Iron in PDB 6q0c: Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
Enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
All present enzymatic activity of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg:
3.2.2.31;
Protein crystallography data
The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg, PDB code: 6q0c
was solved by
V.L.O'shea Murray,
L.P.Russelburg,
M.P.Horvath,
S.S.David,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.30 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
37.860,
86.140,
141.170,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.7 /
27.1
|
Other elements in 6q0c:
The structure of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
(pdb code 6q0c). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg, PDB code: 6q0c:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6q0c
Go back to
Iron Binding Sites List in 6q0c
Iron binding site 1 out
of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:49.1
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
49.1
|
1.0
|
S3
|
A:SF4401
|
2.3
|
50.8
|
1.0
|
S2
|
A:SF4401
|
2.3
|
40.5
|
1.0
|
S4
|
A:SF4401
|
2.3
|
42.3
|
1.0
|
SG
|
A:CYS208
|
2.4
|
51.5
|
1.0
|
HB2
|
A:CYS208
|
2.6
|
45.2
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
47.5
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
45.5
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
47.0
|
1.0
|
CB
|
A:CYS208
|
2.8
|
37.6
|
1.0
|
HB3
|
A:CYS208
|
2.8
|
45.2
|
1.0
|
HA
|
A:CYS205
|
3.3
|
60.1
|
1.0
|
HB2
|
A:CYS198
|
3.8
|
48.1
|
1.0
|
S1
|
A:SF4401
|
3.9
|
42.2
|
1.0
|
HA
|
A:GLN211
|
3.9
|
79.1
|
1.0
|
HG23
|
A:VAL210
|
4.0
|
67.6
|
1.0
|
HG12
|
A:VAL197
|
4.0
|
54.9
|
1.0
|
CA
|
A:CYS205
|
4.2
|
50.1
|
1.0
|
HB3
|
A:CYS205
|
4.2
|
58.6
|
1.0
|
CA
|
A:CYS208
|
4.3
|
50.8
|
1.0
|
HB2
|
A:CYS214
|
4.4
|
74.4
|
1.0
|
HB2
|
A:GLN211
|
4.5
|
74.2
|
1.0
|
HA
|
A:CYS208
|
4.6
|
60.9
|
1.0
|
CB
|
A:CYS205
|
4.6
|
48.8
|
1.0
|
HG22
|
A:VAL210
|
4.6
|
67.6
|
1.0
|
CB
|
A:CYS198
|
4.6
|
40.1
|
1.0
|
HD21
|
A:LEU193
|
4.7
|
55.9
|
1.0
|
HD11
|
A:LEU193
|
4.7
|
50.6
|
1.0
|
CA
|
A:GLN211
|
4.7
|
66.0
|
1.0
|
N
|
A:GLN211
|
4.7
|
61.2
|
1.0
|
H
|
A:VAL210
|
4.7
|
72.3
|
1.0
|
HG11
|
A:VAL197
|
4.7
|
54.9
|
1.0
|
HD23
|
A:LEU154
|
4.8
|
64.8
|
1.0
|
CG2
|
A:VAL210
|
4.8
|
56.4
|
1.0
|
O
|
A:CYS205
|
4.8
|
50.9
|
1.0
|
SG
|
A:CYS205
|
4.8
|
42.9
|
1.0
|
H
|
A:CYS208
|
4.8
|
59.6
|
1.0
|
CG1
|
A:VAL197
|
4.8
|
45.7
|
1.0
|
H
|
A:GLN211
|
4.9
|
73.4
|
1.0
|
HA
|
A:CYS198
|
4.9
|
47.1
|
1.0
|
C
|
A:VAL210
|
4.9
|
64.0
|
1.0
|
HD21
|
A:LEU154
|
4.9
|
64.8
|
1.0
|
SG
|
A:CYS198
|
5.0
|
40.2
|
1.0
|
HB3
|
A:CYS214
|
5.0
|
74.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 6q0c
Go back to
Iron Binding Sites List in 6q0c
Iron binding site 2 out
of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:47.5
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
47.5
|
1.0
|
SG
|
A:CYS205
|
2.2
|
42.9
|
1.0
|
S3
|
A:SF4401
|
2.3
|
50.8
|
1.0
|
S4
|
A:SF4401
|
2.3
|
42.3
|
1.0
|
S1
|
A:SF4401
|
2.3
|
42.2
|
1.0
|
HB3
|
A:CYS205
|
2.6
|
58.6
|
1.0
|
HA
|
A:CYS205
|
2.7
|
60.1
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
49.1
|
1.0
|
CB
|
A:CYS205
|
2.7
|
48.8
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
47.0
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
45.5
|
1.0
|
CA
|
A:CYS205
|
3.2
|
50.1
|
1.0
|
HB2
|
A:PRO203
|
3.5
|
53.1
|
1.0
|
HB2
|
A:CYS205
|
3.7
|
58.6
|
1.0
|
N
|
A:CYS205
|
3.8
|
43.5
|
1.0
|
H
|
A:CYS205
|
3.8
|
52.3
|
1.0
|
S2
|
A:SF4401
|
3.9
|
40.5
|
1.0
|
HB2
|
A:PHE217
|
3.9
|
77.8
|
1.0
|
HB2
|
A:CYS208
|
4.2
|
45.2
|
1.0
|
HB3
|
A:CYS208
|
4.3
|
45.2
|
1.0
|
HG2
|
A:PRO203
|
4.3
|
50.0
|
1.0
|
HB1
|
A:ALA222
|
4.4
|
66.7
|
1.0
|
HB2
|
A:ALA222
|
4.4
|
66.7
|
1.0
|
CB
|
A:PRO203
|
4.4
|
44.2
|
1.0
|
C
|
A:CYS205
|
4.5
|
45.7
|
1.0
|
HD1
|
A:PHE217
|
4.5
|
69.7
|
1.0
|
CB
|
A:CYS208
|
4.6
|
37.6
|
1.0
|
CG
|
A:PRO203
|
4.7
|
41.6
|
1.0
|
SG
|
A:CYS214
|
4.7
|
60.8
|
1.0
|
HG3
|
A:PRO203
|
4.7
|
50.0
|
1.0
|
HD3
|
A:ARG153
|
4.8
|
49.5
|
1.0
|
HB3
|
A:PRO203
|
4.8
|
53.1
|
1.0
|
O
|
A:CYS205
|
4.8
|
50.9
|
1.0
|
CB
|
A:ALA222
|
4.8
|
55.6
|
1.0
|
C
|
A:SER204
|
4.8
|
46.3
|
1.0
|
HB2
|
A:CYS198
|
4.8
|
48.1
|
1.0
|
HA
|
A:CYS198
|
4.8
|
47.1
|
1.0
|
CB
|
A:PHE217
|
4.9
|
64.8
|
1.0
|
HG3
|
A:GLN211
|
5.0
|
78.2
|
1.0
|
SG
|
A:CYS208
|
5.0
|
51.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 6q0c
Go back to
Iron Binding Sites List in 6q0c
Iron binding site 3 out
of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:45.5
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
45.5
|
1.0
|
S2
|
A:SF4401
|
2.3
|
40.5
|
1.0
|
S1
|
A:SF4401
|
2.3
|
42.2
|
1.0
|
S4
|
A:SF4401
|
2.3
|
42.3
|
1.0
|
SG
|
A:CYS198
|
2.5
|
40.2
|
1.0
|
HB2
|
A:CYS198
|
2.6
|
48.1
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
47.0
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
49.1
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
47.5
|
1.0
|
CB
|
A:CYS198
|
3.0
|
40.1
|
1.0
|
HD3
|
A:ARG153
|
3.3
|
49.5
|
1.0
|
HA
|
A:CYS198
|
3.5
|
47.1
|
1.0
|
HH11
|
A:ARG153
|
3.6
|
50.2
|
1.0
|
HB2
|
A:PRO203
|
3.8
|
53.1
|
1.0
|
CA
|
A:CYS198
|
3.8
|
39.3
|
1.0
|
HB3
|
A:CYS198
|
3.9
|
48.1
|
1.0
|
S3
|
A:SF4401
|
3.9
|
50.8
|
1.0
|
HD2
|
A:ARG153
|
4.1
|
49.5
|
1.0
|
CD
|
A:ARG153
|
4.1
|
41.2
|
1.0
|
HB2
|
A:ARG153
|
4.2
|
50.4
|
1.0
|
HB3
|
A:PRO203
|
4.3
|
53.1
|
1.0
|
HB3
|
A:ARG153
|
4.3
|
50.4
|
1.0
|
NH1
|
A:ARG153
|
4.4
|
41.8
|
1.0
|
CB
|
A:PRO203
|
4.5
|
44.2
|
1.0
|
SG
|
A:CYS205
|
4.6
|
42.9
|
1.0
|
HA
|
A:VAL150
|
4.6
|
46.6
|
1.0
|
CB
|
A:ARG153
|
4.6
|
42.0
|
1.0
|
HG22
|
A:VAL150
|
4.7
|
41.3
|
1.0
|
HA
|
A:CYS205
|
4.7
|
60.1
|
1.0
|
HB2
|
A:CYS208
|
4.7
|
45.2
|
1.0
|
N
|
A:CYS198
|
4.8
|
43.2
|
1.0
|
HG12
|
A:VAL197
|
4.8
|
54.9
|
1.0
|
HH12
|
A:ARG153
|
4.8
|
50.2
|
1.0
|
HG3
|
A:PRO203
|
4.8
|
50.0
|
1.0
|
HD23
|
A:LEU154
|
4.9
|
64.8
|
1.0
|
SG
|
A:CYS214
|
4.9
|
60.8
|
1.0
|
SG
|
A:CYS208
|
4.9
|
51.5
|
1.0
|
HB1
|
A:ALA222
|
4.9
|
66.7
|
1.0
|
H
|
A:CYS198
|
4.9
|
51.8
|
1.0
|
C
|
A:CYS198
|
5.0
|
36.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 6q0c
Go back to
Iron Binding Sites List in 6q0c
Iron binding site 4 out
of 4 in the Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Muty Adenine Glycosylase Bound to Dna Containing A Transition State Analog (1N) Paired with Undamaged Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:47.0
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
47.0
|
1.0
|
S1
|
A:SF4401
|
2.3
|
42.2
|
1.0
|
S2
|
A:SF4401
|
2.3
|
40.5
|
1.0
|
S3
|
A:SF4401
|
2.3
|
50.8
|
1.0
|
SG
|
A:CYS214
|
2.4
|
60.8
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
45.5
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
47.5
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
49.1
|
1.0
|
HB2
|
A:CYS214
|
2.9
|
74.4
|
1.0
|
CB
|
A:CYS214
|
3.1
|
62.0
|
1.0
|
HB3
|
A:CYS214
|
3.3
|
74.4
|
1.0
|
HD23
|
A:LEU154
|
3.3
|
64.8
|
1.0
|
HB2
|
A:PHE217
|
3.7
|
77.8
|
1.0
|
S4
|
A:SF4401
|
3.9
|
42.3
|
1.0
|
HB3
|
A:ARG153
|
3.9
|
50.4
|
1.0
|
HA
|
A:GLN211
|
4.1
|
79.1
|
1.0
|
CD2
|
A:LEU154
|
4.2
|
54.0
|
1.0
|
H
|
A:PHE217
|
4.3
|
67.8
|
1.0
|
HD21
|
A:LEU154
|
4.3
|
64.8
|
1.0
|
HB2
|
A:ARG153
|
4.4
|
50.4
|
1.0
|
HB3
|
A:ALA216
|
4.5
|
63.5
|
1.0
|
HB3
|
A:CYS205
|
4.5
|
58.6
|
1.0
|
HA
|
A:LEU154
|
4.5
|
65.5
|
1.0
|
CA
|
A:CYS214
|
4.5
|
65.0
|
1.0
|
HD3
|
A:ARG153
|
4.6
|
49.5
|
1.0
|
CB
|
A:ARG153
|
4.6
|
42.0
|
1.0
|
CB
|
A:PHE217
|
4.6
|
64.8
|
1.0
|
HD22
|
A:LEU154
|
4.6
|
64.8
|
1.0
|
HA
|
A:CYS214
|
4.7
|
78.0
|
1.0
|
HB3
|
A:PHE217
|
4.8
|
77.8
|
1.0
|
SG
|
A:CYS208
|
4.8
|
51.5
|
1.0
|
SG
|
A:CYS205
|
4.8
|
42.9
|
1.0
|
HG23
|
A:VAL210
|
4.8
|
67.6
|
1.0
|
HA
|
A:CYS205
|
4.8
|
60.1
|
1.0
|
N
|
A:PHE217
|
4.9
|
56.5
|
1.0
|
HG
|
A:LEU154
|
4.9
|
63.9
|
1.0
|
SG
|
A:CYS198
|
5.0
|
40.2
|
1.0
|
|
Reference:
L.P.Russelburg,
V.L.O'shea Murray,
M.Demir,
K.R.Knutsen,
S.L.Sehgal,
S.Cao,
S.S.David,
M.P.Horvath.
Structural Basis For Finding Og Lesions and Avoiding Undamaged G By the Dna Glycosylase Muty To Be Published.
Page generated: Wed Aug 7 06:48:04 2024
|