Iron in PDB 1kea: Structure of A Thermostable Thymine-Dna Glycosylase
Protein crystallography data
The structure of Structure of A Thermostable Thymine-Dna Glycosylase, PDB code: 1kea
was solved by
C.D.Mol,
A.S.Arvai,
T.J.Begley,
R.P.Cunningham,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.77 /
2.00
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.215,
68.215,
98.944,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
24.8
|
Other elements in 1kea:
The structure of Structure of A Thermostable Thymine-Dna Glycosylase also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of A Thermostable Thymine-Dna Glycosylase
(pdb code 1kea). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of A Thermostable Thymine-Dna Glycosylase, PDB code: 1kea:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1kea
Go back to
Iron Binding Sites List in 1kea
Iron binding site 1 out
of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:28.6
occ:1.00
|
FE1
|
A:SF4300
|
0.0
|
28.6
|
1.0
|
S3
|
A:SF4300
|
2.2
|
28.2
|
1.0
|
S4
|
A:SF4300
|
2.3
|
28.3
|
1.0
|
SG
|
A:CYS207
|
2.4
|
30.3
|
1.0
|
S2
|
A:SF4300
|
2.4
|
29.2
|
1.0
|
FE4
|
A:SF4300
|
2.7
|
29.3
|
1.0
|
FE2
|
A:SF4300
|
2.7
|
27.3
|
1.0
|
FE3
|
A:SF4300
|
2.8
|
29.1
|
1.0
|
CB
|
A:CYS207
|
3.1
|
31.1
|
1.0
|
S1
|
A:SF4300
|
3.9
|
28.4
|
1.0
|
CZ
|
A:PHE192
|
4.2
|
22.2
|
1.0
|
CA
|
A:CYS207
|
4.6
|
32.8
|
1.0
|
CG
|
A:MET209
|
4.6
|
33.0
|
1.0
|
SG
|
A:CYS204
|
4.7
|
31.4
|
1.0
|
SG
|
A:CYS197
|
4.8
|
25.6
|
1.0
|
CA
|
A:CYS204
|
4.8
|
33.9
|
1.0
|
CE
|
A:MET209
|
4.8
|
33.1
|
1.0
|
CE2
|
A:PHE192
|
4.8
|
22.7
|
1.0
|
N
|
A:SER210
|
4.8
|
33.9
|
1.0
|
CA
|
A:SER210
|
4.9
|
34.9
|
1.0
|
SG
|
A:CYS213
|
4.9
|
31.5
|
1.0
|
CB
|
A:CYS213
|
4.9
|
34.3
|
1.0
|
CG2
|
A:ILE196
|
4.9
|
24.9
|
1.0
|
CB
|
A:CYS197
|
4.9
|
24.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 1kea
Go back to
Iron Binding Sites List in 1kea
Iron binding site 2 out
of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:27.3
occ:1.00
|
FE2
|
A:SF4300
|
0.0
|
27.3
|
1.0
|
S4
|
A:SF4300
|
2.2
|
28.3
|
1.0
|
SG
|
A:CYS197
|
2.3
|
25.6
|
1.0
|
S3
|
A:SF4300
|
2.3
|
28.2
|
1.0
|
S1
|
A:SF4300
|
2.4
|
28.4
|
1.0
|
FE1
|
A:SF4300
|
2.7
|
28.6
|
1.0
|
FE4
|
A:SF4300
|
2.8
|
29.3
|
1.0
|
FE3
|
A:SF4300
|
2.8
|
29.1
|
1.0
|
CB
|
A:CYS197
|
3.1
|
24.9
|
1.0
|
CA
|
A:CYS197
|
3.9
|
24.8
|
1.0
|
S2
|
A:SF4300
|
4.0
|
29.2
|
1.0
|
CB
|
A:PRO202
|
4.3
|
37.4
|
1.0
|
CD
|
A:ARG153
|
4.5
|
29.1
|
1.0
|
CB
|
A:ARG153
|
4.7
|
30.5
|
1.0
|
CE2
|
A:PHE192
|
4.8
|
22.7
|
1.0
|
N
|
A:CYS197
|
4.8
|
24.4
|
1.0
|
SG
|
A:CYS207
|
4.8
|
30.3
|
1.0
|
SG
|
A:CYS204
|
4.8
|
31.4
|
1.0
|
CZ
|
A:PHE192
|
4.9
|
22.2
|
1.0
|
NH1
|
A:ARG153
|
4.9
|
27.8
|
1.0
|
SG
|
A:CYS213
|
4.9
|
31.5
|
1.0
|
CG
|
A:PRO202
|
5.0
|
37.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 1kea
Go back to
Iron Binding Sites List in 1kea
Iron binding site 3 out
of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:29.1
occ:1.00
|
FE3
|
A:SF4300
|
0.0
|
29.1
|
1.0
|
SG
|
A:CYS204
|
2.2
|
31.4
|
1.0
|
S2
|
A:SF4300
|
2.2
|
29.2
|
1.0
|
S1
|
A:SF4300
|
2.3
|
28.4
|
1.0
|
S4
|
A:SF4300
|
2.3
|
28.3
|
1.0
|
FE4
|
A:SF4300
|
2.6
|
29.3
|
1.0
|
FE1
|
A:SF4300
|
2.8
|
28.6
|
1.0
|
FE2
|
A:SF4300
|
2.8
|
27.3
|
1.0
|
CB
|
A:CYS204
|
3.3
|
32.8
|
1.0
|
CA
|
A:CYS204
|
3.7
|
33.9
|
1.0
|
CB
|
A:PRO202
|
4.0
|
37.4
|
1.0
|
S3
|
A:SF4300
|
4.0
|
28.2
|
1.0
|
CG
|
A:PRO202
|
4.1
|
37.9
|
1.0
|
N
|
A:CYS204
|
4.2
|
34.1
|
1.0
|
CD2
|
A:TYR215
|
4.5
|
43.9
|
1.0
|
SG
|
A:CYS213
|
4.7
|
31.5
|
1.0
|
CB
|
A:CYS207
|
4.7
|
31.1
|
1.0
|
SG
|
A:CYS197
|
4.8
|
25.6
|
1.0
|
CE2
|
A:TYR215
|
4.8
|
44.1
|
1.0
|
SG
|
A:CYS207
|
4.8
|
30.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 1kea
Go back to
Iron Binding Sites List in 1kea
Iron binding site 4 out
of 4 in the Structure of A Thermostable Thymine-Dna Glycosylase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of A Thermostable Thymine-Dna Glycosylase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe300
b:29.3
occ:1.00
|
FE4
|
A:SF4300
|
0.0
|
29.3
|
1.0
|
S2
|
A:SF4300
|
2.2
|
29.2
|
1.0
|
S1
|
A:SF4300
|
2.3
|
28.4
|
1.0
|
S3
|
A:SF4300
|
2.4
|
28.2
|
1.0
|
SG
|
A:CYS213
|
2.4
|
31.5
|
1.0
|
FE3
|
A:SF4300
|
2.6
|
29.1
|
1.0
|
FE1
|
A:SF4300
|
2.7
|
28.6
|
1.0
|
FE2
|
A:SF4300
|
2.8
|
27.3
|
1.0
|
CB
|
A:CYS213
|
3.2
|
34.3
|
1.0
|
S4
|
A:SF4300
|
3.8
|
28.3
|
1.0
|
SG
|
A:CYS204
|
4.5
|
31.4
|
1.0
|
CA
|
A:CYS213
|
4.6
|
36.6
|
1.0
|
CB
|
A:TYR216
|
4.6
|
48.1
|
1.0
|
N
|
A:TYR216
|
4.7
|
46.5
|
1.0
|
CD2
|
A:TYR215
|
4.7
|
43.9
|
1.0
|
CB
|
A:TYR215
|
4.7
|
43.8
|
1.0
|
SG
|
A:CYS207
|
4.7
|
30.3
|
1.0
|
SG
|
A:CYS197
|
4.8
|
25.6
|
1.0
|
CB
|
A:ARG153
|
4.9
|
30.5
|
1.0
|
CD1
|
A:TYR154
|
4.9
|
31.6
|
1.0
|
CA
|
A:TYR154
|
4.9
|
32.5
|
1.0
|
N
|
A:TYR154
|
5.0
|
32.0
|
1.0
|
|
Reference:
C.D.Mol,
A.S.Arvai,
T.J.Begley,
R.P.Cunningham,
J.A.Tainer.
Structure and Activity of A Thermostable Thymine-Dna Glycosylase: Evidence For Base Twisting to Remove Mismatched Normal Dna Bases. J.Mol.Biol. V. 315 373 2002.
ISSN: ISSN 0022-2836
PubMed: 11786018
DOI: 10.1006/JMBI.2001.5264
Page generated: Sat Aug 3 09:08:44 2024
|