Iron in PDB 5kn9: Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
Protein crystallography data
The structure of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair, PDB code: 5kn9
was solved by
L.Wang,
S.Chakravarthy,
G.L.Verdine,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
79.88 /
1.93
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.878,
38.759,
82.960,
90.00,
105.66,
90.00
|
R / Rfree (%)
|
16.9 /
22.9
|
Other elements in 5kn9:
The structure of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
(pdb code 5kn9). 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 N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair, PDB code: 5kn9:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5kn9
Go back to
Iron Binding Sites List in 5kn9
Iron binding site 1 out
of 4 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:17.6
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
17.6
|
1.0
|
S4
|
A:SF4301
|
2.2
|
17.3
|
1.0
|
S2
|
A:SF4301
|
2.2
|
18.2
|
1.0
|
S3
|
A:SF4301
|
2.2
|
17.9
|
1.0
|
SG
|
A:CYS205
|
2.3
|
19.6
|
1.0
|
FE4
|
A:SF4301
|
2.8
|
17.9
|
1.0
|
FE3
|
A:SF4301
|
2.8
|
16.5
|
1.0
|
FE2
|
A:SF4301
|
2.9
|
17.0
|
1.0
|
CB
|
A:CYS205
|
3.1
|
20.7
|
1.0
|
CA
|
A:CYS205
|
3.5
|
20.3
|
1.0
|
S1
|
A:SF4301
|
3.8
|
18.1
|
1.0
|
N
|
A:CYS205
|
4.0
|
23.3
|
1.0
|
CB
|
A:PRO203
|
4.3
|
14.5
|
1.0
|
CG
|
A:PRO203
|
4.5
|
18.1
|
1.0
|
CB
|
A:PHE217
|
4.6
|
23.2
|
1.0
|
CB
|
A:CYS208
|
4.7
|
16.6
|
1.0
|
SG
|
A:CYS214
|
4.8
|
20.2
|
1.0
|
C
|
A:CYS205
|
4.9
|
17.1
|
1.0
|
CB
|
A:ALA222
|
4.9
|
13.4
|
1.0
|
SG
|
A:CYS208
|
4.9
|
18.1
|
1.0
|
C
|
A:SER204
|
4.9
|
18.4
|
1.0
|
CD1
|
A:PHE217
|
5.0
|
20.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 5kn9
Go back to
Iron Binding Sites List in 5kn9
Iron binding site 2 out
of 4 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:17.0
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
17.0
|
1.0
|
S3
|
A:SF4301
|
2.2
|
17.9
|
1.0
|
S1
|
A:SF4301
|
2.2
|
18.1
|
1.0
|
S4
|
A:SF4301
|
2.2
|
17.3
|
1.0
|
SG
|
A:CYS198
|
2.4
|
18.9
|
1.0
|
FE4
|
A:SF4301
|
2.8
|
17.9
|
1.0
|
FE3
|
A:SF4301
|
2.8
|
16.5
|
1.0
|
FE1
|
A:SF4301
|
2.9
|
17.6
|
1.0
|
CB
|
A:CYS198
|
3.2
|
15.7
|
1.0
|
S2
|
A:SF4301
|
3.8
|
18.2
|
1.0
|
CA
|
A:CYS198
|
3.9
|
19.3
|
1.0
|
CD
|
A:ARG153
|
3.9
|
15.5
|
1.0
|
NH1
|
A:ARG153
|
4.4
|
16.3
|
1.0
|
CB
|
A:ARG153
|
4.4
|
12.7
|
1.0
|
CB
|
A:PRO203
|
4.6
|
14.5
|
1.0
|
CG
|
A:ARG153
|
4.8
|
19.7
|
1.0
|
SG
|
A:CYS214
|
4.9
|
20.2
|
1.0
|
SG
|
A:CYS208
|
4.9
|
18.1
|
1.0
|
C
|
A:CYS198
|
4.9
|
20.6
|
1.0
|
N
|
A:CYS198
|
4.9
|
18.1
|
1.0
|
NE
|
A:ARG153
|
5.0
|
16.5
|
1.0
|
SG
|
A:CYS205
|
5.0
|
19.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 5kn9
Go back to
Iron Binding Sites List in 5kn9
Iron binding site 3 out
of 4 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:16.5
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
16.5
|
1.0
|
S2
|
A:SF4301
|
2.2
|
18.2
|
1.0
|
S4
|
A:SF4301
|
2.2
|
17.3
|
1.0
|
S1
|
A:SF4301
|
2.2
|
18.1
|
1.0
|
SG
|
A:CYS208
|
2.3
|
18.1
|
1.0
|
FE4
|
A:SF4301
|
2.8
|
17.9
|
1.0
|
FE2
|
A:SF4301
|
2.8
|
17.0
|
1.0
|
FE1
|
A:SF4301
|
2.8
|
17.6
|
1.0
|
CB
|
A:CYS208
|
3.0
|
16.6
|
1.0
|
S3
|
A:SF4301
|
3.8
|
17.9
|
1.0
|
CG2
|
A:VAL210
|
4.4
|
20.6
|
1.0
|
CA
|
A:CYS208
|
4.5
|
15.5
|
1.0
|
CA
|
A:CYS205
|
4.7
|
20.3
|
1.0
|
N
|
A:GLN211
|
4.7
|
21.3
|
1.0
|
CA
|
A:GLN211
|
4.7
|
24.4
|
1.0
|
CG1
|
A:VAL197
|
4.8
|
15.5
|
1.0
|
C
|
A:VAL210
|
4.8
|
15.3
|
1.0
|
SG
|
A:CYS198
|
4.8
|
18.9
|
1.0
|
CB
|
A:CYS198
|
4.9
|
15.7
|
1.0
|
CB
|
A:CYS214
|
4.9
|
18.4
|
1.0
|
SG
|
A:CYS205
|
5.0
|
19.6
|
1.0
|
O
|
A:VAL210
|
5.0
|
22.4
|
1.0
|
CB
|
A:CYS205
|
5.0
|
20.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 5kn9
Go back to
Iron Binding Sites List in 5kn9
Iron binding site 4 out
of 4 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:17.9
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
17.9
|
1.0
|
S1
|
A:SF4301
|
2.2
|
18.1
|
1.0
|
S3
|
A:SF4301
|
2.2
|
17.9
|
1.0
|
S2
|
A:SF4301
|
2.2
|
18.2
|
1.0
|
SG
|
A:CYS214
|
2.4
|
20.2
|
1.0
|
FE2
|
A:SF4301
|
2.8
|
17.0
|
1.0
|
FE3
|
A:SF4301
|
2.8
|
16.5
|
1.0
|
FE1
|
A:SF4301
|
2.8
|
17.6
|
1.0
|
CB
|
A:CYS214
|
3.0
|
18.4
|
1.0
|
S4
|
A:SF4301
|
3.7
|
17.3
|
1.0
|
CB
|
A:PHE217
|
4.3
|
23.2
|
1.0
|
CA
|
A:CYS214
|
4.4
|
15.9
|
1.0
|
CB
|
A:ARG153
|
4.4
|
12.7
|
1.0
|
CD2
|
A:LEU154
|
4.5
|
17.9
|
1.0
|
N
|
A:PHE217
|
4.7
|
23.0
|
1.0
|
SG
|
A:CYS205
|
4.9
|
19.6
|
1.0
|
SG
|
A:CYS208
|
4.9
|
18.1
|
1.0
|
N
|
A:LEU154
|
5.0
|
13.3
|
1.0
|
SG
|
A:CYS198
|
5.0
|
18.9
|
1.0
|
|
Reference:
L.Wang,
S.Chakravarthy,
G.L.Verdine.
Structural Basis For the Lesion-Scanning Mechanism of the Muty Dna Glycosylase. J. Biol. Chem. V. 292 5007 2017.
ISSN: ESSN 1083-351X
PubMed: 28130451
DOI: 10.1074/JBC.M116.757039
Page generated: Tue Aug 6 03:28:39 2024
|