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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:

Magnesium (Mg) 2 atoms

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

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