Calcium in PDB 1s0o: Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Enzymatic activity of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
All present enzymatic activity of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift:
2.7.7.7;
Protein crystallography data
The structure of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift, PDB code: 1s0o
was solved by
H.Ling,
F.Boudsocq,
R.Woodgate,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.301,
103.046,
105.912,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
26.9
|
Other elements in 1s0o:
The structure of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
(pdb code 1s0o). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift, PDB code: 1s0o:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 1 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:37.0
occ:1.00
|
O
|
A:HOH893
|
2.4
|
38.5
|
1.0
|
OE1
|
A:GLU106
|
2.4
|
29.5
|
1.0
|
O2A
|
A:TTP803
|
2.4
|
28.4
|
1.0
|
O
|
A:HOH943
|
2.4
|
39.6
|
1.0
|
OD1
|
A:ASP105
|
2.5
|
24.4
|
1.0
|
OD1
|
A:ASP7
|
2.8
|
30.0
|
1.0
|
OD2
|
A:ASP7
|
2.9
|
35.2
|
1.0
|
CG
|
A:ASP7
|
3.1
|
28.5
|
1.0
|
CG
|
A:ASP105
|
3.3
|
24.8
|
1.0
|
OD2
|
A:ASP105
|
3.3
|
23.2
|
1.0
|
CA
|
A:CA402
|
3.6
|
26.3
|
1.0
|
CD
|
A:GLU106
|
3.6
|
31.1
|
1.0
|
PA
|
A:TTP803
|
3.7
|
34.3
|
1.0
|
O1A
|
A:TTP803
|
3.8
|
33.9
|
1.0
|
O5'
|
A:TTP803
|
4.0
|
30.8
|
1.0
|
CB
|
A:GLU106
|
4.1
|
26.2
|
1.0
|
C5'
|
A:TTP803
|
4.1
|
30.6
|
1.0
|
CG
|
A:GLU106
|
4.2
|
27.2
|
1.0
|
OG
|
A:SER103
|
4.3
|
34.4
|
1.0
|
CB
|
A:ASP7
|
4.5
|
24.9
|
1.0
|
O
|
A:ASP105
|
4.5
|
25.8
|
1.0
|
OE2
|
A:GLU106
|
4.6
|
32.7
|
1.0
|
C
|
A:ASP105
|
4.7
|
24.1
|
1.0
|
CB
|
A:ASP105
|
4.7
|
24.0
|
1.0
|
O
|
A:HOH947
|
4.8
|
58.5
|
1.0
|
NZ
|
A:LYS152
|
4.9
|
33.6
|
1.0
|
N
|
A:GLU106
|
5.0
|
23.7
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 2 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:26.3
occ:1.00
|
OD1
|
A:ASP7
|
2.3
|
30.0
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
23.2
|
1.0
|
O
|
A:PHE8
|
2.3
|
21.5
|
1.0
|
O2A
|
A:TTP803
|
2.4
|
28.4
|
1.0
|
O2B
|
A:TTP803
|
2.6
|
29.8
|
1.0
|
O
|
A:HOH813
|
2.8
|
46.8
|
1.0
|
O3B
|
A:TTP803
|
2.8
|
38.9
|
1.0
|
O1G
|
A:TTP803
|
2.9
|
37.6
|
1.0
|
CG
|
A:ASP7
|
3.3
|
28.5
|
1.0
|
CG
|
A:ASP105
|
3.4
|
24.8
|
1.0
|
PB
|
A:TTP803
|
3.4
|
29.4
|
1.0
|
C
|
A:PHE8
|
3.5
|
23.1
|
1.0
|
CA
|
A:CA401
|
3.6
|
37.0
|
1.0
|
PG
|
A:TTP803
|
3.6
|
33.2
|
1.0
|
PA
|
A:TTP803
|
3.6
|
34.3
|
1.0
|
OD2
|
A:ASP7
|
3.8
|
35.2
|
1.0
|
OD1
|
A:ASP105
|
4.0
|
24.4
|
1.0
|
N
|
A:PHE8
|
4.1
|
23.5
|
1.0
|
O3A
|
A:TTP803
|
4.1
|
34.2
|
1.0
|
O3G
|
A:TTP803
|
4.2
|
33.6
|
1.0
|
C5'
|
A:TTP803
|
4.2
|
30.6
|
1.0
|
C
|
A:ASP7
|
4.3
|
23.9
|
1.0
|
NZ
|
A:LYS159
|
4.3
|
33.3
|
1.0
|
CA
|
A:PHE8
|
4.3
|
22.9
|
1.0
|
O5'
|
A:TTP803
|
4.4
|
30.8
|
1.0
|
CB
|
A:ASP7
|
4.4
|
24.9
|
1.0
|
N
|
A:TYR10
|
4.4
|
22.5
|
1.0
|
N
|
A:ASP9
|
4.4
|
25.3
|
1.0
|
O
|
A:HOH821
|
4.5
|
42.5
|
1.0
|
CA
|
A:ASP9
|
4.5
|
23.2
|
1.0
|
CB
|
A:ASP105
|
4.6
|
24.0
|
1.0
|
O
|
A:ASP7
|
4.6
|
23.8
|
1.0
|
C
|
A:ASP9
|
4.6
|
24.2
|
1.0
|
O1A
|
A:TTP803
|
4.7
|
33.9
|
1.0
|
O
|
A:HOH943
|
4.7
|
39.6
|
1.0
|
CA
|
A:ASP7
|
4.7
|
23.8
|
1.0
|
N
|
A:PHE11
|
4.7
|
22.0
|
1.0
|
O1B
|
A:TTP803
|
4.8
|
32.0
|
1.0
|
O
|
A:ASP105
|
4.8
|
25.8
|
1.0
|
O2G
|
A:TTP803
|
5.0
|
38.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 3 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:52.2
occ:1.00
|
O
|
A:ALA181
|
2.2
|
37.3
|
1.0
|
O
|
A:ILE186
|
2.3
|
33.9
|
1.0
|
C
|
A:ALA181
|
3.4
|
36.5
|
1.0
|
C
|
A:ILE186
|
3.6
|
34.5
|
1.0
|
CA
|
A:ALA181
|
4.2
|
36.3
|
1.0
|
CA
|
A:GLY187
|
4.3
|
37.2
|
1.0
|
N
|
A:GLY187
|
4.4
|
35.7
|
1.0
|
N
|
A:ASP182
|
4.4
|
35.8
|
1.0
|
CB
|
A:ALA181
|
4.4
|
37.7
|
1.0
|
CA
|
A:ASP182
|
4.5
|
34.7
|
1.0
|
CA
|
A:ILE186
|
4.6
|
33.0
|
1.0
|
CB
|
A:ILE186
|
4.6
|
31.8
|
1.0
|
O
|
A:VAL183
|
4.6
|
31.4
|
1.0
|
C
|
A:GLY187
|
4.7
|
39.3
|
1.0
|
OP2
|
C:DC1813
|
4.7
|
47.9
|
1.0
|
O
|
A:GLY187
|
4.9
|
38.2
|
1.0
|
CG2
|
A:ILE186
|
4.9
|
32.9
|
1.0
|
N
|
A:ILE186
|
4.9
|
32.7
|
1.0
|
OD1
|
A:ASP182
|
4.9
|
44.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 4 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:35.4
occ:1.00
|
O
|
B:HOH865
|
1.7
|
82.5
|
1.0
|
O
|
B:HOH806
|
2.2
|
29.4
|
1.0
|
OE1
|
B:GLU106
|
2.2
|
45.7
|
1.0
|
OD1
|
B:ASP7
|
2.3
|
30.9
|
1.0
|
O2A
|
B:TTP804
|
2.4
|
25.1
|
1.0
|
O
|
B:HOH927
|
2.4
|
60.4
|
1.0
|
OD1
|
B:ASP105
|
2.6
|
30.0
|
1.0
|
CG
|
B:GLU106
|
3.0
|
39.7
|
1.0
|
CD
|
B:GLU106
|
3.0
|
39.4
|
1.0
|
CG
|
B:ASP7
|
3.1
|
25.5
|
1.0
|
OD2
|
B:ASP7
|
3.3
|
26.1
|
1.0
|
CG
|
B:ASP105
|
3.5
|
30.3
|
1.0
|
CA
|
B:CA404
|
3.5
|
26.3
|
1.0
|
OD2
|
B:ASP105
|
3.7
|
28.9
|
1.0
|
PA
|
B:TTP804
|
3.7
|
30.1
|
1.0
|
O1A
|
B:TTP804
|
3.8
|
31.0
|
1.0
|
C5'
|
E:DC1813
|
3.8
|
75.7
|
1.0
|
C3'
|
E:DC1813
|
4.0
|
75.4
|
1.0
|
O5'
|
B:TTP804
|
4.1
|
23.6
|
1.0
|
OE2
|
B:GLU106
|
4.2
|
39.1
|
1.0
|
C4'
|
E:DC1813
|
4.3
|
75.2
|
1.0
|
C5'
|
B:TTP804
|
4.3
|
23.0
|
1.0
|
CB
|
B:ASP7
|
4.4
|
28.3
|
1.0
|
CB
|
B:GLU106
|
4.5
|
32.9
|
1.0
|
OP1
|
E:DC1813
|
4.5
|
77.2
|
1.0
|
O3'
|
E:DC1813
|
4.5
|
76.6
|
1.0
|
NZ
|
B:LYS152
|
4.6
|
44.5
|
1.0
|
O
|
B:ASP105
|
4.6
|
29.1
|
1.0
|
OG
|
B:SER103
|
4.7
|
37.5
|
1.0
|
C
|
B:ASP105
|
4.8
|
29.9
|
1.0
|
O5'
|
E:DC1813
|
4.9
|
75.0
|
1.0
|
NZ
|
B:LYS159
|
4.9
|
46.2
|
1.0
|
CB
|
B:ASP105
|
4.9
|
30.3
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 5 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca404
b:26.3
occ:1.00
|
OD2
|
B:ASP7
|
2.1
|
26.1
|
1.0
|
OD2
|
B:ASP105
|
2.2
|
28.9
|
1.0
|
O
|
B:PHE8
|
2.3
|
26.2
|
1.0
|
O2A
|
B:TTP804
|
2.3
|
25.1
|
1.0
|
O2B
|
B:TTP804
|
2.4
|
24.4
|
1.0
|
O
|
B:HOH890
|
2.5
|
84.4
|
1.0
|
O3B
|
B:TTP804
|
2.8
|
36.3
|
1.0
|
O
|
B:HOH927
|
2.9
|
60.4
|
1.0
|
CG
|
B:ASP105
|
3.2
|
30.3
|
1.0
|
PB
|
B:TTP804
|
3.3
|
26.4
|
1.0
|
CG
|
B:ASP7
|
3.3
|
25.5
|
1.0
|
O1G
|
B:TTP804
|
3.3
|
39.4
|
1.0
|
PA
|
B:TTP804
|
3.5
|
30.1
|
1.0
|
C
|
B:PHE8
|
3.5
|
26.9
|
1.0
|
O
|
B:HOH827
|
3.5
|
33.2
|
1.0
|
CA
|
B:CA403
|
3.5
|
35.4
|
1.0
|
OD1
|
B:ASP105
|
3.6
|
30.0
|
1.0
|
PG
|
B:TTP804
|
3.8
|
34.7
|
1.0
|
OD1
|
B:ASP7
|
3.8
|
30.9
|
1.0
|
O3A
|
B:TTP804
|
3.9
|
31.1
|
1.0
|
C5'
|
B:TTP804
|
3.9
|
23.0
|
1.0
|
N
|
B:PHE8
|
4.0
|
25.5
|
1.0
|
O5'
|
B:TTP804
|
4.2
|
23.6
|
1.0
|
CA
|
B:PHE8
|
4.3
|
26.0
|
1.0
|
C
|
B:ASP7
|
4.3
|
27.1
|
1.0
|
O
|
B:HOH865
|
4.3
|
82.5
|
1.0
|
NZ
|
B:LYS159
|
4.4
|
46.2
|
1.0
|
O3G
|
B:TTP804
|
4.4
|
38.0
|
1.0
|
CB
|
B:ASP7
|
4.5
|
28.3
|
1.0
|
N
|
B:ASP9
|
4.5
|
26.7
|
1.0
|
N
|
B:TYR10
|
4.5
|
24.5
|
1.0
|
CB
|
B:ASP105
|
4.5
|
30.3
|
1.0
|
O1A
|
B:TTP804
|
4.6
|
31.0
|
1.0
|
CA
|
B:ASP9
|
4.6
|
27.3
|
1.0
|
O1B
|
B:TTP804
|
4.7
|
29.7
|
1.0
|
O
|
B:ASP7
|
4.7
|
28.1
|
1.0
|
N
|
B:PHE11
|
4.7
|
26.1
|
1.0
|
C
|
B:ASP9
|
4.7
|
26.6
|
1.0
|
CA
|
B:ASP7
|
4.8
|
26.7
|
1.0
|
O
|
B:ASP105
|
4.8
|
29.1
|
1.0
|
O
|
B:HOH806
|
4.8
|
29.4
|
1.0
|
CB
|
B:PHE8
|
4.9
|
22.9
|
1.0
|
CB
|
B:PHE11
|
5.0
|
24.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1s0o
Go back to
Calcium Binding Sites List in 1s0o
Calcium binding site 6 out
of 6 in the Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Snapshots of Replication Through An Abasic Lesion: Structural Basis For Base Substitution and Frameshift within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca405
b:41.5
occ:1.00
|
O
|
B:ALA181
|
2.4
|
34.1
|
1.0
|
O
|
E:HOH124
|
2.5
|
38.3
|
1.0
|
O
|
B:ILE186
|
2.5
|
30.8
|
1.0
|
C
|
B:ALA181
|
3.6
|
33.9
|
1.0
|
C
|
B:ILE186
|
3.7
|
31.9
|
1.0
|
OP2
|
E:DT1812
|
4.0
|
43.4
|
1.0
|
CA
|
B:ALA181
|
4.4
|
34.6
|
1.0
|
CA
|
B:GLY187
|
4.4
|
34.2
|
1.0
|
N
|
B:ASP182
|
4.5
|
34.4
|
1.0
|
N
|
B:GLY187
|
4.6
|
33.2
|
1.0
|
CB
|
B:ALA181
|
4.6
|
35.9
|
1.0
|
CA
|
B:ASP182
|
4.6
|
35.3
|
1.0
|
O
|
B:VAL183
|
4.7
|
29.8
|
1.0
|
CB
|
B:ILE186
|
4.8
|
32.1
|
1.0
|
CA
|
B:ILE186
|
4.8
|
31.8
|
1.0
|
C
|
B:GLY187
|
4.8
|
35.7
|
1.0
|
|
Reference:
H.Ling,
F.Boudsocq,
R.Woodgate,
W.Yang.
Snapshots of Replication Through An Abasic Lesion; Structural Basis For Base Substitutions and Frameshifts. Mol.Cell V. 13 751 2004.
ISSN: ISSN 1097-2765
PubMed: 15023344
DOI: 10.1016/S1097-2765(04)00101-7
Page generated: Thu Jul 11 22:23:13 2024
|