Iron in PDB 2ddg: Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
Protein crystallography data
The structure of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna, PDB code: 2ddg
was solved by
H.Kosaka,
N.Nakagawa,
R.Masui,
J.Hoseki,
S.Kuramitsu,
Riken Structuralgenomics/Proteomics Initiative (Rsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.16 /
2.10
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.927,
150.174,
93.408,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.8 /
24
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
(pdb code 2ddg). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna, PDB code: 2ddg:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2ddg
Go back to
Iron Binding Sites List in 2ddg
Iron binding site 1 out
of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe220
b:28.4
occ:1.00
|
FE1
|
A:SF4220
|
0.0
|
28.4
|
1.0
|
S3
|
A:SF4220
|
2.3
|
26.8
|
1.0
|
S2
|
A:SF4220
|
2.3
|
25.4
|
1.0
|
S4
|
A:SF4220
|
2.3
|
25.5
|
1.0
|
SG
|
A:CYS13
|
2.4
|
28.3
|
1.0
|
FE4
|
A:SF4220
|
2.7
|
29.4
|
1.0
|
FE2
|
A:SF4220
|
2.7
|
27.4
|
1.0
|
FE3
|
A:SF4220
|
2.7
|
29.0
|
1.0
|
CB
|
A:CYS13
|
3.4
|
26.7
|
1.0
|
NE1
|
A:TRP133
|
3.8
|
27.8
|
1.0
|
S1
|
A:SF4220
|
3.8
|
28.2
|
1.0
|
N
|
A:LEU15
|
4.1
|
32.2
|
1.0
|
CD1
|
A:TRP133
|
4.2
|
25.7
|
1.0
|
C
|
A:CYS13
|
4.3
|
29.8
|
1.0
|
CB
|
A:LEU15
|
4.3
|
33.4
|
1.0
|
CA
|
A:CYS13
|
4.5
|
27.9
|
1.0
|
N
|
A:ARG14
|
4.5
|
30.3
|
1.0
|
O
|
A:CYS13
|
4.5
|
29.9
|
1.0
|
CG
|
A:LEU15
|
4.7
|
34.8
|
1.0
|
CA
|
A:LEU15
|
4.8
|
32.2
|
1.0
|
CD1
|
A:LEU15
|
4.8
|
34.0
|
1.0
|
N
|
A:CYS16
|
4.9
|
30.3
|
1.0
|
SG
|
A:CYS115
|
4.9
|
22.3
|
1.0
|
SG
|
A:CYS16
|
4.9
|
26.9
|
1.0
|
SG
|
A:CYS130
|
4.9
|
26.1
|
1.0
|
CE2
|
A:TRP133
|
5.0
|
26.1
|
1.0
|
CA
|
A:ARG14
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 2ddg
Go back to
Iron Binding Sites List in 2ddg
Iron binding site 2 out
of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe220
b:27.4
occ:1.00
|
FE2
|
A:SF4220
|
0.0
|
27.4
|
1.0
|
S4
|
A:SF4220
|
2.2
|
25.5
|
1.0
|
S3
|
A:SF4220
|
2.3
|
26.8
|
1.0
|
S1
|
A:SF4220
|
2.3
|
28.2
|
1.0
|
SG
|
A:CYS130
|
2.4
|
26.1
|
1.0
|
FE1
|
A:SF4220
|
2.7
|
28.4
|
1.0
|
FE4
|
A:SF4220
|
2.7
|
29.4
|
1.0
|
FE3
|
A:SF4220
|
2.7
|
29.0
|
1.0
|
CB
|
A:CYS130
|
3.2
|
26.9
|
1.0
|
CA
|
A:CYS130
|
3.8
|
26.8
|
1.0
|
S2
|
A:SF4220
|
3.8
|
25.4
|
1.0
|
CD1
|
A:TRP133
|
3.9
|
25.7
|
1.0
|
N
|
A:ARG114
|
4.2
|
22.7
|
1.0
|
NE1
|
A:TRP133
|
4.4
|
27.8
|
1.0
|
N
|
A:CYS130
|
4.4
|
27.5
|
1.0
|
CB
|
A:ARG114
|
4.4
|
23.2
|
1.0
|
CA
|
A:ARG114
|
4.7
|
23.2
|
1.0
|
SG
|
A:CYS13
|
4.8
|
28.3
|
1.0
|
SG
|
A:CYS115
|
4.9
|
22.3
|
1.0
|
SG
|
A:CYS16
|
4.9
|
26.9
|
1.0
|
N
|
A:CYS115
|
5.0
|
21.4
|
1.0
|
CG
|
A:ARG114
|
5.0
|
23.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 2ddg
Go back to
Iron Binding Sites List in 2ddg
Iron binding site 3 out
of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe220
b:29.0
occ:1.00
|
FE3
|
A:SF4220
|
0.0
|
29.0
|
1.0
|
S1
|
A:SF4220
|
2.3
|
28.2
|
1.0
|
S2
|
A:SF4220
|
2.3
|
25.4
|
1.0
|
S4
|
A:SF4220
|
2.3
|
25.5
|
1.0
|
SG
|
A:CYS115
|
2.5
|
22.3
|
1.0
|
FE1
|
A:SF4220
|
2.7
|
28.4
|
1.0
|
FE4
|
A:SF4220
|
2.7
|
29.4
|
1.0
|
FE2
|
A:SF4220
|
2.7
|
27.4
|
1.0
|
CB
|
A:CYS115
|
3.2
|
21.5
|
1.0
|
S3
|
A:SF4220
|
3.8
|
26.8
|
1.0
|
N
|
A:CYS115
|
4.1
|
21.4
|
1.0
|
CA
|
A:CYS115
|
4.2
|
21.0
|
1.0
|
CG
|
A:PRO42
|
4.5
|
23.7
|
1.0
|
C
|
A:ARG114
|
4.5
|
23.0
|
1.0
|
NH2
|
A:ARG23
|
4.7
|
26.2
|
1.0
|
CB
|
A:PRO42
|
4.8
|
22.6
|
1.0
|
SG
|
A:CYS13
|
4.8
|
28.3
|
1.0
|
SG
|
A:CYS130
|
4.9
|
26.1
|
1.0
|
O
|
A:ARG114
|
4.9
|
21.8
|
1.0
|
N
|
A:ARG114
|
5.0
|
22.7
|
1.0
|
SG
|
A:CYS16
|
5.0
|
26.9
|
1.0
|
CD1
|
A:LEU19
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 2ddg
Go back to
Iron Binding Sites List in 2ddg
Iron binding site 4 out
of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/dd/2ddg-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe220
b:29.4
occ:1.00
|
FE4
|
A:SF4220
|
0.0
|
29.4
|
1.0
|
S3
|
A:SF4220
|
2.3
|
26.8
|
1.0
|
S1
|
A:SF4220
|
2.3
|
28.2
|
1.0
|
S2
|
A:SF4220
|
2.3
|
25.4
|
1.0
|
SG
|
A:CYS16
|
2.5
|
26.9
|
1.0
|
FE1
|
A:SF4220
|
2.7
|
28.4
|
1.0
|
FE2
|
A:SF4220
|
2.7
|
27.4
|
1.0
|
FE3
|
A:SF4220
|
2.7
|
29.0
|
1.0
|
CB
|
A:CYS16
|
3.2
|
29.4
|
1.0
|
N
|
A:CYS16
|
3.7
|
30.3
|
1.0
|
S4
|
A:SF4220
|
3.8
|
25.5
|
1.0
|
CA
|
A:CYS16
|
4.1
|
28.6
|
1.0
|
CD1
|
A:LEU19
|
4.5
|
22.4
|
1.0
|
CB
|
A:LEU15
|
4.5
|
33.4
|
1.0
|
C
|
A:LEU15
|
4.6
|
32.0
|
1.0
|
CB
|
A:CYS130
|
4.7
|
26.9
|
1.0
|
N
|
A:LEU15
|
4.7
|
32.2
|
1.0
|
CB
|
A:ALA129
|
4.7
|
27.6
|
1.0
|
SG
|
A:CYS13
|
4.8
|
28.3
|
1.0
|
SG
|
A:CYS130
|
4.8
|
26.1
|
1.0
|
CA
|
A:LEU15
|
4.8
|
32.2
|
1.0
|
N
|
A:CYS130
|
4.9
|
27.5
|
1.0
|
O
|
A:GLU126
|
4.9
|
27.1
|
1.0
|
SG
|
A:CYS115
|
5.0
|
22.3
|
1.0
|
|
Reference:
H.Kosaka,
J.Hoseki,
N.Nakagawa,
S.Kuramitsu,
R.Masui.
Crystal Structure of Family 5 Uracil-Dna Glycosylase Bound to Dna. J.Mol.Biol. V. 373 839 2007.
ISSN: ISSN 0022-2836
PubMed: 17870091
DOI: 10.1016/J.JMB.2007.08.022
Page generated: Sat Aug 3 20:43:20 2024
|