Iron in PDB 8dwf: Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
Enzymatic activity of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
All present enzymatic activity of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine:
3.2.2.31;
Protein crystallography data
The structure of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine, PDB code: 8dwf
was solved by
L.P.Russelburg,
M.Demir,
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)
|
73.00 /
2.60
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.08,
137.9,
74.52,
90,
101.44,
90
|
|
R / Rfree (%)
|
20.7 /
25.3
|
Other elements in 8dwf:
The structure of Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
(pdb code 8dwf). 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine, PDB code: 8dwf:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 1 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:52.9
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
52.9
|
1.0
|
|
S3
|
A:SF4401
|
2.2
|
61.8
|
1.0
|
|
S2
|
A:SF4401
|
2.3
|
55.4
|
1.0
|
|
S4
|
A:SF4401
|
2.3
|
54.6
|
1.0
|
|
SG
|
A:CYS208
|
2.4
|
49.7
|
1.0
|
|
FE4
|
A:SF4401
|
2.7
|
54.1
|
1.0
|
|
FE3
|
A:SF4401
|
2.7
|
52.0
|
1.0
|
|
FE2
|
A:SF4401
|
2.8
|
59.5
|
1.0
|
|
HB2
|
A:CYS208
|
2.9
|
65.6
|
1.0
|
|
CB
|
A:CYS208
|
3.1
|
53.3
|
1.0
|
|
HB3
|
A:CYS208
|
3.2
|
65.6
|
1.0
|
|
HA
|
A:CYS205
|
3.5
|
71.1
|
1.0
|
|
HG23
|
A:VAL210
|
3.7
|
55.7
|
1.0
|
|
S1
|
A:SF4401
|
3.9
|
49.5
|
1.0
|
|
HB2
|
A:CYS198
|
4.0
|
60.6
|
1.0
|
|
HA
|
A:GLN211
|
4.0
|
70.7
|
1.0
|
|
HG12
|
A:VAL197
|
4.1
|
59.0
|
1.0
|
|
HB2
|
A:CYS214
|
4.3
|
63.3
|
1.0
|
|
HG22
|
A:VAL210
|
4.4
|
55.7
|
1.0
|
|
CA
|
A:CYS205
|
4.4
|
58.6
|
1.0
|
|
HD11
|
A:LEU193
|
4.5
|
53.3
|
1.0
|
|
CG2
|
A:VAL210
|
4.5
|
44.1
|
1.0
|
|
HB2
|
A:GLN211
|
4.5
|
81.0
|
1.0
|
|
CA
|
A:CYS208
|
4.5
|
56.7
|
1.0
|
|
H
|
A:VAL210
|
4.6
|
69.9
|
1.0
|
|
HD21
|
A:LEU193
|
4.7
|
56.5
|
1.0
|
|
HB3
|
A:CYS205
|
4.7
|
64.6
|
1.0
|
|
HG11
|
A:VAL197
|
4.7
|
59.0
|
1.0
|
|
CA
|
A:GLN211
|
4.7
|
62.7
|
1.0
|
|
CB
|
A:CYS198
|
4.7
|
51.8
|
1.0
|
|
SG
|
A:CYS214
|
4.7
|
53.1
|
1.0
|
|
HA
|
A:CYS208
|
4.8
|
69.2
|
1.0
|
|
N
|
A:GLN211
|
4.8
|
60.4
|
1.0
|
|
SG
|
A:CYS198
|
4.8
|
48.2
|
1.0
|
|
C
|
A:VAL210
|
4.8
|
54.7
|
1.0
|
|
O
|
A:VAL210
|
4.8
|
57.4
|
1.0
|
|
SG
|
A:CYS205
|
4.8
|
55.8
|
1.0
|
|
HA
|
A:CYS198
|
4.8
|
64.3
|
1.0
|
|
CG1
|
A:VAL197
|
4.8
|
46.5
|
1.0
|
|
O
|
A:CYS205
|
4.9
|
60.5
|
1.0
|
|
CB
|
A:CYS205
|
4.9
|
53.5
|
1.0
|
|
CB
|
A:CYS214
|
5.0
|
53.5
|
1.0
|
|
Iron binding site 2 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 2 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:59.5
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
59.5
|
1.0
|
|
S1
|
A:SF4401
|
2.2
|
49.5
|
1.0
|
|
SG
|
A:CYS205
|
2.2
|
55.8
|
1.0
|
|
S3
|
A:SF4401
|
2.3
|
61.8
|
1.0
|
|
S4
|
A:SF4401
|
2.3
|
54.6
|
1.0
|
|
FE3
|
A:SF4401
|
2.7
|
52.0
|
1.0
|
|
FE4
|
A:SF4401
|
2.7
|
54.1
|
1.0
|
|
HA
|
A:CYS205
|
2.7
|
71.1
|
1.0
|
|
FE1
|
A:SF4401
|
2.8
|
52.9
|
1.0
|
|
CB
|
A:CYS205
|
3.0
|
53.5
|
1.0
|
|
HB3
|
A:CYS205
|
3.1
|
64.6
|
1.0
|
|
CA
|
A:CYS205
|
3.3
|
58.6
|
1.0
|
|
HB2
|
A:PRO203
|
3.5
|
68.5
|
1.0
|
|
S2
|
A:SF4401
|
3.9
|
55.4
|
1.0
|
|
N
|
A:CYS205
|
3.9
|
61.2
|
1.0
|
|
HB2
|
A:CYS205
|
3.9
|
64.6
|
1.0
|
|
H
|
A:CYS205
|
3.9
|
74.5
|
1.0
|
|
HB2
|
A:PHE217
|
4.1
|
84.0
|
1.0
|
|
HB2
|
A:CYS208
|
4.2
|
65.6
|
1.0
|
|
HG2
|
A:PRO203
|
4.3
|
68.8
|
1.0
|
|
CB
|
A:PRO203
|
4.4
|
56.2
|
1.0
|
|
HD1
|
A:PHE217
|
4.4
|
91.5
|
1.0
|
|
HA
|
A:CYS198
|
4.5
|
64.3
|
1.0
|
|
C
|
A:CYS205
|
4.6
|
63.2
|
1.0
|
|
SG
|
A:CYS214
|
4.6
|
53.1
|
1.0
|
|
HD3
|
A:ARG153
|
4.6
|
60.9
|
1.0
|
|
HB1
|
A:ALA222
|
4.7
|
70.0
|
1.0
|
|
HB3
|
A:CYS208
|
4.7
|
65.6
|
1.0
|
|
CG
|
A:PRO203
|
4.7
|
56.9
|
1.0
|
|
HB3
|
A:PRO203
|
4.7
|
68.5
|
1.0
|
|
SG
|
A:CYS198
|
4.8
|
48.2
|
1.0
|
|
HG3
|
A:PRO203
|
4.8
|
68.8
|
1.0
|
|
HB2
|
A:ALA222
|
4.8
|
70.0
|
1.0
|
|
CB
|
A:CYS208
|
4.8
|
53.3
|
1.0
|
|
C
|
A:SER204
|
4.8
|
56.3
|
1.0
|
|
O
|
A:CYS205
|
4.9
|
60.5
|
1.0
|
|
SG
|
A:CYS208
|
4.9
|
49.7
|
1.0
|
|
HB2
|
A:CYS198
|
4.9
|
60.6
|
1.0
|
|
Iron binding site 3 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 3 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:52.0
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
52.0
|
1.0
|
|
S4
|
A:SF4401
|
2.2
|
54.6
|
1.0
|
|
S1
|
A:SF4401
|
2.3
|
49.5
|
1.0
|
|
SG
|
A:CYS198
|
2.3
|
48.2
|
1.0
|
|
S2
|
A:SF4401
|
2.3
|
55.4
|
1.0
|
|
FE4
|
A:SF4401
|
2.7
|
54.1
|
1.0
|
|
FE2
|
A:SF4401
|
2.7
|
59.5
|
1.0
|
|
FE1
|
A:SF4401
|
2.7
|
52.9
|
1.0
|
|
HB2
|
A:CYS198
|
2.7
|
60.6
|
1.0
|
|
CB
|
A:CYS198
|
3.0
|
51.8
|
1.0
|
|
HA
|
A:CYS198
|
3.2
|
64.3
|
1.0
|
|
HD3
|
A:ARG153
|
3.4
|
60.9
|
1.0
|
|
CA
|
A:CYS198
|
3.6
|
55.2
|
1.0
|
|
HH11
|
A:ARG153
|
3.8
|
59.8
|
1.0
|
|
S3
|
A:SF4401
|
3.8
|
61.8
|
1.0
|
|
HB3
|
A:CYS198
|
3.8
|
60.6
|
1.0
|
|
HB2
|
A:PRO203
|
3.9
|
68.5
|
1.0
|
|
HD2
|
A:ARG153
|
4.0
|
60.9
|
1.0
|
|
CD
|
A:ARG153
|
4.2
|
51.5
|
1.0
|
|
HB3
|
A:ARG153
|
4.2
|
66.5
|
1.0
|
|
HB2
|
A:ARG153
|
4.3
|
66.5
|
1.0
|
|
HB3
|
A:PRO203
|
4.4
|
68.5
|
1.0
|
|
NH1
|
A:ARG153
|
4.5
|
50.3
|
1.0
|
|
N
|
A:CYS198
|
4.5
|
53.1
|
1.0
|
|
CB
|
A:PRO203
|
4.6
|
56.2
|
1.0
|
|
HA
|
A:VAL150
|
4.6
|
56.2
|
1.0
|
|
SG
|
A:CYS205
|
4.7
|
55.8
|
1.0
|
|
CB
|
A:ARG153
|
4.7
|
56.3
|
1.0
|
|
HG12
|
A:VAL197
|
4.7
|
59.0
|
1.0
|
|
SG
|
A:CYS214
|
4.7
|
53.1
|
1.0
|
|
HA
|
A:CYS205
|
4.8
|
71.1
|
1.0
|
|
HG22
|
A:VAL150
|
4.8
|
52.6
|
1.0
|
|
C
|
A:CYS198
|
4.8
|
55.8
|
1.0
|
|
H
|
A:CYS198
|
4.8
|
61.6
|
1.0
|
|
HG13
|
A:VAL150
|
4.8
|
54.0
|
1.0
|
|
SG
|
A:CYS208
|
4.9
|
49.7
|
1.0
|
|
HH12
|
A:ARG153
|
5.0
|
59.8
|
1.0
|
|
HG3
|
A:PRO203
|
5.0
|
68.8
|
1.0
|
|
Iron binding site 4 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 4 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:54.1
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
54.1
|
1.0
|
|
S2
|
A:SF4401
|
2.2
|
55.4
|
1.0
|
|
SG
|
A:CYS214
|
2.2
|
53.1
|
1.0
|
|
S3
|
A:SF4401
|
2.2
|
61.8
|
1.0
|
|
S1
|
A:SF4401
|
2.3
|
49.5
|
1.0
|
|
FE3
|
A:SF4401
|
2.7
|
52.0
|
1.0
|
|
FE1
|
A:SF4401
|
2.7
|
52.9
|
1.0
|
|
FE2
|
A:SF4401
|
2.7
|
59.5
|
1.0
|
|
HB2
|
A:CYS214
|
3.0
|
63.3
|
1.0
|
|
CB
|
A:CYS214
|
3.2
|
53.5
|
1.0
|
|
HB3
|
A:CYS214
|
3.6
|
63.3
|
1.0
|
|
HB2
|
A:PHE217
|
3.6
|
84.0
|
1.0
|
|
HB3
|
A:ARG153
|
3.7
|
66.5
|
1.0
|
|
S4
|
A:SF4401
|
3.8
|
54.6
|
1.0
|
|
HD23
|
A:LEU154
|
3.9
|
51.4
|
1.0
|
|
H
|
A:PHE217
|
4.3
|
72.4
|
1.0
|
|
HD3
|
A:ARG153
|
4.4
|
60.9
|
1.0
|
|
HA
|
A:GLN211
|
4.4
|
70.7
|
1.0
|
|
HB2
|
A:ARG153
|
4.5
|
66.5
|
1.0
|
|
CB
|
A:ARG153
|
4.5
|
56.3
|
1.0
|
|
CB
|
A:PHE217
|
4.5
|
69.2
|
1.0
|
|
CA
|
A:CYS214
|
4.6
|
55.4
|
1.0
|
|
SG
|
A:CYS198
|
4.6
|
48.2
|
1.0
|
|
HD21
|
A:LEU154
|
4.6
|
51.4
|
1.0
|
|
HB3
|
A:ALA216
|
4.6
|
72.4
|
1.0
|
|
HA
|
A:CYS214
|
4.6
|
65.6
|
1.0
|
|
HB3
|
A:PHE217
|
4.6
|
84.0
|
1.0
|
|
CD2
|
A:LEU154
|
4.6
|
41.1
|
1.0
|
|
HG
|
A:LEU154
|
4.6
|
58.2
|
1.0
|
|
SG
|
A:CYS205
|
4.7
|
55.8
|
1.0
|
|
N
|
A:PHE217
|
4.8
|
58.8
|
1.0
|
|
HA
|
A:LEU154
|
4.8
|
56.6
|
1.0
|
|
HG23
|
A:VAL210
|
4.8
|
55.7
|
1.0
|
|
HA
|
A:CYS205
|
5.0
|
71.1
|
1.0
|
|
SG
|
A:CYS208
|
5.0
|
49.7
|
1.0
|
|
HB3
|
A:CYS205
|
5.0
|
64.6
|
1.0
|
|
Iron binding site 5 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 5 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:50.9
occ:1.00
|
FE1
|
D:SF4401
|
0.0
|
50.9
|
1.0
|
|
S4
|
D:SF4401
|
2.2
|
47.5
|
1.0
|
|
S2
|
D:SF4401
|
2.3
|
48.9
|
1.0
|
|
S3
|
D:SF4401
|
2.3
|
59.1
|
1.0
|
|
SG
|
D:CYS208
|
2.3
|
49.5
|
1.0
|
|
FE3
|
D:SF4401
|
2.7
|
51.9
|
1.0
|
|
FE2
|
D:SF4401
|
2.7
|
59.1
|
1.0
|
|
FE4
|
D:SF4401
|
2.7
|
49.5
|
1.0
|
|
HB2
|
D:CYS208
|
2.9
|
64.8
|
1.0
|
|
CB
|
D:CYS208
|
3.1
|
56.0
|
1.0
|
|
HB3
|
D:CYS208
|
3.3
|
64.8
|
1.0
|
|
HA
|
D:CYS205
|
3.6
|
73.0
|
1.0
|
|
HG23
|
D:VAL210
|
3.7
|
66.1
|
1.0
|
|
S1
|
D:SF4401
|
3.9
|
49.6
|
1.0
|
|
HA
|
D:GLN211
|
3.9
|
79.5
|
1.0
|
|
HG22
|
D:VAL210
|
4.1
|
66.1
|
1.0
|
|
CG2
|
D:VAL210
|
4.3
|
57.4
|
1.0
|
|
HB2
|
D:CYS198
|
4.3
|
52.6
|
1.0
|
|
HG12
|
D:VAL197
|
4.3
|
65.3
|
1.0
|
|
HB2
|
D:CYS214
|
4.3
|
76.4
|
1.0
|
|
HD21
|
D:LEU193
|
4.4
|
58.6
|
1.0
|
|
HD11
|
D:LEU193
|
4.5
|
55.6
|
1.0
|
|
HB2
|
D:GLN211
|
4.5
|
78.0
|
1.0
|
|
CA
|
D:CYS208
|
4.5
|
58.5
|
1.0
|
|
CA
|
D:CYS205
|
4.6
|
67.4
|
1.0
|
|
CA
|
D:GLN211
|
4.6
|
69.2
|
1.0
|
|
N
|
D:GLN211
|
4.7
|
64.8
|
1.0
|
|
H
|
D:VAL210
|
4.7
|
71.9
|
1.0
|
|
HA
|
D:CYS208
|
4.7
|
67.5
|
1.0
|
|
HB3
|
D:CYS205
|
4.7
|
66.6
|
1.0
|
|
HG21
|
D:VAL210
|
4.7
|
66.1
|
1.0
|
|
HG11
|
D:VAL197
|
4.8
|
65.3
|
1.0
|
|
SG
|
D:CYS205
|
4.8
|
69.6
|
1.0
|
|
H
|
D:GLN211
|
4.8
|
74.9
|
1.0
|
|
SG
|
D:CYS214
|
4.8
|
47.7
|
1.0
|
|
SG
|
D:CYS198
|
4.9
|
53.7
|
1.0
|
|
HD21
|
D:LEU154
|
4.9
|
60.4
|
1.0
|
|
CB
|
D:CYS205
|
4.9
|
62.5
|
1.0
|
|
C
|
D:VAL210
|
4.9
|
66.1
|
1.0
|
|
CB
|
D:CYS214
|
5.0
|
61.4
|
1.0
|
|
Iron binding site 6 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 6 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:59.1
occ:1.00
|
FE2
|
D:SF4401
|
0.0
|
59.1
|
1.0
|
|
S4
|
D:SF4401
|
2.2
|
47.5
|
1.0
|
|
SG
|
D:CYS205
|
2.3
|
69.6
|
1.0
|
|
S1
|
D:SF4401
|
2.3
|
49.6
|
1.0
|
|
S3
|
D:SF4401
|
2.3
|
59.1
|
1.0
|
|
FE4
|
D:SF4401
|
2.7
|
49.5
|
1.0
|
|
FE3
|
D:SF4401
|
2.7
|
51.9
|
1.0
|
|
FE1
|
D:SF4401
|
2.7
|
50.9
|
1.0
|
|
HA
|
D:CYS205
|
2.8
|
73.0
|
1.0
|
|
CB
|
D:CYS205
|
3.1
|
62.5
|
1.0
|
|
HB3
|
D:CYS205
|
3.1
|
66.6
|
1.0
|
|
CA
|
D:CYS205
|
3.4
|
67.4
|
1.0
|
|
HB2
|
D:PRO203
|
3.5
|
66.7
|
1.0
|
|
HB2
|
D:PHE217
|
3.8
|
80.1
|
1.0
|
|
S2
|
D:SF4401
|
3.8
|
48.9
|
1.0
|
|
HB2
|
D:CYS205
|
4.0
|
66.6
|
1.0
|
|
N
|
D:CYS205
|
4.0
|
67.8
|
1.0
|
|
H
|
D:CYS205
|
4.1
|
73.5
|
1.0
|
|
HB2
|
D:CYS208
|
4.1
|
64.8
|
1.0
|
|
HD1
|
D:PHE217
|
4.3
|
86.6
|
1.0
|
|
CB
|
D:PRO203
|
4.5
|
59.1
|
1.0
|
|
HB2
|
D:ALA222
|
4.6
|
78.0
|
1.0
|
|
HG2
|
D:PRO203
|
4.6
|
66.1
|
1.0
|
|
HB1
|
D:ALA222
|
4.6
|
78.0
|
1.0
|
|
HD3
|
D:ARG153
|
4.7
|
56.7
|
1.0
|
|
HB3
|
D:CYS208
|
4.7
|
64.8
|
1.0
|
|
C
|
D:CYS205
|
4.7
|
71.2
|
1.0
|
|
CB
|
D:CYS208
|
4.7
|
56.0
|
1.0
|
|
SG
|
D:CYS214
|
4.7
|
47.7
|
1.0
|
|
HA
|
D:CYS198
|
4.8
|
64.0
|
1.0
|
|
HB3
|
D:PRO203
|
4.8
|
66.7
|
1.0
|
|
CB
|
D:PHE217
|
4.8
|
67.4
|
1.0
|
|
SG
|
D:CYS208
|
4.8
|
49.5
|
1.0
|
|
SG
|
D:CYS198
|
4.8
|
53.7
|
1.0
|
|
C
|
D:SER204
|
4.9
|
60.1
|
1.0
|
|
O
|
D:CYS205
|
4.9
|
71.9
|
1.0
|
|
CG
|
D:PRO203
|
4.9
|
59.2
|
1.0
|
|
HG3
|
D:PRO203
|
4.9
|
66.1
|
1.0
|
|
CD1
|
D:PHE217
|
5.0
|
74.2
|
1.0
|
|
Iron binding site 7 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 7 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:51.9
occ:1.00
|
FE3
|
D:SF4401
|
0.0
|
51.9
|
1.0
|
|
S2
|
D:SF4401
|
2.2
|
48.9
|
1.0
|
|
S4
|
D:SF4401
|
2.3
|
47.5
|
1.0
|
|
S1
|
D:SF4401
|
2.3
|
49.6
|
1.0
|
|
SG
|
D:CYS198
|
2.4
|
53.7
|
1.0
|
|
FE1
|
D:SF4401
|
2.7
|
50.9
|
1.0
|
|
FE4
|
D:SF4401
|
2.7
|
49.5
|
1.0
|
|
FE2
|
D:SF4401
|
2.7
|
59.1
|
1.0
|
|
HB2
|
D:CYS198
|
3.1
|
52.6
|
1.0
|
|
CB
|
D:CYS198
|
3.3
|
47.2
|
1.0
|
|
HD3
|
D:ARG153
|
3.5
|
56.7
|
1.0
|
|
HA
|
D:CYS198
|
3.6
|
64.0
|
1.0
|
|
S3
|
D:SF4401
|
3.8
|
59.1
|
1.0
|
|
HH11
|
D:ARG153
|
3.9
|
67.8
|
1.0
|
|
HD2
|
D:ARG153
|
3.9
|
56.7
|
1.0
|
|
CA
|
D:CYS198
|
4.0
|
57.2
|
1.0
|
|
HB3
|
D:CYS198
|
4.1
|
52.6
|
1.0
|
|
CD
|
D:ARG153
|
4.2
|
41.7
|
1.0
|
|
HB2
|
D:ARG153
|
4.2
|
57.8
|
1.0
|
|
HB3
|
D:ARG153
|
4.2
|
57.8
|
1.0
|
|
HB2
|
D:PRO203
|
4.3
|
66.7
|
1.0
|
|
CB
|
D:ARG153
|
4.6
|
42.5
|
1.0
|
|
HA
|
D:VAL150
|
4.6
|
50.0
|
1.0
|
|
NH1
|
D:ARG153
|
4.7
|
51.0
|
1.0
|
|
HB3
|
D:PRO203
|
4.7
|
66.7
|
1.0
|
|
SG
|
D:CYS214
|
4.7
|
47.7
|
1.0
|
|
HG22
|
D:VAL150
|
4.8
|
50.4
|
1.0
|
|
SG
|
D:CYS205
|
4.8
|
69.6
|
1.0
|
|
SG
|
D:CYS208
|
4.8
|
49.5
|
1.0
|
|
HG13
|
D:VAL150
|
4.8
|
54.7
|
1.0
|
|
N
|
D:CYS198
|
4.9
|
62.7
|
1.0
|
|
CB
|
D:PRO203
|
4.9
|
59.1
|
1.0
|
|
HG12
|
D:VAL197
|
4.9
|
65.3
|
1.0
|
|
HA
|
D:CYS205
|
4.9
|
73.0
|
1.0
|
|
HD21
|
D:LEU193
|
5.0
|
58.6
|
1.0
|
|
Iron binding site 8 out
of 8 in 8dwf
Go back to
Iron Binding Sites List in 8dwf
Iron binding site 8 out
of 8 in the Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine
 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 E43S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Adenine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:49.5
occ:1.00
|
FE4
|
D:SF4401
|
0.0
|
49.5
|
1.0
|
|
S3
|
D:SF4401
|
2.3
|
59.1
|
1.0
|
|
S1
|
D:SF4401
|
2.3
|
49.6
|
1.0
|
|
S2
|
D:SF4401
|
2.3
|
48.9
|
1.0
|
|
SG
|
D:CYS214
|
2.3
|
47.7
|
1.0
|
|
FE2
|
D:SF4401
|
2.7
|
59.1
|
1.0
|
|
FE3
|
D:SF4401
|
2.7
|
51.9
|
1.0
|
|
FE1
|
D:SF4401
|
2.7
|
50.9
|
1.0
|
|
HB2
|
D:CYS214
|
3.0
|
76.4
|
1.0
|
|
CB
|
D:CYS214
|
3.2
|
61.4
|
1.0
|
|
HB2
|
D:PHE217
|
3.4
|
80.1
|
1.0
|
|
HB3
|
D:CYS214
|
3.4
|
76.4
|
1.0
|
|
HB3
|
D:ARG153
|
3.8
|
57.8
|
1.0
|
|
HD23
|
D:LEU154
|
3.8
|
60.4
|
1.0
|
|
S4
|
D:SF4401
|
3.8
|
47.5
|
1.0
|
|
H
|
D:PHE217
|
4.0
|
83.1
|
1.0
|
|
HB3
|
D:PHE217
|
4.1
|
80.1
|
1.0
|
|
CB
|
D:PHE217
|
4.2
|
67.4
|
1.0
|
|
HA
|
D:GLN211
|
4.3
|
79.5
|
1.0
|
|
HB3
|
D:ALA216
|
4.4
|
78.4
|
1.0
|
|
HB2
|
D:ARG153
|
4.5
|
57.8
|
1.0
|
|
HD3
|
D:ARG153
|
4.5
|
56.7
|
1.0
|
|
HD21
|
D:LEU154
|
4.5
|
60.4
|
1.0
|
|
CD2
|
D:LEU154
|
4.6
|
50.0
|
1.0
|
|
CB
|
D:ARG153
|
4.6
|
42.5
|
1.0
|
|
CA
|
D:CYS214
|
4.6
|
63.7
|
1.0
|
|
SG
|
D:CYS205
|
4.6
|
69.6
|
1.0
|
|
N
|
D:PHE217
|
4.6
|
69.4
|
1.0
|
|
HG
|
D:LEU154
|
4.7
|
65.2
|
1.0
|
|
HA
|
D:CYS214
|
4.7
|
79.2
|
1.0
|
|
HG23
|
D:VAL210
|
4.8
|
66.1
|
1.0
|
|
HA
|
D:LEU154
|
4.8
|
70.7
|
1.0
|
|
HB3
|
D:CYS205
|
4.9
|
66.6
|
1.0
|
|
SG
|
D:CYS208
|
4.9
|
49.5
|
1.0
|
|
HB2
|
D:ALA222
|
4.9
|
78.0
|
1.0
|
|
SG
|
D:CYS198
|
4.9
|
53.7
|
1.0
|
|
CA
|
D:PHE217
|
5.0
|
73.1
|
1.0
|
|
Reference:
L.P.Russelburg,
M.Demir,
K.Cedeno,
S.S.David,
M.P.Horvath.
Structural Basis For Base Engagement and Stereochemistry Revealed By Alteration of Catalytic Residue GLU43 in Dna Repair Glycosylase Muty To Be Published.
Page generated: Sat Aug 10 00:27:54 2024
|
