
|
23.9
|
0.5
|
CB
|
A:CYS205
|
2.8
|
47.9
|
0.5
|
HA
|
A:CYS205
|
2.8
|
57.4
|
0.5
|
HA
|
A:CYS205
|
2.9
|
57.1
|
0.5
|
S4
|
A:SF4401
|
2.9
|
23.1
|
0.5
|
HB3
|
A:CYS205
|
2.9
|
56.5
|
0.5
|
CB
|
A:CYS205
|
3.0
|
47.1
|
0.5
|
HB2
|
A:PRO203
|
3.0
|
49.6
|
1.0
|
CA
|
A:CYS205
|
3.3
|
47.8
|
0.5
|
CA
|
A:CYS205
|
3.3
|
47.6
|
0.5
|
HB2
|
A:CYS205
|
3.3
|
57.4
|
0.5
|
HB3
|
A:CYS205
|
3.4
|
57.4
|
0.5
|
S3
|
A:SF4401
|
3.6
|
22.6
|
0.5
|
FE3
|
A:SF4401
|
3.6
|
22.9
|
0.5
|
N
|
A:CYS205
|
3.8
|
45.4
|
1.0
|
H
|
A:CYS205
|
3.8
|
54.4
|
0.5
|
H
|
A:CYS205
|
3.8
|
54.4
|
0.5
|
HB2
|
A:CYS205
|
3.9
|
56.5
|
0.5
|
S2
|
A:SF4401
|
3.9
|
22.9
|
0.5
|
CB
|
A:PRO203
|
3.9
|
41.4
|
1.0
|
FE4
|
A:SF4401
|
4.0
|
25.2
|
0.5
|
HB1
|
A:ALA222
|
4.1
|
51.6
|
1.0
|
HB2
|
A:ALA222
|
4.1
|
51.6
|
1.0
|
FE1
|
A:SF4401
|
4.1
|
23.4
|
0.5
|
HG2
|
A:PRO203
|
4.1
|
38.2
|
1.0
|
HB2
|
A:PHE217
|
4.2
|
68.6
|
1.0
|
HB3
|
A:PRO203
|
4.2
|
49.6
|
1.0
|
HB2
|
A:CYS208
|
4.3
|
54.4
|
0.5
|
CB
|
A:ALA222
|
4.4
|
43.1
|
1.0
|
CG
|
A:PRO203
|
4.5
|
31.9
|
1.0
|
HB3
|
A:ALA222
|
4.5
|
51.6
|
1.0
|
HB2
|
A:CYS208
|
4.5
|
49.2
|
0.5
|
HG3
|
A:PRO203
|
4.6
|
38.2
|
1.0
|
HA
|
A:CYS198
|
4.6
|
34.5
|
0.5
|
HD3
|
A:ARG153
|
4.6
|
36.2
|
1.0
|
HA
|
A:CYS198
|
4.6
|
34.7
|
0.5
|
C
|
A:SER204
|
4.7
|
36.4
|
1.0
|
C
|
A:CYS205
|
4.7
|
42.6
|
1.0
|
SG
|
A:CYS214
|
4.8
|
38.0
|
0.5
|
SG
|
A:CYS208
|
4.8
|
32.8
|
0.5
|
C
|
A:PRO203
|
4.8
|
48.4
|
1.0
|
HB3
|
A:CYS208
|
4.8
|
54.4
|
0.5
|
CB
|
A:CYS208
|
4.8
|
45.3
|
0.5
|
HD1
|
A:PHE217
|
4.8
|
64.0
|
1.0
|
SG
|
A:CYS198
|
4.9
|
27.5
|
0.5
|
O
|
A:PRO203
|
4.9
|
46.5
|
1.0
|
HB3
|
A:CYS208
|
4.9
|
49.2
|
0.5
|
N
|
A:SER204
|
5.0
|
39.8
|
1.0
|
CA
|
A:PRO203
|
5.0
|
35.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 4 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:25.0
occ:0.47
|
FE2
|
A:SF4401
|
0.0
|
25.0
|
0.5
|
FE2
|
A:SF4401
|
1.5
|
25.9
|
0.5
|
FE1
|
A:SF4401
|
1.5
|
23.9
|
0.5
|
S3
|
A:SF4401
|
1.5
|
23.5
|
0.5
|
FE4
|
A:SF4401
|
1.8
|
25.3
|
0.5
|
S1
|
A:SF4401
|
2.2
|
23.9
|
0.5
|
SG
|
A:CYS205
|
2.2
|
42.3
|
0.5
|
S4
|
A:SF4401
|
2.3
|
23.1
|
0.5
|
S3
|
A:SF4401
|
2.3
|
22.6
|
0.5
|
S4
|
A:SF4401
|
2.4
|
23.1
|
0.5
|
FE3
|
A:SF4401
|
2.4
|
22.9
|
0.5
|
S1
|
A:SF4401
|
2.6
|
23.9
|
0.5
|
S2
|
A:SF4401
|
2.6
|
22.9
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.2
|
0.5
|
FE1
|
A:SF4401
|
2.8
|
23.4
|
0.5
|
HA
|
A:CYS205
|
3.1
|
57.4
|
0.5
|
HA
|
A:CYS205
|
3.2
|
57.1
|
0.5
|
HB3
|
A:CYS205
|
3.5
|
56.5
|
0.5
|
CB
|
A:CYS205
|
3.6
|
47.9
|
0.5
|
SG
|
A:CYS205
|
3.6
|
34.8
|
0.5
|
SG
|
A:CYS208
|
3.7
|
32.8
|
0.5
|
CB
|
A:CYS205
|
3.8
|
47.1
|
0.5
|
CA
|
A:CYS205
|
3.8
|
47.6
|
0.5
|
CA
|
A:CYS205
|
3.8
|
47.8
|
0.5
|
HB3
|
A:CYS205
|
3.9
|
57.4
|
0.5
|
S2
|
A:SF4401
|
3.9
|
23.2
|
0.5
|
HB2
|
A:CYS208
|
3.9
|
54.4
|
0.5
|
HB2
|
A:CYS208
|
3.9
|
49.2
|
0.5
|
HB2
|
A:PHE217
|
3.9
|
68.6
|
1.0
|
SG
|
A:CYS214
|
4.0
|
38.0
|
0.5
|
HB3
|
A:CYS208
|
4.1
|
54.4
|
0.5
|
HB3
|
A:CYS208
|
4.1
|
49.2
|
0.5
|
CB
|
A:CYS208
|
4.2
|
45.3
|
0.5
|
HB2
|
A:PRO203
|
4.2
|
49.6
|
1.0
|
HB2
|
A:CYS205
|
4.3
|
57.4
|
0.5
|
SG
|
A:CYS214
|
4.3
|
49.5
|
0.5
|
CB
|
A:CYS208
|
4.4
|
41.0
|
0.5
|
HB2
|
A:CYS214
|
4.4
|
60.1
|
0.5
|
HA
|
A:GLN211
|
4.4
|
58.6
|
0.5
|
HB2
|
A:CYS214
|
4.5
|
60.4
|
0.5
|
N
|
A:CYS205
|
4.6
|
45.4
|
1.0
|
SG
|
A:CYS208
|
4.6
|
37.7
|
0.5
|
SG
|
A:CYS198
|
4.6
|
27.2
|
0.5
|
HB2
|
A:CYS198
|
4.6
|
35.6
|
0.5
|
HB3
|
A:CYS214
|
4.6
|
60.4
|
0.5
|
CB
|
A:CYS214
|
4.7
|
50.1
|
0.5
|
HB3
|
A:CYS214
|
4.7
|
60.1
|
0.5
|
SG
|
A:CYS198
|
4.7
|
27.5
|
0.5
|
HA
|
A:GLN211
|
4.7
|
61.5
|
0.5
|
HB2
|
A:CYS205
|
4.7
|
56.5
|
0.5
|
HD3
|
A:ARG153
|
4.7
|
36.2
|
1.0
|
CB
|
A:CYS214
|
4.8
|
50.4
|
0.5
|
HA
|
A:CYS198
|
4.8
|
34.5
|
0.5
|
HA
|
A:CYS198
|
4.8
|
34.7
|
0.5
|
HB2
|
A:ALA222
|
4.9
|
51.6
|
1.0
|
H
|
A:CYS205
|
4.9
|
54.4
|
0.5
|
H
|
A:CYS205
|
4.9
|
54.4
|
0.5
|
CB
|
A:PHE217
|
4.9
|
57.2
|
1.0
|
HG12
|
A:VAL197
|
4.9
|
43.1
|
1.0
|
C
|
A:CYS205
|
4.9
|
42.6
|
1.0
|
HB3
|
A:ARG153
|
5.0
|
40.1
|
1.0
|
O
|
A:CYS205
|
5.0
|
53.3
|
1.0
|
HB1
|
A:ALA222
|
5.0
|
51.6
|
1.0
|
|
Iron binding site 5 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 5 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:22.9
occ:0.53
|
FE3
|
A:SF4401
|
0.0
|
22.9
|
0.5
|
FE3
|
A:SF4401
|
1.3
|
22.9
|
0.5
|
S1
|
A:SF4401
|
1.9
|
23.9
|
0.5
|
S4
|
A:SF4401
|
2.2
|
23.1
|
0.5
|
S1
|
A:SF4401
|
2.3
|
23.9
|
0.5
|
S4
|
A:SF4401
|
2.3
|
23.1
|
0.5
|
S2
|
A:SF4401
|
2.3
|
22.9
|
0.5
|
SG
|
A:CYS198
|
2.3
|
27.5
|
0.5
|
FE2
|
A:SF4401
|
2.4
|
25.0
|
0.5
|
SG
|
A:CYS198
|
2.4
|
27.2
|
0.5
|
FE1
|
A:SF4401
|
2.7
|
23.9
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.3
|
0.5
|
FE2
|
A:SF4401
|
2.7
|
25.9
|
0.5
|
HB2
|
A:CYS198
|
2.9
|
35.6
|
0.5
|
HD3
|
A:ARG153
|
3.0
|
36.2
|
1.0
|
HA
|
A:CYS198
|
3.1
|
34.5
|
0.5
|
CB
|
A:CYS198
|
3.1
|
29.7
|
0.5
|
HA
|
A:CYS198
|
3.2
|
34.7
|
0.5
|
FE4
|
A:SF4401
|
3.4
|
25.2
|
0.5
|
CB
|
A:CYS198
|
3.4
|
28.8
|
0.5
|
HH11
|
A:ARG153
|
3.4
|
34.3
|
1.0
|
FE1
|
A:SF4401
|
3.5
|
23.4
|
0.5
|
HB2
|
A:CYS198
|
3.5
|
34.5
|
0.5
|
S2
|
A:SF4401
|
3.6
|
23.2
|
0.5
|
CA
|
A:CYS198
|
3.7
|
28.9
|
0.5
|
CA
|
A:CYS198
|
3.7
|
28.8
|
0.5
|
HB2
|
A:PRO203
|
3.8
|
49.6
|
1.0
|
S3
|
A:SF4401
|
3.9
|
23.5
|
0.5
|
CD
|
A:ARG153
|
3.9
|
30.2
|
1.0
|
SG
|
A:CYS205
|
4.0
|
42.3
|
0.5
|
HB3
|
A:CYS198
|
4.0
|
35.6
|
0.5
|
HB3
|
A:ARG153
|
4.1
|
40.1
|
1.0
|
HD2
|
A:ARG153
|
4.1
|
36.2
|
1.0
|
NH1
|
A:ARG153
|
4.1
|
28.6
|
1.0
|
HB3
|
A:PRO203
|
4.1
|
49.6
|
1.0
|
HB2
|
A:ARG153
|
4.2
|
40.1
|
1.0
|
S3
|
A:SF4401
|
4.2
|
22.6
|
0.5
|
HB3
|
A:CYS198
|
4.2
|
34.5
|
0.5
|
CB
|
A:PRO203
|
4.4
|
41.4
|
1.0
|
HH12
|
A:ARG153
|
4.5
|
34.3
|
1.0
|
CB
|
A:ARG153
|
4.5
|
33.5
|
1.0
|
HB1
|
A:ALA222
|
4.5
|
51.6
|
1.0
|
HA
|
A:VAL150
|
4.7
|
34.8
|
1.0
|
SG
|
A:CYS208
|
4.7
|
32.8
|
0.5
|
N
|
A:CYS198
|
4.7
|
30.0
|
1.0
|
CG
|
A:ARG153
|
4.7
|
33.6
|
1.0
|
C
|
A:CYS198
|
4.7
|
29.0
|
1.0
|
NE
|
A:ARG153
|
4.7
|
38.8
|
1.0
|
HG12
|
A:VAL197
|
4.8
|
43.1
|
1.0
|
SG
|
A:CYS214
|
4.8
|
38.0
|
0.5
|
CZ
|
A:ARG153
|
4.8
|
31.1
|
1.0
|
SG
|
A:CYS205
|
4.8
|
34.8
|
0.5
|
HA
|
A:CYS205
|
4.9
|
57.4
|
0.5
|
HA
|
A:CYS205
|
4.9
|
57.1
|
0.5
|
SG
|
A:CYS214
|
4.9
|
49.5
|
0.5
|
HG3
|
A:PRO203
|
4.9
|
38.2
|
1.0
|
HG2
|
A:ARG153
|
5.0
|
40.4
|
1.0
|
|
Iron binding site 6 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 6 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:22.9
occ:0.47
|
FE3
|
A:SF4401
|
0.0
|
22.9
|
0.5
|
S2
|
A:SF4401
|
1.2
|
22.9
|
0.5
|
FE3
|
A:SF4401
|
1.3
|
22.9
|
0.5
|
SG
|
A:CYS198
|
2.2
|
27.2
|
0.5
|
S4
|
A:SF4401
|
2.2
|
23.1
|
0.5
|
S1
|
A:SF4401
|
2.3
|
23.9
|
0.5
|
S2
|
A:SF4401
|
2.3
|
23.2
|
0.5
|
FE1
|
A:SF4401
|
2.5
|
23.9
|
0.5
|
HB2
|
A:CYS198
|
2.6
|
35.6
|
0.5
|
SG
|
A:CYS198
|
2.7
|
27.5
|
0.5
|
FE2
|
A:SF4401
|
2.7
|
25.0
|
0.5
|
FE1
|
A:SF4401
|
2.7
|
23.4
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.2
|
0.5
|
FE4
|
A:SF4401
|
2.7
|
25.3
|
0.5
|
S4
|
A:SF4401
|
3.0
|
23.1
|
0.5
|
CB
|
A:CYS198
|
3.1
|
29.7
|
0.5
|
S1
|
A:SF4401
|
3.2
|
23.9
|
0.5
|
HB2
|
A:CYS198
|
3.2
|
34.5
|
0.5
|
CB
|
A:CYS198
|
3.3
|
28.8
|
0.5
|
FE2
|
A:SF4401
|
3.6
|
25.9
|
0.5
|
HA
|
A:CYS198
|
3.7
|
34.5
|
0.5
|
HD3
|
A:ARG153
|
3.7
|
36.2
|
1.0
|
HB3
|
A:CYS198
|
3.8
|
35.6
|
0.5
|
HA
|
A:CYS198
|
3.8
|
34.7
|
0.5
|
S3
|
A:SF4401
|
3.9
|
22.6
|
0.5
|
S3
|
A:SF4401
|
4.0
|
23.5
|
0.5
|
HB2
|
A:ARG153
|
4.0
|
40.1
|
1.0
|
HA
|
A:VAL150
|
4.1
|
34.8
|
1.0
|
CA
|
A:CYS198
|
4.1
|
28.8
|
0.5
|
HB3
|
A:CYS198
|
4.1
|
34.5
|
0.5
|
CA
|
A:CYS198
|
4.1
|
28.9
|
0.5
|
HB3
|
A:ARG153
|
4.1
|
40.1
|
1.0
|
SG
|
A:CYS208
|
4.1
|
32.8
|
0.5
|
HH11
|
A:ARG153
|
4.2
|
34.3
|
1.0
|
HG13
|
A:VAL150
|
4.3
|
39.1
|
1.0
|
HG22
|
A:VAL150
|
4.3
|
35.3
|
1.0
|
HD2
|
A:ARG153
|
4.5
|
36.2
|
1.0
|
CD
|
A:ARG153
|
4.5
|
30.2
|
1.0
|
HD21
|
A:LEU193
|
4.5
|
49.3
|
1.0
|
CB
|
A:ARG153
|
4.5
|
33.5
|
1.0
|
SG
|
A:CYS214
|
4.6
|
49.5
|
0.5
|
SG
|
A:CYS214
|
4.6
|
38.0
|
0.5
|
HG
|
A:LEU154
|
4.7
|
53.6
|
1.0
|
SG
|
A:CYS205
|
4.7
|
42.3
|
0.5
|
SG
|
A:CYS208
|
4.7
|
37.7
|
0.5
|
HG12
|
A:VAL197
|
4.8
|
43.1
|
1.0
|
HB2
|
A:CYS208
|
4.8
|
49.2
|
0.5
|
HG
|
A:LEU193
|
4.9
|
42.7
|
1.0
|
N
|
A:CYS198
|
4.9
|
30.0
|
1.0
|
HB2
|
A:CYS214
|
4.9
|
60.1
|
0.5
|
HG23
|
A:VAL210
|
5.0
|
49.9
|
0.5
|
HD23
|
A:LEU154
|
5.0
|
54.8
|
1.0
|
CA
|
A:VAL150
|
5.0
|
29.0
|
1.0
|
HD21
|
A:LEU154
|
5.0
|
54.8
|
1.0
|
HG23
|
A:VAL210
|
5.0
|
50.1
|
0.5
|
|
Iron binding site 7 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 7 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:25.3
occ:0.53
|
FE4
|
A:SF4401
|
0.0
|
25.3
|
0.5
|
S1
|
A:SF4401
|
1.3
|
23.9
|
0.5
|
FE4
|
A:SF4401
|
1.5
|
25.2
|
0.5
|
FE2
|
A:SF4401
|
1.8
|
25.0
|
0.5
|
S3
|
A:SF4401
|
2.3
|
23.5
|
0.5
|
S1
|
A:SF4401
|
2.3
|
23.9
|
0.5
|
S2
|
A:SF4401
|
2.3
|
22.9
|
0.5
|
SG
|
A:CYS214
|
2.3
|
38.0
|
0.5
|
S3
|
A:SF4401
|
2.4
|
22.6
|
0.5
|
SG
|
A:CYS214
|
2.6
|
49.5
|
0.5
|
FE1
|
A:SF4401
|
2.7
|
23.9
|
0.5
|
FE2
|
A:SF4401
|
2.7
|
25.9
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
HB2
|
A:CYS214
|
3.2
|
60.1
|
0.5
|
FE1
|
A:SF4401
|
3.3
|
23.4
|
0.5
|
HB2
|
A:PHE217
|
3.3
|
68.6
|
1.0
|
SG
|
A:CYS205
|
3.3
|
42.3
|
0.5
|
CB
|
A:CYS214
|
3.3
|
50.1
|
0.5
|
HB2
|
A:CYS214
|
3.3
|
60.4
|
0.5
|
CB
|
A:CYS214
|
3.4
|
50.4
|
0.5
|
S2
|
A:SF4401
|
3.4
|
23.2
|
0.5
|
HB3
|
A:CYS214
|
3.4
|
60.4
|
0.5
|
HB3
|
A:CYS214
|
3.6
|
60.1
|
0.5
|
S4
|
A:SF4401
|
3.6
|
23.1
|
0.5
|
HB3
|
A:ARG153
|
3.6
|
40.1
|
1.0
|
S4
|
A:SF4401
|
3.9
|
23.1
|
0.5
|
H
|
A:PHE217
|
4.2
|
58.8
|
1.0
|
CB
|
A:PHE217
|
4.2
|
57.2
|
1.0
|
HD3
|
A:ARG153
|
4.2
|
36.2
|
1.0
|
HB3
|
A:ALA216
|
4.3
|
57.5
|
1.0
|
HD23
|
A:LEU154
|
4.4
|
54.8
|
1.0
|
HB2
|
A:ALA222
|
4.4
|
51.6
|
1.0
|
CB
|
A:ARG153
|
4.4
|
33.5
|
1.0
|
HA
|
A:GLN211
|
4.4
|
58.6
|
0.5
|
HB3
|
A:PHE217
|
4.5
|
68.6
|
1.0
|
HB2
|
A:ARG153
|
4.5
|
40.1
|
1.0
|
HB3
|
A:CYS205
|
4.5
|
56.5
|
0.5
|
N
|
A:PHE217
|
4.6
|
49.0
|
1.0
|
SG
|
A:CYS205
|
4.6
|
34.8
|
0.5
|
SG
|
A:CYS198
|
4.7
|
27.2
|
0.5
|
HA
|
A:CYS205
|
4.7
|
57.4
|
0.5
|
HA
|
A:GLN211
|
4.7
|
61.5
|
0.5
|
CA
|
A:CYS214
|
4.7
|
59.1
|
0.5
|
HA
|
A:CYS205
|
4.8
|
57.1
|
0.5
|
SG
|
A:CYS208
|
4.8
|
32.8
|
0.5
|
HA
|
A:PHE217
|
4.8
|
73.0
|
1.0
|
HB1
|
A:ALA222
|
4.8
|
51.6
|
1.0
|
CA
|
A:CYS214
|
4.8
|
59.2
|
0.5
|
CB
|
A:CYS205
|
4.8
|
47.9
|
0.5
|
CA
|
A:PHE217
|
4.8
|
60.9
|
1.0
|
SG
|
A:CYS198
|
4.8
|
27.5
|
0.5
|
HA
|
A:CYS214
|
4.9
|
70.9
|
0.5
|
HB3
|
A:CYS205
|
4.9
|
57.4
|
0.5
|
|
Iron binding site 8 out
of 8 in 9bs2
Go back to
Iron Binding Sites List in 9bs2
Iron binding site 8 out
of 8 in the Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Glycosylase Muty Variant R149Q in Complex with Dna Containing D(8-Oxo- G) Paired with A Product Analog (Thf) to 1.51 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:25.2
occ:0.47
|
FE4
|
A:SF4401
|
0.0
|
25.2
|
0.5
|
FE4
|
A:SF4401
|
1.5
|
25.3
|
0.5
|
S2
|
A:SF4401
|
1.7
|
22.9
|
0.5
|
HB2
|
A:CYS214
|
2.2
|
60.1
|
0.5
|
SG
|
A:CYS214
|
2.3
|
49.5
|
0.5
|
S3
|
A:SF4401
|
2.3
|
22.6
|
0.5
|
S2
|
A:SF4401
|
2.3
|
23.2
|
0.5
|
S1
|
A:SF4401
|
2.3
|
23.9
|
0.5
|
SG
|
A:CYS214
|
2.3
|
38.0
|
0.5
|
HB2
|
A:CYS214
|
2.4
|
60.4
|
0.5
|
FE2
|
A:SF4401
|
2.7
|
25.0
|
0.5
|
FE1
|
A:SF4401
|
2.7
|
23.4
|
0.5
|
CB
|
A:CYS214
|
2.7
|
50.1
|
0.5
|
CB
|
A:CYS214
|
2.7
|
50.4
|
0.5
|
FE3
|
A:SF4401
|
2.7
|
22.9
|
0.5
|
FE1
|
A:SF4401
|
2.9
|
23.9
|
0.5
|
S3
|
A:SF4401
|
3.0
|
23.5
|
0.5
|
HD23
|
A:LEU154
|
3.0
|
54.8
|
1.0
|
HB3
|
A:CYS214
|
3.1
|
60.4
|
0.5
|
HB3
|
A:CYS214
|
3.2
|
60.1
|
0.5
|
FE3
|
A:SF4401
|
3.4
|
22.9
|
0.5
|
S1
|
A:SF4401
|
3.6
|
23.9
|
0.5
|
HD21
|
A:LEU154
|
3.6
|
54.8
|
1.0
|
CD2
|
A:LEU154
|
3.7
|
45.6
|
1.0
|
S4
|
A:SF4401
|
3.8
|
23.1
|
0.5
|
HB3
|
A:ARG153
|
3.9
|
40.1
|
1.0
|
HA
|
A:GLN211
|
4.0
|
58.6
|
0.5
|
HA
|
A:CYS214
|
4.0
|
70.9
|
0.5
|
CA
|
A:CYS214
|
4.0
|
59.1
|
0.5
|
FE2
|
A:SF4401
|
4.0
|
25.9
|
0.5
|
HB2
|
A:PHE217
|
4.0
|
68.6
|
1.0
|
HG
|
A:LEU154
|
4.0
|
53.6
|
1.0
|
CA
|
A:CYS214
|
4.1
|
59.2
|
0.5
|
HA
|
A:CYS214
|
4.1
|
71.0
|
0.5
|
HG23
|
A:VAL210
|
4.1
|
50.1
|
0.5
|
HA
|
A:LEU154
|
4.1
|
52.2
|
1.0
|
HA
|
A:GLN211
|
4.2
|
61.5
|
0.5
|
HG23
|
A:VAL210
|
4.2
|
49.9
|
0.5
|
CG
|
A:LEU154
|
4.5
|
44.7
|
1.0
|
SG
|
A:CYS208
|
4.5
|
32.8
|
0.5
|
HD22
|
A:LEU154
|
4.5
|
54.8
|
1.0
|
HB2
|
A:ARG153
|
4.5
|
40.1
|
1.0
|
SG
|
A:CYS205
|
4.6
|
42.3
|
0.5
|
S4
|
A:SF4401
|
4.6
|
23.1
|
0.5
|
H
|
A:PHE217
|
4.6
|
58.8
|
1.0
|
CB
|
A:ARG153
|
4.7
|
33.5
|
1.0
|
O
|
A:VAL210
|
4.7
|
46.8
|
0.5
|
SG
|
A:CYS198
|
4.7
|
27.2
|
0.5
|
O
|
A:VAL210
|
4.8
|
46.7
|
0.5
|
SG
|
A:CYS208
|
4.8
|
37.7
|
0.5
|
N
|
A:CYS214
|
4.8
|
56.9
|
0.5
|
HB3
|
A:PHE217
|
4.8
|
68.6
|
1.0
|
N
|
A:LEU154
|
4.8
|
37.1
|
1.0
|
CB
|
A:PHE217
|
4.9
|
57.2
|
1.0
|
N
|
A:CYS214
|
4.9
|
56.9
|
0.5
|
CA
|
A:LEU154
|
4.9
|
43.6
|
1.0
|
CA
|
A:GLN211
|
4.9
|
48.8
|
0.5
|
H
|
A:CYS214
|
4.9
|
68.2
|
0.5
|
H
|
A:CYS214
|
4.9
|
68.3
|
0.5
|
HB3
|
A:ALA216
|
4.9
|
57.5
|
1.0
|
HD3
|
A:ARG153
|
5.0
|
36.2
|
1.0
|
|
Reference:
C.H.Trasvina-Arenas,
U.C.Dissanayake,
N.Tamayo,
S.M.Hashemian,
W.J.Lin,
M.Demir,
N.Hoyos-Gonzalez,
A.J.Fisher,
G.A.Cisneros,
M.P.Horvath,
S.S.David.
Structural and Functional Profiling of Mutyh Cancer-Associated Variants Reveal An Allosteric Role For Its [4FE-4S] Cluster Cofactor To Be Published.
Page generated: Wed Nov 13 10:37:40 2024
|