Calcium in PDB 1rys: Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Enzymatic activity of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
All present enzymatic activity of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution:
2.7.7.7;
Protein crystallography data
The structure of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution, PDB code: 1rys
was solved by
H.Ling,
F.Boudsocq,
B.Plosky,
R.Woodgate,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.90 /
2.03
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.732,
102.290,
106.069,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.1 /
25.6
|
Other elements in 1rys:
The structure of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
(pdb code 1rys). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Replication of A Cis-Syn Thymine Dimer at Atomic Resolution, PDB code: 1rys:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 1rys
Go back to
Calcium Binding Sites List in 1rys
Calcium binding site 1 out
of 5 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca805
b:50.3
occ:1.00
|
O
|
A:HOH2003
|
2.2
|
45.4
|
1.0
|
OP2
|
C:DT1811
|
2.3
|
39.7
|
1.0
|
O
|
A:HOH1933
|
2.3
|
57.2
|
1.0
|
OD2
|
A:ASP294
|
2.5
|
49.4
|
1.0
|
O
|
A:HOH1862
|
2.5
|
72.1
|
1.0
|
O
|
A:HOH1920
|
2.6
|
68.7
|
1.0
|
O
|
A:HOH2029
|
2.7
|
51.9
|
1.0
|
CG
|
A:ASP294
|
3.5
|
52.2
|
1.0
|
P
|
C:DT1811
|
3.6
|
40.1
|
1.0
|
O
|
C:HOH607
|
3.8
|
40.2
|
1.0
|
OD1
|
A:ASP294
|
3.9
|
52.8
|
1.0
|
C3'
|
C:DA1810
|
4.2
|
41.2
|
1.0
|
OP1
|
C:DT1811
|
4.2
|
42.7
|
1.0
|
O3'
|
C:DA1810
|
4.2
|
40.0
|
1.0
|
O
|
A:ILE295
|
4.3
|
44.7
|
1.0
|
O
|
C:HOH653
|
4.3
|
45.3
|
1.0
|
N
|
A:ILE295
|
4.6
|
48.4
|
1.0
|
C2'
|
C:DA1810
|
4.6
|
39.9
|
1.0
|
O5'
|
C:DT1811
|
4.7
|
39.8
|
1.0
|
CB
|
A:ASP294
|
4.8
|
50.2
|
1.0
|
|
Calcium binding site 2 out
of 5 in 1rys
Go back to
Calcium Binding Sites List in 1rys
Calcium binding site 2 out
of 5 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:37.0
occ:1.00
|
O
|
A:HOH1945
|
2.1
|
37.8
|
1.0
|
O2B
|
A:ATP1814
|
2.2
|
84.0
|
1.0
|
OD1
|
A:ASP7
|
2.3
|
32.1
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
41.0
|
1.0
|
O
|
A:PHE8
|
2.4
|
29.0
|
1.0
|
O
|
A:HOH2060
|
2.4
|
53.5
|
1.0
|
CG
|
A:ASP7
|
3.4
|
31.4
|
1.0
|
PB
|
A:ATP1814
|
3.5
|
83.1
|
1.0
|
CG
|
A:ASP105
|
3.5
|
34.4
|
1.0
|
C
|
A:PHE8
|
3.5
|
29.4
|
1.0
|
O2G
|
A:ATP1814
|
3.8
|
82.3
|
1.0
|
O3B
|
A:ATP1814
|
3.9
|
83.8
|
1.0
|
OD2
|
A:ASP7
|
3.9
|
33.6
|
1.0
|
CA
|
A:CA802
|
3.9
|
54.3
|
1.0
|
O1G
|
A:ATP1814
|
3.9
|
84.5
|
1.0
|
O
|
A:HOH1881
|
4.0
|
51.6
|
1.0
|
PG
|
A:ATP1814
|
4.1
|
83.7
|
1.0
|
N
|
A:PHE8
|
4.1
|
28.5
|
1.0
|
O
|
A:HOH1934
|
4.2
|
36.8
|
1.0
|
O
|
A:HOH1902
|
4.2
|
30.1
|
1.0
|
OD1
|
A:ASP105
|
4.3
|
30.9
|
1.0
|
CB
|
A:ASP105
|
4.3
|
30.3
|
1.0
|
NZ
|
A:LYS159
|
4.4
|
39.5
|
1.0
|
N
|
A:TYR10
|
4.4
|
27.4
|
1.0
|
CA
|
A:PHE8
|
4.4
|
29.9
|
1.0
|
C
|
A:ASP7
|
4.4
|
28.4
|
1.0
|
O3A
|
A:ATP1814
|
4.4
|
86.0
|
1.0
|
N
|
A:ASP9
|
4.5
|
30.6
|
1.0
|
CA
|
A:ASP9
|
4.5
|
31.5
|
1.0
|
O
|
A:ASP105
|
4.6
|
32.0
|
1.0
|
O1B
|
A:ATP1814
|
4.6
|
85.5
|
1.0
|
CB
|
A:ASP7
|
4.6
|
29.6
|
1.0
|
O
|
A:HOH2058
|
4.7
|
73.9
|
1.0
|
C
|
A:ASP9
|
4.7
|
30.7
|
1.0
|
N
|
A:PHE11
|
4.8
|
29.7
|
1.0
|
O
|
A:ASP7
|
4.8
|
30.1
|
1.0
|
CA
|
A:ASP7
|
4.9
|
29.5
|
1.0
|
CB
|
A:PHE8
|
5.0
|
29.2
|
1.0
|
|
Calcium binding site 3 out
of 5 in 1rys
Go back to
Calcium Binding Sites List in 1rys
Calcium binding site 3 out
of 5 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:54.3
occ:1.00
|
O
|
A:HOH1881
|
2.3
|
51.6
|
1.0
|
O
|
A:HOH1826
|
2.4
|
65.6
|
1.0
|
O
|
A:HOH1935
|
2.5
|
45.2
|
1.0
|
OD1
|
A:ASP105
|
2.6
|
30.9
|
1.0
|
O
|
A:HOH2058
|
2.7
|
73.9
|
1.0
|
OD2
|
A:ASP105
|
2.8
|
41.0
|
1.0
|
O3A
|
A:ATP1814
|
3.0
|
86.0
|
1.0
|
CG
|
A:ASP105
|
3.1
|
34.4
|
1.0
|
O2B
|
A:ATP1814
|
3.1
|
84.0
|
1.0
|
O1A
|
A:ATP1814
|
3.5
|
87.5
|
1.0
|
PB
|
A:ATP1814
|
3.6
|
83.1
|
1.0
|
PA
|
A:ATP1814
|
3.8
|
86.2
|
1.0
|
O5'
|
A:ATP1814
|
3.9
|
87.2
|
1.0
|
CA
|
A:CA801
|
3.9
|
37.0
|
1.0
|
CG
|
A:GLU106
|
4.2
|
40.1
|
1.0
|
CD
|
A:GLU106
|
4.2
|
43.2
|
1.0
|
OE2
|
A:GLU106
|
4.3
|
45.1
|
1.0
|
O
|
A:HOH1945
|
4.4
|
37.8
|
1.0
|
OG
|
A:SER103
|
4.4
|
39.9
|
1.0
|
O3B
|
A:ATP1814
|
4.5
|
83.8
|
1.0
|
O3'
|
C:DA1814
|
4.6
|
54.6
|
1.0
|
CB
|
A:ASP105
|
4.6
|
30.3
|
1.0
|
C5'
|
A:ATP1814
|
4.6
|
87.4
|
1.0
|
C4'
|
A:ATP1814
|
4.6
|
88.7
|
1.0
|
OE1
|
A:GLU106
|
4.7
|
50.2
|
1.0
|
OD1
|
A:ASP7
|
4.8
|
32.1
|
1.0
|
O1B
|
A:ATP1814
|
4.8
|
85.5
|
1.0
|
O2G
|
A:ATP1814
|
4.9
|
82.3
|
1.0
|
|
Calcium binding site 4 out
of 5 in 1rys
Go back to
Calcium Binding Sites List in 1rys
Calcium binding site 4 out
of 5 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca803
b:38.0
occ:1.00
|
OD2
|
B:ASP105
|
2.3
|
38.8
|
1.0
|
OD1
|
B:ASP7
|
2.3
|
35.1
|
1.0
|
O
|
B:PHE8
|
2.3
|
33.2
|
1.0
|
O1B
|
B:ATP1815
|
2.6
|
50.3
|
1.0
|
O3B
|
B:ATP1815
|
2.7
|
55.8
|
1.0
|
PB
|
B:ATP1815
|
3.3
|
48.6
|
1.0
|
CG
|
B:ASP105
|
3.4
|
37.4
|
1.0
|
O1G
|
B:ATP1815
|
3.4
|
59.1
|
1.0
|
CG
|
B:ASP7
|
3.4
|
36.3
|
1.0
|
C
|
B:PHE8
|
3.5
|
34.0
|
1.0
|
PG
|
B:ATP1815
|
3.7
|
55.6
|
1.0
|
OD2
|
B:ASP7
|
4.0
|
39.2
|
1.0
|
O2G
|
B:ATP1815
|
4.0
|
54.3
|
1.0
|
O3A
|
B:ATP1815
|
4.0
|
51.4
|
1.0
|
N
|
B:PHE8
|
4.1
|
32.4
|
1.0
|
OD1
|
B:ASP105
|
4.1
|
35.8
|
1.0
|
O
|
B:HOH1837
|
4.1
|
48.0
|
1.0
|
CB
|
B:ASP105
|
4.3
|
32.1
|
1.0
|
NZ
|
B:LYS159
|
4.3
|
44.4
|
1.0
|
CA
|
B:PHE8
|
4.4
|
33.1
|
1.0
|
O
|
B:HOH1817
|
4.4
|
45.4
|
1.0
|
C
|
B:ASP7
|
4.4
|
33.9
|
1.0
|
N
|
B:TYR10
|
4.5
|
31.3
|
1.0
|
N
|
B:ASP9
|
4.5
|
33.2
|
1.0
|
O2B
|
B:ATP1815
|
4.5
|
47.0
|
1.0
|
CA
|
B:ASP9
|
4.5
|
34.1
|
1.0
|
O
|
B:ASP105
|
4.6
|
34.0
|
1.0
|
CB
|
B:ASP7
|
4.7
|
35.1
|
1.0
|
C
|
B:ASP9
|
4.7
|
32.3
|
1.0
|
O1A
|
B:ATP1815
|
4.7
|
50.8
|
1.0
|
O
|
B:ASP7
|
4.8
|
35.3
|
1.0
|
N
|
B:PHE11
|
4.8
|
27.0
|
1.0
|
CA
|
B:ASP7
|
4.9
|
33.2
|
1.0
|
CB
|
B:PHE8
|
4.9
|
30.9
|
1.0
|
|
Calcium binding site 5 out
of 5 in 1rys
Go back to
Calcium Binding Sites List in 1rys
Calcium binding site 5 out
of 5 in the Replication of A Cis-Syn Thymine Dimer at Atomic Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Replication of A Cis-Syn Thymine Dimer at Atomic Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca806
b:41.2
occ:1.00
|
O
|
B:HOH1836
|
1.9
|
45.2
|
1.0
|
O
|
B:HOH1910
|
2.1
|
33.9
|
1.0
|
O
|
B:ALA181
|
2.3
|
42.6
|
1.0
|
O
|
E:HOH151
|
2.4
|
36.4
|
1.0
|
O
|
B:HOH2008
|
2.4
|
53.6
|
1.0
|
O
|
E:HOH298
|
2.4
|
36.5
|
1.0
|
O
|
B:ILE186
|
2.7
|
39.1
|
1.0
|
O
|
B:HOH1854
|
2.9
|
52.1
|
1.0
|
C
|
B:ALA181
|
3.5
|
41.7
|
1.0
|
C
|
B:ILE186
|
3.9
|
37.3
|
1.0
|
CA
|
B:ALA181
|
4.3
|
40.9
|
1.0
|
OP1
|
E:DC1813
|
4.4
|
33.4
|
1.0
|
CA
|
B:GLY187
|
4.4
|
36.2
|
1.0
|
N
|
B:ASP182
|
4.4
|
39.9
|
1.0
|
CA
|
B:ASP182
|
4.5
|
40.9
|
1.0
|
CB
|
B:ALA181
|
4.5
|
42.4
|
1.0
|
OP2
|
E:DC1813
|
4.6
|
33.2
|
1.0
|
N
|
B:GLY187
|
4.7
|
34.6
|
1.0
|
C
|
B:GLY187
|
4.7
|
38.6
|
1.0
|
O
|
B:HOH1951
|
4.8
|
57.4
|
1.0
|
O
|
B:VAL183
|
4.9
|
36.0
|
1.0
|
CA
|
B:ILE186
|
5.0
|
37.4
|
1.0
|
O
|
B:GLY187
|
5.0
|
36.8
|
1.0
|
|
Reference:
H.Ling,
F.Boudsocq,
B.Plosky,
R.Woodgate,
W.Yang.
Replication of A Cis-Syn Thymine Dimer at Atomic Resolution Nature V. 424 1083 2003.
ISSN: ISSN 0028-0836
PubMed: 12904819
DOI: 10.1038/NATURE01919
Page generated: Thu Jul 11 22:19:41 2024
|