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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:

Sodium (Na) 1 atom

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

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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

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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

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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: Sat Dec 12 03:18:14 2020

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